hrbrmstr · May 31, 2018 01:45
diff --git a/cran-r-pkgs-system-calls.R b/cran-r-pkgs-system-calls.R
 system(paste(".", pathtoms, "ms 10", 1000*numloc, "-t tbs -r tbs tbs -eN tbs tbs -eN tbs tbs < bottpost |", ".", pathtoms, "sample_stats > ss_postb.txt", sep=""))
 system(paste(".", pathtoms, "ms 10", formatC(numsim*numloc,digit=7), " -t tbs -r tbs tbs < const |", ".", pathtoms, "sample_stats > afr-const.txt", sep=""))
 system(paste(".", pathtoms, "ms 10", formatC(numsim*numloc,digit=7), " -t tbs -r tbs tbs -eN tbs tbs < exp | ", ".", pathtoms, "sample_stats > afr-exp.txt", sep=""))
 system(paste(".", pathtoms, "ms 10", formatC(numsim*numloc,digit=7), " -t tbs -r tbs tbs -eN tbs tbs -eN tbs tbs < bott | ", ".", pathtoms, "sample_stats > afr-bott.txt", sep=""))
 system(paste("jags ",run.file,sep=""))
 system("cmd /c ver",intern=TRUE,invisible=TRUE)
 system("uname -rps",intern=TRUE)
 system("rm Rlisting001.tmp")
 system("rm Rlisting001.tmp")
 system("rm Rlisting001.tmp")
 system(paste(command,"&"))
 system(paste("ps aux|grep '",command,"'",sep=""),intern=TRUE)
 system(paste("kill",pid1,pid2,pid3,pid4,pid5,pid6,pid7))
 system("xdpyinfo  | grep 'dimensions:'", intern=TRUE, ignore.stderr=TRUE)
 system(paste(Sys.getenv("ImageMagick"),"identify -format %r \"",filename,"\"",sep=""),intern=TRUE)
 system(paste(convert.path," -compress None \"",filename,"\" \"",tmpfile,"\"",sep=""),wait=TRUE)
 system(paste(Sys.getenv("ImageMagick"),"identify -format %c \"",name,"\" ",sep=""),intern=TRUE)
 system(paste(convert.path,
           " -compress None -comment \"",img$description,"\" \"",
           tmpfile,"\" \"",file,"\"",sep=""),wait=TRUE)
 system(paste(Sys.getenv("ImageMagick"),
 "mogrify -comment \"",img$description,"\" \"",tmpfile,"\"",sep=""),wait=TRUE)
 system(paste(convert.path,
       " -compress None -comment \"",img$description,"\" \"",
         tmpfile,"\" \"",filename,"\"",sep=""),wait=TRUE)
 system(paste("dcraw", opt1, opt2, opt3, opt4, tmpfile))
 system(paste("dcraw -i -v", filename),intern=TRUE)
 system('admb simple.tpl')
 system('simple -nohess')
 system('simple')
 system('simple -hbf 1')
 system('simple')
 system(paste(model, "-mceval -noest -nohess"), ignore.stdout=FALSE)
 system(cmd, ignore.stdout=!verbose)
 system(cmd, ignore.stdout=!verbose)
 system(paste(exec, opts, filename))
 system(
      paste(
        file.path2(getOption("lattePath"), "latte-maximize"), 
        opts, 
        file.path2(dir2, "maxCode 2> out.txt")
      ),
      intern = FALSE, ignore.stderr = FALSE
    )
 system(
      paste(
        paste0("cmd.exe /c env.exe"),
        file.path(getOption("lattePath"), "latte-maximize"), 
        opts, 
        matFile
      ),
      intern = FALSE, ignore.stderr = FALSE
    )
 system(
      paste(
        file.path2(getOption("lattePath"), "latte-minimize"), 
        opts, 
        file.path2(dir2, "minCode 2> out.txt")
      ),
      intern = FALSE, ignore.stderr = FALSE
    )
 system(
      paste(
        paste0("cmd.exe /c env.exe"),
        file.path(getOption("lattePath"), "latte-minimize"), 
        opts, 
        matFile
      ),
      intern = FALSE, ignore.stderr = FALSE
    )
 system('ls /Applications/', intern = TRUE)
 system('ls ~/', intern = TRUE)
 system(paste(wexe, s), TRUE)
 system(paste("open", shQuote(getAmelia("wdForLastImputation"))))
 system(paste("xdg-open", shQuote(getAmelia("wdForLastImputation"))))
 system(cmd, intern = TRUE)
 system(cmd)
 system(paste0('wc -l ',pedFile.f), intern=T)
 system(sprintf('%s %s', shQuote(normalizePath(getOption('pdfviewer'))),
               'Sweave_animation.pdf'))
 system(paste('open ', shQuote(output)))
 system(paste('xdg-open ', shQuote(output)))
 system(sprintf('%s %s', pdflatex, latex.filename))
 system(
            sprintf('%s %s', shQuote(normalizePath(getOption('pdfviewer'))),
                    sprintf('%s.pdf', sub('([^.]+)\\.[[:alnum:]]+$', '\\1', latex.filename)))
          )
 system(convert)
 system(paste(tool, '--version'), intern = TRUE)
 system(convert)
 system(convert)
 system(cmd)
 system(cmd)
 system(paste(ffmpeg, '-version'), intern = TRUE)
 system(ffmpeg)
 system(cmd)
 system(cmd)
 system(cmd)
 system(cmd, ...)
 system(paste0("xdg-open \"", filename, "\""))
 system(paste0("open \"", filename, "\""))
 system(cmd[i])
 system(paste(exec, "-h"))
 system(paste(exec, opts), ignore.stdout = quiet)
 system(paste(exec, "-help"))
 system(paste(exec, opts), ignore.stdout = quiet)
 system(exec)
 system(paste(exec, opts))
 system(exec)
 system(paste(exec, opts))
 system(exec, intern = TRUE, input = c("W", "A", "Y"))
 system("rm -r LOG")
 system("rm -r MAPPING")
 system("rm -r MCMC")
 system("rm -r RESULT")
 system(saint.command)
 system("rm -r LOG")
 system("rm -r MAPPING")
 system("rm -r MCMC")
 system("rm -r RESULT")
 system(saint.command2)
 system("rm -r LOG")
 system("rm -r MAPPING")
 system("rm -r MCMC")
 system("rm -r RESULT")
 system(saint.command.norm)
 system("rm -r LOG")
 system("rm -r MAPPING")
 system("rm -r MCMC")
 system("rm -r RESULT")
 system(saint.commandp1)
 system("rm -r LOG")
 system("rm -r MAPPING")
 system("rm -r MCMC")
 system("rm -r RESULT")
 system(saint.commandp1)
 system("rm -r LOG")
 system("rm -r MAPPING")
 system("rm -r MCMC")
 system("rm -r RESULT")
 system( paste( apsim, " \"", sim_file_name, "\"", sep = "" ), 
 				show.output.on.console = FALSE )
 system(paste(exe,addCommas(files[i]), sep = " "), show.output.on.console = FALSE)
 system(string, intern=TRUE)
 system(python_cmd, input=python_code, intern=TRUE)
 system(python_cmd, input=python_code, intern=TRUE)
 system(command)
 system("ls" ,intern=TRUE)
 system(paste("mkdir ", path,"/ARTIVAsubnet", sep=""))
 system( "ls ",intern=TRUE)
 system(paste("mkdir ",outputPath, sep=""))
 system(paste( "ls ",outputPath),intern=TRUE)
 system(paste("mkdir ",outputPath,"/Estimations",sep=""))
 system(paste( "ls ",outputPath),intern=TRUE)
 system(paste("mkdir ",outputPath,"/Pictures",sep=""))
 system("ls" ,intern=TRUE)
 system("mkdir ARTIVAnet")
 system( "ls ",intern=TRUE)
 system(paste("mkdir ", outputPath, sep=""))
 system("ls" ,intern=TRUE)
 system("mkdir ARTIVAsubnet", ignore.stderr = TRUE)
 system( "ls ",intern=TRUE)
 system(paste("mkdir ", outputPath, sep=""))
 system(paste( "ls ",outputPath),intern=TRUE)
 system(paste("mkdir ",outputPath,"/Iterations",sep=""))
 system(paste( "ls ",outputPath),intern=TRUE)
 system(paste("mkdir ",outputPath,"/Estimations",sep=""))
 system(paste(shell, script.file, sep=" "))
 system(command, intern=intern)
 system("cmp zaki.data makebin.data")
 system("cmp zaki.conf makebin.conf")
 system(cmd, wait = TRUE)
 system(paste(shQuote("open"), shQuote(dfile)), wait = FALSE, ignore.stderr = TRUE)
 system(paste(shQuote("/usr/bin/xdg-open"), shQuote(dfile)), wait = FALSE, ignore.stderr = TRUE)
 system("sw_vers -productVersion", intern = TRUE)
 system(paste(dir,"open the_audiolyzr_mac_v5/the_audiolyzr_mac_v5.app", sep="; "))
 system(paste("cd",output,";","open .."))
 system(paste("unzip", paste(directory, "the_audiolyzr_mac_v5", "the_audiolyzr_mac_v5.zip", sep="/"),
                     "-d", paste (directory,"the_audiolyzr_mac_v5",sep="/"), sep=" "), 
               ignore.stdout=TRUE)
 system("killall -9 the_audiolyzR_mac_v5", ignore.stderr=TRUE)
 system(paste(awk, "--version"),
                           intern = TRUE, ignore.stderr = TRUE)
 system("which awk", intern = TRUE, ignore.stderr = TRUE)
 system(paste(awk, "--version"),
                           intern = TRUE, ignore.stderr = TRUE)
 system(cmd, intern = TRUE)
 system("system_profiler -detailLevel mini | grep \"  Memory:\"", 
            intern = TRUE)
 system(cmd, intern = TRUE)
 system("wmic MemoryChip get Capacity", intern = TRUE)
 system("which hmmbuild",intern = T)
 system(command = sub_hmm_command, wait = T)
 system(command = leftover_hmm_command, wait = T)
 system("svn checkout svn://scm.r-forge.r-project.org/svnroot/bayesr/pkg/BayesXsrc BayesXsrc")
 system('sh ./get_BayesXsrc.sh')
 system("svn checkout svn://scm.r-forge.r-project.org/svnroot/bayesr/pkg/BayesXsrc BayesXsrc")
 system('sh ./get_BayesXsrc.sh')
 system("which xclip", ignore.stdout = TRUE, ignore.stderr = TRUE)
 system("which pbcopy", ignore.stdout = TRUE, ignore.stderr = TRUE)
 system("which xclip", ignore.stdout = TRUE,
                              ignore.stderr = TRUE)
 system("which pbcopy", ignore.stdout = TRUE,
                              ignore.stderr = TRUE)
 system(paste(Rwin(), "--vanilla <", rfile), wait=FALSE)
 system(i)
 system(cmdstr)
 system(bin, ...)
 system(paste(bin, " ", dir, "/", prg.name, sep = ""), 
          intern = TRUE, show.output.on.console = FALSE, ...)
 system(paste(bin, " ", dir, "/", prg.name, 
          " > ", dir, "/bayesx.log", sep = ""), intern = FALSE, ...)
 system(paste(bin, " ", dir, "/", prg.name, sep = ""), intern = FALSE, ...)
 system(paste("cat ",folders[1],"/",list.files(folders[1],pattern = "1_Summary")," > ",name,"/1_Summary.txt",sep=""))
 system(paste("cat ",folders[1],"/",list.files(folders[1],pattern = "2_IMGT-gapped-nt-sequences")," > ",name,"/2_IMGT-gapped-nt-sequences.txt",sep=""))
 system(paste("cat ",folders[1],"/",list.files(folders[1],pattern = "3_Nt-sequences")," > ",name,"/3_Nt-sequences.txt",sep=""))
 system(paste("cat ",folders[1],"/",list.files(folders[1],pattern = "4_IMGT-gapped-AA-sequences")," > ",name,"/4_IMGT-gapped-AA-sequences.txt",sep=""))
 system(paste("cat ",folders[1],"/",list.files(folders[1],pattern = "5_AA-sequences")," > ",name,"/5_AA-sequences.txt",sep=""))
 system(paste("cat ",folders[1],"/",list.files(folders[1],pattern = "6_Junction")," > ",name,"/6_Junction.txt",sep=""))
 system(paste("cat ",folders[1],"/",list.files(folders[1],pattern = "7_V-REGION-mutation-and-AA-change-table")," > ",name,"/7_V-REGION-mutation-and-AA-change-table.txt",sep=""))
 system(paste("cat ",folders[1],"/",list.files(folders[1],pattern = "8_V-REGION-nt-mutation-statistics")," > ",name,"/8_V-REGION-nt-mutation-statistics.txt",sep=""))
 system(paste("cat ",folders[1],"/",list.files(folders[1],pattern = "9_V-REGION-AA-change-statistics")," > ",name,"/9_V-REGION-AA-change-statistics.txt",sep=""))
 system(paste("cat ",folders[1],"/",list.files(folders[1],pattern = "10_V-REGION-mutation-hotspots")," > ",name,"/10_V-REGION-mutation-hotspots.txt",sep=""))
 system(paste("cat ",folders[i],"/",list.files(folders[i],pattern = "1_Summary")," | tail -n+2 >> ",name,"/1_Summary.txt",sep=""))
 system(paste("cat ",folders[i],"/",list.files(folders[i],pattern = "2_IMGT-gapped-nt-sequences")," | tail -n+2 >> ",name,"/2_IMGT-gapped-nt-sequences.txt",sep=""))
 system(paste("cat ",folders[i],"/",list.files(folders[i],pattern = "3_Nt-sequences")," | tail -n+2 >> ",name,"/3_Nt-sequences.txt",sep=""))
 system(paste("cat ",folders[i],"/",list.files(folders[i],pattern = "4_IMGT-gapped-AA-sequences")," | tail -n+2 >> ",name,"/4_IMGT-gapped-AA-sequences.txt",sep=""))
 system(paste("cat ",folders[i],"/",list.files(folders[i],pattern = "5_AA-sequences")," | tail -n+2 >> ",name,"/5_AA-sequences.txt",sep=""))
 system(paste("cat ",folders[i],"/",list.files(folders[i],pattern = "6_Junction")," | tail -n+2 >> ",name,"/6_Junction.txt",sep=""))
 system(paste("cat ",folders[i],"/",list.files(folders[i],pattern = "7_V-REGION-mutation-and-AA-change-table")," | tail -n+2 >> ",name,"/7_V-REGION-mutation-and-AA-change-table.txt",sep=""))
 system(paste("cat ",folders[i],"/",list.files(folders[i],pattern = "8_V-REGION-nt-mutation-statistics")," | tail -n+2 >> ",name,"/8_V-REGION-nt-mutation-statistics.txt",sep=""))
 system(paste("cat ",folders[i],"/",list.files(folders[i],pattern = "9_V-REGION-AA-change-statistics")," | tail -n+2 >> ",name,"/9_V-REGION-AA-change-statistics.txt",sep=""))
 system(paste("cat ",folders[i],"/",list.files(folders[i],pattern = "10_V-REGION-mutation-hotspots")," | tail -n+2 >> ",name,"/10_V-REGION-mutation-hotspots.txt",sep=""))
 system( "WMIC CPU Get DeviceID,NumberOfCores", intern = TRUE )
 system( cmd, TRUE )
 system(paste0("bash -c 'tabix -H ", file.name, "'"), wait = TRUE, intern = TRUE, ignore.stdout = FALSE, ignore.stderr = FALSE)
 system(command , wait = TRUE, intern = TRUE, ignore.stdout = FALSE, ignore.stderr = FALSE)
 system(paste("head ", region.file[[1]]))
 system("tabix --help")
 system(command , wait = TRUE, intern = intern, ignore.stdout = FALSE, ignore.stderr = FALSE)
 system(command , wait = TRUE, intern = intern, ignore.stdout = FALSE, ignore.stderr = FALSE)
 system(paste("head ", input.files[[i]]))
 system("sort --version", intern = TRUE)
 system(command, intern = TRUE)
 system(command, intern = TRUE)
 system(paste("vlc -Idummy --no-loop --no-repeat --playlist-autostart --no-media-library --play-and-exit", fname), 
         ignore.stdout = TRUE, ignore.stderr=TRUE,wait = FALSE)
 system(paste("paplay ", fname), ignore.stdout = TRUE, ignore.stderr=TRUE,wait = FALSE)
 system(paste("aplay --buffer-time=48000 -N -q", fname), ignore.stdout = TRUE, ignore.stderr=TRUE,wait = FALSE)
 system(cmd, intern=TRUE)
 system(cmd, intern=TRUE)
 system("sysctl -n machdep.cpu.vendor", intern=TRUE)
 system("sysctl -n machdep.cpu.brand_string", intern=TRUE)
 system("wmic cpu get name", intern=TRUE)
 system("wmic cpu get manufacturer", intern=TRUE)
 system(cmd_blas, intern=TRUE)
 system(cmd_lapack, intern=TRUE)
 system(cmd, intern=TRUE)
 system("sysctl hw.memsize", intern = TRUE)
 system(cmd, intern=TRUE)
 system("wmic MemoryChip get Capacity", intern=TRUE)
 system(cmd)
 system(command)
 system(command)
 system(command)
 system(VOScommand)
 system("svn checkout svn://scm.r-forge.r-project.org/svnroot/bigmemory",
         intern=!verbose, ignore.stderr=!verbose)
 system("REFBLAS=1 R CMD INSTALL bigalgebra",intern=!verbose, ignore.stderr=!verbose)
 system("rm -rf bigmemory", intern=!verbose, ignore.stderr=!verbose)
 system(paste(exefile, "--version"),
                     ignore.stderr = TRUE, ignore.stdout = TRUE)
 system(paste(exefile, "--version"),
                       ignore.stderr = TRUE, ignore.stdout = TRUE)
 system(cmd,
                        ignore.stderr = !verbose, ignore.stdout = !verbose)
 system(cmd)
 system( paste(exefile," -f",outfile," ",infile,sep="") )
 system(paste(exefile, "--version"),
                   ignore.stderr = TRUE, ignore.stdout = TRUE)
 system(cmd, ignore.stderr = !verbose, ignore.stdout = !verbose)
 system(cmd)
 system(cmd)
 system(paste(exefile, ver),
                     ignore.stderr = TRUE, ignore.stdout = TRUE)
 system(cmd)
 system(cmd)
 system(paste(exefile, ver),
                     ignore.stderr = TRUE, ignore.stdout = TRUE)
 system(cmd)
 system(paste(exefile, ver),
                     ignore.stderr = TRUE, ignore.stdout = TRUE)
 system(cmd)
 system(paste(exefile, ver),
                   ignore.stderr = TRUE, ignore.stdout = TRUE)
 system(cmd, ignore.stderr = !verbose, ignore.stdout = !verbose)
 system(paste("pdflatex", texfile))
 system(cmdstr)
 system(cmdstr)
 system(cmd)
 system("command -v java", intern=TRUE )
 system( "java", intern=TRUE )
 system(command = maxent.command, wait = TRUE, intern=TRUE)
 system(command = maxent.command, wait = TRUE, intern=TRUE)
 system(command=paste("java ",
                         ifelse(is.null([email protected]$memory_allocated),"",paste("-mx",[email protected]$memory_allocated,"m",sep="")),
                         " -jar ", file.path([email protected]$path_to_maxent.jar, "maxent.jar"), 
                         " environmentallayers=\"", MWD$m_backgroundFile,
                         "\" samplesfile=\"", MWD$m_speciesFile,
                         "\" projectionlayers=\"", gsub(", ",",",toString(MWD$m_predictFile)), 
                         "\" outputdirectory=\"", MWD$m_outdir, "\"",
                         " outputformat=logistic ",
                         #                            "jackknife maximumiterations=",[email protected]$maximumiterations,
                         ifelse(length(categorial_var), 
                                paste(" togglelayertype=",categorial_var, collapse=" ",sep=""), 
                                ""),
                         " redoifexists",
                         " visible=", [email protected]$visible,
                         " linear=", [email protected]$linear,
                         " quadratic=", [email protected]$quadratic,
                         " product=", [email protected]$product,
                         " threshold=", [email protected]$threshold,
                         " hinge=", [email protected]$hinge,
                         " lq2lqptthreshold=", [email protected]$lq2lqptthreshold,
                         " l2lqthreshold=", [email protected]$l2lqthreshold,
                         " hingethreshold=", [email protected]$hingethreshold,
                         " beta_threshold=", [email protected]$beta_threshold,
                         " beta_categorical=", [email protected]$beta_categorical,
                         " beta_lqp=", [email protected]$beta_lqp,
                         " beta_hinge=", [email protected]$beta_hinge,
                         " betamultiplier=", [email protected]$betamultiplier,
                         " defaultprevalence=", [email protected]$defaultprevalence,
                         " autorun nowarnings notooltips noaddsamplestobackground", sep=""), wait = TRUE, intern = TRUE,
           ignore.stdout = FALSE, ignore.stderr = FALSE)
 system(system.str)
 system(command = command, intern = TRUE)
 system(cmd)
 system(paste("open ",.libPaths(), "/Blaunet/scripts/command.pdf", sep=""))
 system(paste("xdg-open ",.libPaths(), "/Blaunet/scripts/command.pdf", sep=""))
 system(paste("open ",.libPaths(), "/Blaunet/scripts/graphic.pdf", sep=""))
 system(paste("xdg-open ",.libPaths(), "/Blaunet/scripts/graphic.pdf", sep=""))
 system(
                    'cat /proc/$PPID/stat | cut -d " " -f 14-17',
                    intern=TRUE
                )
 system(cmd, intern = intern)
 system(cmd, intern = intern)
 system(cmd)
 system('brew update && brew reinstall hugo')
 system(paste("perl",text2krona,out_krona))
 system(paste("rm",out_krona))
 system(paste0("ls -R ",x," | grep ':$' | sed -e 's/:$//' -e 's/[^-][^\\/]*\\//--/g' -e 's/^/ /' -e 's/-/|/'"))
 system("rm tempFile*")
 system("wmic desktopmonitor get screenwidth", intern=TRUE)
 system("wmic desktopmonitor get screenheight", intern=TRUE)
 system("xrandr | grep '*' | awk '{print $1}'", intern=TRUE)
 system( paste("open", file) )
 system(paste("cd", pkgpath, "; make", fileflag, target),
           ignore.stdout=quiet, ignore.stderr=quiet,
           intern=FALSE)
 system(sprintf("cat %s | ./pmws > %s", datfile, outfilepath))
 system(shcmd)
 system("echo \"modelQuit()\" | /usr/local/lib/OpenBUGS/lib/../bin/OpenBUGS", intern=TRUE)
 system(cmd, wait = FALSE)
 system(paste("open", path))
 system(command.tmp, intern=TRUE)
 system(command.tmp2b, intern=TRUE)
 system(command.tmp, show.output.on.console = FALSE, intern = TRUE)
 system(command.tmp,  intern=TRUE)
 system(command.tmp, intern=TRUE)
 system(command.tmp, intern=TRUE)
 system(cmdWinEdt, wait = FALSE)
 system("mageck -h",intern=FALSE, ignore.stdout = FALSE, ignore.stderr = FALSE,
                   wait = TRUE, input = NULL, show.output.on.console = FALSE,
                   minimized = FALSE, invisible = TRUE)
 system("pandoc -h",intern=FALSE, ignore.stdout = FALSE, ignore.stderr = FALSE,
                   wait = TRUE, input = NULL, show.output.on.console = FALSE,
                   minimized = FALSE, invisible = TRUE)
 system("bowtie2 -h",intern=FALSE, ignore.stdout = FALSE, ignore.stderr = FALSE,
                   wait = TRUE, input = NULL, show.output.on.console = FALSE,
                   minimized = FALSE, invisible = TRUE)
 system("bowtie2-build -h",intern=FALSE, ignore.stdout = TRUE, ignore.stderr = TRUE,
                   wait = TRUE, input = NULL, show.output.on.console = FALSE,
                   minimized = FALSE, invisible = TRUE)
 system(mageckstring)
 system(paste("perl", paste("'",extractstring, "'", sep=""),paste("'", pattern,"'", sep=""), filearg, reversecomplement, paste("'", machinepattern, "'", sep=""), sep=" "))
 system(paste("bowtie2-build", "-f", filearg, paste(bt2index, bowtieparams, sep=" ")))
 system(paste("bowtie2", "-x", filearg.reference, "-U", filearg.fastq, "-S", filearg.sam,  bowtie2.params, sep=" "))
 system(paste("perl", extractstring, filearg.reference, filearg.sam, match, sep=" "))
 system("date")
 system("date")
 system(strdotcall, intern=TRUE, ignore.stderr=TRUE)
 system(strevincecall, intern=FALSE, wait=FALSE, ignore.stderr=TRUE)
 system(strdotcall, intern=TRUE, ignore.stderr=TRUE)
 system(strevincecall, intern=TRUE, ignore.stderr=TRUE)
 system(strdotcall, intern=TRUE, ignore.stderr=TRUE)
 system(strevincecall, intern=TRUE, ignore.stderr=TRUE)
 system("join -j 1 gi.txt gi.taxid.txt > gi.taxid.match")
 system(syscmd)
 system(paste(mycat,' "',file,'" | wc -l',sep=""),intern=TRUE)
 system(paste(mycat,' "',file,'" | grep -n "^>" | cut -f 1 -d ":"',sep=""),intern=TRUE)
 system(paste(mycat,' "',file,'"',sep=""),intern=TRUE)
 system(cmd)
 system(paste0("dd if=/dev/zero of=", fn, " count=1 bs=",
                civis:::MIN_MULTIPART_SIZE + 1))
 system(pandoc.cmd)
 system(paste("echo '", qhullout(mat), "' | qconvex QbB i"), TRUE)
 system(ssh_cmd, wait=TRUE, ignore.stdout=TRUE, ignore.stderr=TRUE)
 system("sbatch", input=filled, ignore.stdout=TRUE)
 system(paste("scancel --jobname", private$job_id),
                       ignore.stdout=clean, ignore.stderr=clean)
 system("qsub", input=filled, ignore.stdout=TRUE)
 system(paste("qdel", private$job_id),
                       ignore.stdout=clean, ignore.stderr=clean)
 system("bsub", input=filled, ignore.stdout=TRUE)
 system(paste("bkill -J", private$job_id),
                       ignore.stdout=clean, ignore.stderr=clean)
 system("R CMD build --resave-data .")
 system(splinefile, intern=TRUE)
 system(paste0(R.home(component = "bin"), "/R CMD SHLIB ", filename), intern = TRUE)
 system(paste0(R.home(component = "bin"), "/R CMD SHLIB ", filename, " -leinspline"), intern = TRUE)
 system("rm -rf codemetar_copy")
 system(cmd)
 system(sprintf(...))
 system( paste( "command -v ", names(available.clipboard.commands)[i], sep=""), intern=TRUE )
 system(paste("perl",plFile,GSEid,user,password,host,port,dbname))
 system(paste("perl",plFile,id,user,password,host,port,dbname))
 system(paste("perl -I",paste(dataLoc,"/BigMac/COMPENDIUM",sep=""),plFile,GSEid,dataLoc,scriptLoc,user,password,host,port,dbname,GPLid))
 system(paste("Rscript",scriptLoc,x,"gse.new 0",sep=" "))
 system(paste("perl",plFile,GSEid,GPLid,scriptLoc,user,password,host,port,dbname))
 system(paste("perl -I",paste(dataLoc,"/BigMac/COMPENDIUM",sep=""),plFile,GSEid,dataLoc,scriptLoc))
 system(text.cmd, intern = TRUE)
 system(phantomScript)
 system("free -m|grep Mem|awk '{print $2}' > memory.limits ")
 system("top -l 1|grep 'PhysMem'|awk '{print $2+$6}' > memory.limits ")
 system(paste("pdfcrop --pdftexcmd pdftex", f, f, "1>/dev/null 2>&1"),
           intern=FALSE)
 system(paste("elki-cli -dbc.in ",path,"/configs.txt -algorithm clustering.OPTICS -optics.minpts ",minpts," -optics.epsilon ",epsilon," -resulthandler ResultWriter -out ",path,"/opticsout -out.silentoverwrite",sep=""))
 system(paste("mkdir",timeid))
 system(paste("qsub  -cwd -V -sync y -l virtual_free=2G -t 1-",ncores,":1 rjob.sh",sep=""))
 system(paste("qsub  -cwd -V -sync y ",qmem," -t 1-",ncores,":1 rjob.sh",sep=""))
 system(paste("rm -rf",timeid))
 system(command)
 system("touch ssmtest.cpp")
 system("touch ssmtest.cpp")
 system(cmd)
 system(cmd)
 system(paste(R.home("bin"), "R --vanilla CMD config CC", sep="/"),
        intern = TRUE)
 system(full, intern = FALSE, ignore.stderr = quiet, ignore.stdout = quiet, ...)
 system(full, intern = TRUE, ignore.stderr = quiet, ...)
 system('uname',intern=TRUE)
 system('free',intern=TRUE)
 system('top -l1 -n 20 | grep -Ei "mem|vm"',intern=TRUE)
 system("tput colors 2>/dev/null", intern = TRUE)
 system(paste("crontab", file))
 system(paste("crontab -u", user, file))
 system("crontab -l", intern=TRUE, ignore.stderr=TRUE)
 system(paste("crontab -u", user, "-l", intern=TRUE, ignore.stderr=TRUE))
 system(sprintf('nohup %s &', cmd))
 system( paste("crontab -r") )
 system( paste("crontab", tempfile) )
 system("crontab -l", intern=TRUE, ignore.stderr=TRUE)
 system( paste("crontab", tempfile) )
 system("crontab -r")
 system("crontab -r")
 system(paste("epstool --copy --bbox --quiet", f, f., "1>/dev/null 2>&1; mv", f., f))
 system(paste("pdfcrop --pdftexcmd pdftex", f, f, "1>/dev/null 2>&1"))
 system(paste("mogrify -trim", f, f, "1>/dev/null 2>&1"))
 system(paste("command -v", command, ">/dev/null 2>&1"))
 system("stty -echo", ignore.stdout=TRUE, ignore.stderr=TRUE)
 system("stty echo", ignore.stdout=TRUE, ignore.stderr=TRUE)
 system(plink.comm)
 system(paste0("rm ",tmpdir,'/*.*'))
 system(paste0("rm ",tmpdir,'/*.*'))
 system(paste0("rm ",tmpdir,'/*.*'))
 system(paste0("rm ",tmpdir,'/*.*'))
 system(paste0("rm ",tmpdir,'/*.*'))
 system(paste0("rm ",tmpdir,'/*.*'))
 system(paste0("rm ",tmpdir,'/*.*'))
 system(paste0("rm ",tmpdir,'/*.*'))
 system(paste0("rm ",tmpdir,'/*.*'))
 system(paste0("Rscript --slave --no-restore -e source(\'",tmpdir,"/stanplottemp.R\')"),wait=FALSE)
 system(paste0(R.home(component = "home"),"/Rscript --slave --no-restore -e source\\(\\\'",tmpdir,"\\/stanplottemp.R\\\'\\)"),wait=FALSE)
 system(paste0("rm ",tmpdir,'/',stanseed,"samples_",chaini,".csv"))
 system(paste0('rm ',tmpdir,'/stanplottemp.R'))
 system(g1, intern=TRUE)
 system(g2, intern=TRUE)
 system("git log --pretty=format:'%H' -n 1", intern = TRUE)
 system( S[kk] )
 system ( outs, intern = TRUE )
 system(paste("lpr", file))
 system(paste("lpr", file))
 system("rm extras/Cyclops.pdf")
 system("R CMD Rd2pdf ./ --output=extras/Cyclops.pdf")
 system(paste("open",filename,sep = " "))
 system(paste(shQuote(getOption("pdfviewer")), shQuote(pdf)), wait = FALSE)
 system(paste(arg0, "-c pass", sep = ""))
 system(csv2xls.cmd)
 system("top -b -n 1", intern=TRUE)
 system(cmd)
 system(paste("fallocate -l", csvsize, csvfile))
 system('id -u', intern=TRUE)
 system(paste('(', input, ') > ', tt, sep=""))
 system(sprintf('dat create %s', dir))
 system(sprintf('dat share %s', dir), wait = FALSE)
 system(sprintf('dat clone %s %s', link, dir))
 system('dat pull')
 system('dat sync')
 system(sprintf('dat log %s', path))
 system('dat status')
 system(paste0('SETX /M PATH "%PATH%;',
     paste0(normalizedPath, destpath), '"'))
 system(sprintf("echo 'export PATH=$PATH:%s' >> ~/.profile", normalizedPath))
 system(command, TRUE)
 system(paste("open",pdffilename,sep = " "))
 system("
       cd data-raw
       git clone https://github.com/mapbox/earcut.hpp
       cp earcut.hpp/include/mapbox/earcut.hpp ../src/
       cp earcut.hpp/LICENSE ../inst/earcut_source/
       cd earcut.hpp
       git log -n 5  >  ../mapbox-earcut.hpp.git.log
       ")
 system("R CMD SHLIB dede_lv.c")
 system("R CMD SHLIB dede_lvF.f dedeUtils.c")
 system("R CMD SHLIB dede_lv2.c")
 system("R CMD SHLIB dede_lv2F.f dedeUtils.c")
 system("R CMD SHLIB dedesimple.c")
 system("R CMD SHLIB dedesimpleF.f dedeUtils.c")
 system("bash")
 system(full, intern = quiet, ignore.stderr = quiet, ...)
 system(full, intern = TRUE, ignore.stderr = quiet, ...)
 system(paste0("mogrify -fill black -pointsize 36 -annotate +50+68 '", location, " ", ystart, "' ", file.path(md, fname)))
 system(paste0("mogrify -fill black -pointsize 36 -annotate +50+68 '", location, " ", y, "' ", file.path(md, fname)))
 system("ffmpeg -y -f image2 -r 25 -i movie%08d.png -vcodec libx264 -pix_fmt yuv420p movie.mp4")
 system('git log -1 --pretty=format:"%h %aD"', intern=TRUE)
 system(cmd)
 system(myCommand)
 system(paste("ls ", myDir, "/web/newalldetails*.html", sep=''), TRUE)
 system(call)
 system(tt)
 system(tt)
 system(tt)
 system(tt)
 system(tt)
 system(tt)
 system(paste(pdfV,fileN),wait=FALSE)
 system(paste(pngV,fileN),wait=FALSE)
 system(paste0(R.home(component = "bin"), "/R CMD SHLIB ", paste(filename, "c", sep = ".")), intern = TRUE)
 system(paste("ssh", m, "cat /proc/loadavg"), intern = TRUE)
 system(paste("ssh", m, "nproc"), intern = TRUE)
 system("cat /proc/loadavg", intern = TRUE)
 system("nproc", intern = TRUE)
 system(paste0("ssh ", machine[m], " ls ", filename[m], "_folder/ | grep -x ", filename[m], "_result.RData"), 
             intern = TRUE)
 system(paste0("scp ", machine[m], ":", filename[m], "_folder/", filename[m], "_result.RData ./"), ignore.stdout = TRUE, ignore.stderr = TRUE)
 system(paste0("ssh ", machine[m], " rm -r ", filename[m], "_folder"))
 system(paste0("rm ", filename0, "*"))
 system(paste0("ssh ", machine[m], " mkdir ", filename[m], "_folder/"), ignore.stdout = TRUE, ignore.stderr = TRUE)
 system(paste0("ssh ", machine[m], " rm ", filename[m], "_folder/*"), ignore.stdout = TRUE, ignore.stderr = TRUE)
 system(paste0("scp ", getwd(), "/", filename0, ".RData* ", machine[m], ":", filename[m], "_folder/"))
 system(paste0("scp ", getwd(), "/", filename[m], ".R* ", machine[m], ":", filename[m], "_folder/"))
 system(paste0("scp ", getwd(), "/*.c ", getwd(), "/*.cpp ", machine[m], ":", filename[m], "_folder/"))
 system(paste0("scp ", getwd(), "/*.so ", machine[m], ":", filename[m], "_folder/"))
 system(paste0("ssh ", machine[m], " R CMD BATCH --vanilla ", filename[m], "_folder/", filename[m], ".R"), intern = FALSE, wait = wait)
 system(paste0("ssh ", machine, " ls ", filename0, "_folder/ | grep result.RData"), 
             intern = TRUE)
 system(paste0("scp ", machine, ":", filename0, "_folder/*", "_result.RData ./"), ignore.stdout = TRUE, ignore.stderr = TRUE)
 system(paste0("rm ", filename0, "*"), wait = TRUE)
 system(paste0("ssh ", machine, " rm -r ", filename0, "*"), wait = TRUE)
 system(paste0("ssh ", machine, " mkdir ", filename0, "_folder/"), ignore.stdout = TRUE, ignore.stderr = TRUE)
 system(paste0("ssh ", machine, " rm ", filename0, "_folder/*"), ignore.stdout = TRUE, ignore.stderr = TRUE)
 system(paste0("scp ", getwd(), "/", filename0, ".RData* ", machine, ":", filename0, "_folder/"))
 system(paste0("scp ", getwd(), "/", filename0, "*.R* ", machine, ":", filename0, "_folder/"))
 system(paste0("scp ", getwd(), "/", filename0, "*.moab ", machine, ":"))
 system(paste0("scp ", getwd(), "/*.c ", getwd(), "/*.cpp ", machine, ":", filename0, "_folder/"))
 system(paste0("ssh ", machine, " 'module load math/R; R CMD SHLIB ", filename0, "_folder/*.c ", filename0,  "_folder/*.cpp -o ", filename0, "_folder/", filename0, ".so'"))
 system(paste0("scp ", getwd(), "/*.so ", machine, ":", filename0, "_folder/"))
 system(paste0("ssh ", machine, " msub ", filename[m], ".moab"), intern = FALSE)
 system(eval(paste("R CMD build --no-build-vignettes", source)))
 system(eval(paste0("scp ", dModPkg, " ", sshtarget, ":~/")))
 system(eval(paste("ssh", sshtarget, "R CMD INSTALL", dModPkg)))
 system(command = paste(command, filename))
 system(paste0(R.home(component = "bin"), "/R CMD SHLIB ", files[i], " ", args))
 system(paste0(R.home(component = "bin"), "/R CMD SHLIB ", paste(files, collapse = " "), " -o ", output, .so, " ", args))
 system(paste("wc -l",f),intern=TRUE)
 system(paste0("perl -ne 'print if (rand() < ",perc,")' ",file,
                  " > ",file,".tmp.csv"))
 system(ffmpeg_local[i])
 system(convert_local[i])
 system(paste0("R CMD check -o ",chkdir," ",pkgdir),intern=!display)
 system(paste0("R CMD build --resave-data ",pkgdir),intern=!display)
 system(paste0("R CMD check -o ",chkdir," ",pkgdir),intern=!display)
 system(paste0("R CMD build --resave-data ",pkgdir),intern=!display)
 system(cmd, input=stdInput)
 system(cmd)
 system(paste(c(Rbin,args),collapse=" "),intern=FALSE,wait=FALSE)
 system(matlabCall, ignore.stdout = TRUE, ignore.stderr = TRUE)
 system("git pull")
 system(cmd)
 system(paste(getOption("pdfviewer"), "fernTree2.pdf"))
 system( "gsl-config --cflags" , intern = TRUE )
 system( "gsl-config --libs"   , intern = TRUE )
 system(cmd, intern=!verbose)
 system(command)
 system("zenity --file-selection --directory", intern = TRUE)
 system("osascript -e 'tell app \"RStudio\" to POSIX path of (choose folder with prompt \"Choose Folder:\")' > /tmp/R_folder",
             intern = FALSE, ignore.stderr = TRUE)
 system("cat /tmp/R_folder && rm -f /tmp/R_folder", intern = TRUE)
 system(plink_Call)
 system(paste("zcat ",object@fileIn," | wc -l",sep=""),intern=TRUE)
 system(sprintf("wc -l %s",object@fileIn),intern=TRUE)
 system(paste("bgzip ",fileOut,sep=""))
 system(paste("tabix ",strTabixParam, " ", fileOut,sep=""))
 system(plink_Call)
 system(pingCmd, intern=TRUE,
               show.output.on.console=show.output.on.console)
 system(pingCmd, intern=TRUE,
               show.output.on.console=show.output.on.console)
 system(shQuote(paste(path.package("SWATmodel"),libarch,swatbin, sep = "/")))
 system(shQuote(paste(path.package("SWATmodel"), libarch, swatbin, sep = "/")))
 system(shQuote(paste(path.package("SWATmodel"), libarch, swatbin, sep = "/")))
 system(shQuote(paste(path.package("SWATmodel"), libarch, swatbin, sep = "/")))
 system("zip HMM_data.zip MAFFT.fasta hmmsearch.txt hmmbuild.hmm Readme.txt")
 system("ls", intern = TRUE)
 system(cmd)
 system(cmd)
 system("ls", intern = TRUE)
 system(string, intern = TRUE)
 system(paste(google[which(file.exists(google))],kmlD@fName,'&',sep=" "),ignore.stdout=TRUE,ignore.stderr=TRUE)
 system(paste(google[which(file.exists(google))],kmlD@fName,'&',sep=" "),ignore.stdout=TRUE,ignore.stderr=TRUE)
 system(paste(grass.cor.map[i], 
            " | awk '$3>0 {sum=sum+($1*$3*$2);np=np+$3} END{print sum/np}'"), intern = T)
 system(paste(grass.cor.map2[i], 
            " | awk '$3>0 {sum=sum+($1*$3*$2);np=np+$3} END{print sum/np}'"), intern = T)
 system(paste(grass.cor.map[i], 
            " | awk '{sum=sum+($1*$2)} END{print sum}'"), intern = T)
 system(paste("r.stats -1 ", i, ",", 
            presences_map, " | awk '{s=s+$1*$2;n=n+$2} END{print s/n}'", sep = ""), 
            intern = T)
 system(paste(grass.cor.map[i], 
            " | awk '{sum=sum+($1*$2)/", numberpixel, "} END{print sum}'"), intern = T)
 system(paste("r.mapcalc --overwrite 'pond_", i, " = ", i, " *", presences_map, 
            " / ", number_presences, "'", sep = ""))
 system(paste(grass.cor.map[i], 
            " | awk '{sum=sum+($1*$2)} END{print sum}'"), intern = T)
 system(calc)
 system(paste("r.mapcalc --overwrite", li.calc[i], sep = ""))
 system(calc.pred)
 system(calc.hsm)
 system(paste(CMD, "-dnum -s1 -e1 -cY -v0", tmpfile))
 system(
              paste(
                shQuote(msconvert_path),
                shQuote(rawfile),
 				filtered0,
                filtered1,
                filtered2,
                there2
              )
      ,intern=notintern)
 system(
              paste(
                shQuote(msconvert_path),
                shQuote(there1),
 				filtered0,
                filtered1,
                filtered2,
                there2
              )
          ,intern=notintern)
 system(gdalinfo_str, intern = TRUE)
 system(gdalinfo_str, intern = TRUE)
 system(gdal_str)
 system(paste0("rm -rf ", tempDir))
 system("R CMD Rd2pdf --no-preview --encoding=UTF-8 --force  NEWS.Rd")
 system("gswin64c -q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -dEmbedAllFonts=true -dPDFSETTINGS=/screen -sColorConversionStrategy=/RGB -sOutputICCProfile=srgb.icc -dCompatibilityLevel=1.5 -dAutoRotatePages=/None -sOutputFile=NEWSx.pdf NEWS.pdf")
 system("qpdf --stream-data=compress --object-streams=generate NEWSx.pdf NEWS.pdf")
 system(command,ignore.stderr = T,ignore.stdout = T)
 system(command,ignore.stderr = T,ignore.stdout = T)
 system(command,ignore.stderr = T,ignore.stdout = T)
 system(paste(shcmd, "pdfcrop --clip", paste0(name, ".pdf"), paste0(name, ".pdf")), ignore.stdout = TRUE)
 system(paste(shcmd, "pdf2svg", paste0(name, ".pdf"), paste0(name, if(nt > 1) "_%d" else NULL, ".svg"), "all"), ignore.stdout = TRUE)
 system(paste(shQuote(getOption("pdfviewer")), shQuote(out_pdf)), wait = FALSE)
 system(paste(sh, cmd), ...)
 system("tesseract -psm 6 .tesseract-temp-image.png .tesseract-temp-text",
    ignore.stderr = TRUE)
 system(paste(shQuote(getOption("pdfviewer")), shQuote(out)), wait = FALSE)
 system(command, ignore.stdout = TRUE,
    ignore.stderr = TRUE, show.output.on.console = FALSE)
 system(command, ignore.stdout = TRUE,
                   ignore.stderr = TRUE, show.output.on.console = FALSE)
 system(command, intern = TRUE)
 system(command, intern = TRUE)
 system(command, intern=intern, ...)
 system(paste0("open ", path))
 system(paste0("xdg-open ", path))
 system(paste("ln -s", XmLib, tmpLink))
 system(paste0("open ", path))
 system(paste0("xdg-open ", path))
 system(cmd)
 system("head -20 ddd.txt ddd.csv")
 system("head SomeData.txt SomeData.csv")
 system("hostname -s", TRUE)
 system("rm -fr package-Ch3")
 system("rm -fr package-Ch4")
 system("R CMD SHLIB chambers-1980.c")
 system("rm -fr package-Ch7")
 system("rm -fr package-ChA")
 system("rm -fr package-Ch5")
 system("rm -fr package-Ch9")
 system("rm -fr package-Ch2")
 system("rm -fr package-Ch6")
 system("rm -fr package-Ch9")
 system("./closure")
 system( paste( "cp", FBATSOURCE, FBAT ) )
 system( paste( sh, filename ), intern=FALSE, ... )
 system( paste( sh, filename, ">", output ), intern=FALSE, ... )
 system( paste( sh, filename ), intern=intern, ... )
 system( paste( sh, filename, ">", output ), intern=intern, ... )
 system( paste( "pdflatex", filename ) )
 system( paste( pdf, pdfname ) )
 system( "tar -zxvf fbat.tgz" )
 system( paste( "mv ", fbat.extrapath(), "* .", sep="" ) )
 system( "rtools.exe" )
 system(cmd, input=filelist, intern=TRUE)
 system(cmd, intern=TRUE)
 system(cmd, intern=TRUE)
 system(cmd, intern=TRUE)
 system(cmd, intern=TRUE)
 system(paste(shQuote(getOption("pdfviewer")), shQuote(pdfManual)), wait = FALSE)
 system(cmd, intern = intern)
 system(cmd, intern = intern)
 system(cmd, intern = intern)
 system("unzip \\*.zip")
 system("mv *.zip ../.archive/zip_files/")
 system(paste('awk -F "," ' , "'NR!=1 {filename=$1; sub($1FS,blank); print >> filename",'".csv"',"}'" , file, sep=" "))
 system(paste("mv ", file, " ../.archive/csv_files/", file, sep=""))
 system(paste("echo ", header," > ", fullpathfile, sep=""))
 system(paste("cat ", file, " >> ", fullpathfile, sep=""))
 system(paste("rm gold_prices.xls"))
 system("wget http://www.gold.org/download/get/value/stats/statistics/xls/gold_prices.xls")
 system(paste('echo "', Sys.time(), ' configureTRTH job.name: ', .TRTH$job.name, '" > ', 
                 paste(.TRTH$path.output, "current.job.txt", sep=""), 
                 sep=""))
 system(paste('TMPDIR=', .TRTH$tmp, 
                         ' R --no-site-file --no-init-file --quiet', sep=""))
 system(paste('echo "', Sys.time(), ' download_reut job.name: ', .TRTH$job.name, '" > ', 
                 paste(.TRTH$path.output, "current.job.txt", sep=""), 
                 sep=""))
 system(paste("curl ftp://tickhistory-ftp.thomsonreuters.com:15500/results/ -u ",
                                .TRTH$username,":",.TRTH$password," --ftp-ssl -k -l",sep=""),intern=TRUE)
 system(paste("curl -m 10800 --max-filesize 1610612736 ftp://tickhistory-ftp.thomsonreuters.com:15500/results/", 
                                    filename.gz, " -u ", .TRTH$username, ":", .TRTH$password, " --ssl -k > ", .TRTH$archive_dir, filename.gz, sep=""))
 system(paste("curl ftp://tickhistory-ftp.thomsonreuters.com:15500/results/",
                        Reuters.report[grep(alias,Reuters.report)], " -u ", .TRTH$username, ":", .TRTH$password,
                        " --ftp-ssl -k > ", .TRTH$archive_dir, Reuters.report[grep(alias,Reuters.report)], sep=""))
 system(paste('echo "', Sys.time(), ' splitCSV job.name: ', .TRTH$job.name, '" > ', 
                 paste(.TRTH$path.output, "current.job.txt", sep=""), 
                 sep=""))
 system(paste("gunzip -f < ", .TRTH$archive_dir, filename.gz, " > ", .TRTH$tmp_archive_dir, filename.csv, sep=""))
 system(paste('awk -v f2="" -F "," '," '",'{f1 = $1"."$2".csv";if(f1 != f2) { print >> f1; close(f2); f2=f1; } }',"' ",filename.csv, sep=""))
 system(paste('tail -1 "', files.header, '" > header.csv', sep=""))
 system(paste('mv header.csv "', files.header, '"', sep=""))
 system(paste('cp "', files.header, '" ', paste(.TRTH$tmp_archive_dir, fl, sep=""), sep=""))
 system(paste('awk -v f2="" -F "," '," '",'{f1 = $1"."$2".csv";print >> f1; if(f1 != f2) { close(f2); f2=f1; } }',"' ",filename.csv, sep=""))
 system(paste("mv -fv ", name.csv, " ", .TRTH$csv_dir, date.format, "/", date.format, ".", name.new, ".csv", sep=""))
 system(paste("mv -nv ", name.csv, " ", .TRTH$csv_dir, date.format, "/", date.format, ".", name.new, ".csv", sep=""))
 system(paste('echo "', Sys.time(), ' FEreut2xts job.name: ', .TRTH$job.name, '" > ', 
                 paste(.TRTH$path.output, "current.job.txt", sep=""), 
                 sep=""))
 system(paste("gzip -d -f ", CSV.name, ".gz", sep=""))
 system(paste("gzip -f ", CSV.name, sep=""))
 system("rm DJUBS_full_hist.xls")
 system("wget http://www.djindexes.com/mdsidx/downloads/xlspages/ubsci_public/DJUBS_full_hist.xls")
 system(path, intern=TRUE, input=python_code, ignore.stderr=TRUE)
 system(paste(Editor.name,control.path),invisible=F,wait=F)
 system(NONMEM.command,wait=F)
 system(NONMEM.command,wait=F)
 system(paste(Editor.name,paste(dir.name,"\\",file.id,sep="")),wait=F)
 system(NONMEM.command,invisible=F,show.output.on.console=F,wait=F)
 system(NONMEM.command,invisible=F,show.output.on.console=F,wait=F)
 system("Rgui")
 system(random.command,invisible=F,show.output.on.console=F)
 system(VPC.command,invisible=F,show.output.on.console=F)
 system(Boot.command,invisible=F,show.output.on.console=F)
 system(wam.command,invisible=F,show.output.on.console=F)
 system(CDD.command,invisible=F,show.output.on.console=F)
 system(CV.command,invisible=F,show.output.on.console=F)
 system(CV.command,invisible=F,show.output.on.console=F)
 system(NM.command,invisible=F,show.output.on.console=F)
 system("env")
 system(paste0("head -n100 ", x), intern = TRUE)
 system(paste0("tail -n100 ", x), intern = TRUE)
 system(cmd, intern = TRUE)
 system(sprintf("echo %s ", jobj@format), intern=TRUE)
 system(cmds[i], intern = TRUE)
 system(paste(convert.path,"-version"),FALSE)
 system("convert -version",TRUE,TRUE)
 system( paste( sascmd, tmpProg ) )
 system(paste("ls -l ", tmpProgLog))
 system(command, intern=TRUE)
 system(paste(solver, "-v"), intern=TRUE)
 system(command, intern=TRUE)
 system(paste(solver, "-v"), intern=TRUE)
 system(command, intern=TRUE)
 system(paste(solver, "-v"), intern=TRUE)
 system(command, show.output.on.console = TRUE)
 system(command, intern=TRUE)
 system(command, intern=TRUE)
 system(paste(solver, "-v"), intern=TRUE)
 system(command, intern=TRUE)
 system(paste(solver, "-v"), intern=TRUE)
 system(header)
 system(cmd)
 system(cmd)
 system(cmd)
 system(old_reset)
 system(cmd, intern = TRUE)
 system(cmd)
 system(old_reset)
 system(cmd)
 system(cmd, intern = intern, ...)
 system(old_reset)
 system( fullCommand, intern = TRUE )
 system(cmd)
 system(cmd, intern=intern)
 system(cmd)
 system(cmd, intern=intern)
 system(cmd, intern=intern)
 system(cmd, intern = intern)
 system(cmd, intern = TRUE)
 system(cmd, intern = intern)
 system(cmd, intern = intern)
 system(cmd, intern = intern)
 system(cmd, intern = TRUE)
 system(cmd, intern = TRUE)
 system(cmd, intern = intern)
 system(cmd, intern = intern)
 system(cmd, intern = intern)
 system(cmd, intern = intern)
 system(cmd, intern = intern)
 system(cmd, intern = TRUE)
 system(cmd, intern = intern)
 system(cmd, intern = intern)
 system(cmd, intern = intern)
 system(cmd, intern = TRUE)
 system(cmd)
 system(cmd, intern = FALSE)
 system(cmd, intern = intern)
 system(cmd, intern = FALSE)
 system(cmd, intern=intern)
 system(cmd, intern=intern)
 system(cmd, intern=intern)
 system(cmd)
 system(cmd, intern=intern)
 system("shutdown -h now")
 system("gunzip go_DATE-termdb-tables.tar.gz")
 system("tar -xf go_DATE-termdb-tables.tar")
 system(file.path(bin, pkg), intern = TRUE)
 system(local_cmd, wait = FALSE, input = input)
 system(cmd, intern=TRUE)
 system(cmd,      intern=TRUE)
 system(cmd,      intern=TRUE)
 system(cmd,      intern=TRUE)
 system(cmd,      intern=TRUE)
 system(cmdgpu, intern=TRUE)
 system("sudo apt-get -y --force-yes install libatlas3gf-base", intern=TRUE, ignore.stderr=TRUE)
 system("sudo apt-get -y --force-yes purge libatlas3gf-base", intern=TRUE, ignore.stderr=TRUE)
 system("sudo apt-get -y --force-yes install revolution-mkl r-revolution-revobase revolution-r", intern=TRUE, ignore.stderr=TRUE)
 system("sudo apt-get -y --force-yes purge revolution-mkl r-revolution-revobase revolution-r", intern=TRUE, ignore.stderr=TRUE)
 system("sudo wajig -y install /var/spool/gotoblas2-helper/archive/gotoblas2_1.13-1_amd64.deb", intern=TRUE, ignore.stderr=TRUE)
 system("sudo apt-get -y --force-yes purge gotoblas2", intern=TRUE, ignore.stderr=TRUE)
 system("sudo wajig -y install /var/spool/atlas39/libatlas39_3.9.25-1_amd64.deb", intern=TRUE, ignore.stderr=TRUE)
 system("sudo apt-get -y --force-yes purge libatlas39", intern=TRUE, ignore.stderr=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(cmd, intern=!verbose)
 system(cmd, intern=TRUE, ignore.stderr=TRUE)
 system(cmd, intern=TRUE)
 system(cmd, intern=TRUE)
 system("which PATHd8", ignore.stdout=TRUE)
 system(paste("PATHd8 -n", infile, "-pn >", outfile, sep=" "))
 system(paste("grep \"d8 tree\" ", outfile, ">", parsed.outfile, sep=" "))
 system(command, intern = T)
 system("which df", intern = TRUE)
 system(cmd, intern = TRUE)
 system("rm -r ./demo.genos")
 system(paste("cut -d \"", ped.sep ,"\" -f 1-", num.nonsnp.col, " ", ped.dir, "/", ped.file, " > ", tmp.file, sep=""))
 system(paste("cut -d \"", ped.sep ,"\" -f ", (G.start[g]+num.nonsnp.col), " ", ped.dir, "/", ped.file, " > ", tmp.file, sep=""))
 system(paste("cut -d \"", ped.sep ,"\" -f ", (G.start[g]+num.nonsnp.col), "-", (G.end[g]+num.nonsnp.col), " ", ped.dir, "/", ped.file, " > ", tmp.file, sep=""))
 system(combo)
 system(todelete)
 system(step.call)
 system(paste("cd ", dir.debug, " ; ls -v *mlgeno > all.txt", sep=""))
 system(paste("cd ", dir.debug, " ; cat $(ls -v *mlgeno) > ", touse, sep=""))
 system(paste("cp", fromfile, touse, sep=" "))
 system(command.rem)
 system(command.dis.status)
 system(command.paste)
 system(cut.call)
 system(cut.data)
 system(cut.delim)
 system(cut.combo)
 system(uncomp.call)
 system(paste("rm", ped.name.cols, names$ped, ped.name.data, ped.name.delim, ped.name.combo,  sep=" "))
 system(step2)
 system(paste("gzip -d ", possible.mlgeno,  sep=""))
 system(step1)
 system(uncomp.call)
 system(cut.call)
 system(cut.space)
 system(cut.data)
 system(cut.delim)
 system(cut.combo)
 system(paste("rm", ped.name, ped.name.cols, ped.name.cols.space, ped.name.data, ped.name.delim, sep=" "))
 system(paste("wc ", genome.file, sep=""), intern=TRUE)
 system(paste("cut -f ", (num.nonsnp.col+1), "-", col.genos, " ", curr.file, " > ", tmp.names[i], sep=""))
 system(paste("cut -f 1-", col.genos, " --complement ", curr.file, " > ", disease.name, sep=""))
 system(to.paste)
 system(shred.comand)
 system(paste("tar -xjf ", dir.in, "/", fname[i], " -C ", dir.out, sep=""))
 system(command)
 system(command)
 system(command)
 system(cmd_vcftools)
 system(paste("cp", sort_by_chr, "."))
 system(cmd_finding_snps)
 system(cmd_grandmaster_snps)
 system(paste("gpsbabel -i csv -f", container, 
      "-x transform -o gpx -F", filename))
 system(paste("gpsbabel -i csv -f", container, 
      "-x transform,rte=wpt,del -o gpx -F", filename))
 system(paste("gpsbabel -i csv -f", container, 
      "-x transform,trk=wpt,del -o gpx -F", filename))
 system(paste("chmod u+x", tmpskipanaskra))
 system(tmpskipanaskra)
 system(call)
 system(command = Argument, ...)
 system(paste("sed -e 's/NCOLS/ncols/g'",name,">",namen[1]))
 system(paste("sed -e 's/NROWS/nrows/g'",namen[1],">",namen[2]))
 system(paste("sed -e 's/XLLCORNER/xllcorner/g'",namen[2],">",namen[3]))
 system(paste("sed -e 's/YLLCORNER/yllcorner/g'",namen[3],">",namen[4]))
 system(paste("sed -e 's/CELLSIZE/cellsize/g'",namen[4],">",namen[5]))
 system(cmd, intern = TRUE)
 system(cmd, ignore.stdout = TRUE, ignore.stderr = TRUE, show.output.on.console = FALSE)
 system(cmd, ignore.stdout = TRUE, ignore.stderr = TRUE)
 system(syscmd, intern=TRUE)
 system(paste0("perl ", perlscript," ",fname),intern=T,ignore.stderr=T)
 system('taskkill /f /im java.exe', show.output.on.console = F)
 system('taskkill /f /im phantomjs.exe', show.output.on.console = F)
 system('killall -1 phantomjs > /dev/null 2>&1')
 system(cmd_line, wait=F)
 system(cmd)
 system("git remote -v", intern = TRUE)
 system("git config remote.origin.fetch", intern = TRUE)
 system("git config --add remote.origin.fetch +refs/merge-requests/*/head:refs/remotes/origin/merge-requests/*")
 system("git fetch origin")
 system("git branch ", intern = TRUE)
 system(paste0("git checkout -b ", dat[["un"]], " origin/merge-requests/", dat[["id"]]))
 system(paste0("git branch -d -r origin/merge-requests/", dat[["id"]]))
 system(paste0("git push --set-upstream origin ", dat["un"]))
 system(cmd, intern = TRUE)
 system(cmd, intern = TRUE)
 system("git config --global --list", intern = TRUE)
 system(.)
 system("git config --global --list", intern = TRUE)
 system("git config --global --list", intern = TRUE)
 system("git config --global credential.helper osxkeychain")
 system("git config --global credential.helper wincred")
 system("git config --global credential.helper 'cache --timeout=32000000'")
 system("git config --global --list", intern = TRUE)
 system(cmd)
 system("git branch -a", intern = TRUE)
 system(.)
 system(paste("git checkout", into))
 system(paste("git merge", from))
 system("git merge --abort")
 system(.)
 system(paste0("git branch -d -r origin/", branch))
 system("git checkout master")
 system(.)
 system("git branch --all", intern = TRUE)
 system(paste0("git checkout ", sub("remotes/origin/","",input$branch_checkout_name)))
 system("git remote -v", intern = TRUE)
 system("git remote -v", intern = TRUE)
 system(paste("git remote add upstream", input$sync_from))
 system("git fetch upstream")
 system("git checkout master")
 system("git merge upstream/master")
 system("git merge --abort")
 system("git remote remove upstream")
 system("git config remote.origin.fetch", intern = TRUE)
 system(paste0("R CMD INSTALL --build ", f))
 system(paste0(Sys.which("R"), " -e \"source('~/gh/gitgadget/build/build_mac.R')\""))
 system("git add --all .")
 system(paste0("git commit -m '",mess,"'"))
 system("git push")
 system(paste0("R CMD INSTALL --build ", f))
 system(sprintf('rm -rf gitter/build/%s', targz))
 system(sprintf('%s CMD build gitter', R_PATH))
 system(sprintf('mv %s gitter/build/%s', targz, targz))
 system(sprintf('%s CMD INSTALL gitter/build/%s', R_PATH, targz))
 system(
      "find /store/patrick/ -name OpenBUGS",
      TRUE)
 system(
      "find /store/patrick/ -name OpenBUGS",
    TRUE)
 system(paste("pdflatex", file))
 system(cmd, intern=TRUE)
 system(paste(py, doc), intern = TRUE)
 system('rm queries.fasta')
 system('rm toCompute_gphmm.csv')
 system('rm toCompute.csv')
 system('rm train.csv')
 system('rm train.fasta')
 system('rm train_paramgphmm.json')
 system('rm train_llgphmm.json')
 system(paste('eps2png ',path,'/',fileName, '.eps',sep=''))
 system(paste('eps2png ', pathfilename, sep=''))
 system(paste('eps2png ', pathfilename, sep=''))
 system(paste('eps2png ', pathfilename, sep=''))
 system(paste('convert -delay 80 ',path,'/',filename,'*.png ', path,'/',filename,'.gif', sep=''))
 system(paste('eps2png ', path,'/gpCovariance.eps', sep=''))
 system(paste('eps2png ', path,'/',filename,'.eps', sep=''))
 system(paste('eps2png ', pathfilename, sep=''))
 system(paste('convert -delay 80 ',path,'/',filename,'*.png ', path,'/',filename,'.gif', sep=''))
 system(paste('eps2png ', pathfilename, sep=''))
 system(paste('eps2png ', pathfilename, sep=''))
 system(paste('convert -delay 80 ',path,'/',filename,'*.png ', path,'/',filename,'.gif', sep=''))
 system(paste('eps2png ',path,'/',fileName, '.eps',sep=''))
 system(paste('eps2png ',path,'/',filename,'1_',as.character(figNo),'.eps',sep=''))
 system(paste('eps2png ',path,'/',filename,'2_', as.character(figNo), '.eps',sep=''))
 system(paste('convert -delay 80 ',path,'/',filename,'1_*.png ', path,'/',filename,'1.gif', sep=''))
 system(paste('convert -delay 80 ',path,'/',filename,'2_*.png ', path,'/',filename,'2.gif', sep=''))
 system(paste('eps2png ',path,'/',filename,'_1.eps',sep=''))
 system(str_c("diff ", e1, " ", e2))
 system( paste('java -Xmx800m -jar ',dir,'beagle.jar data=',dir, 'dat.bgl scale=',m,' shift=',b,' out=D', sep=''))
 system(cmd, intern=intern, ignore.stderr = ignore.stderr)
 system(op)
 system(paste('chmod u=rw,g=rw,o=', paste(shQuote(paths), collapse=' ')))
 system(paste('scp ', paste(shQuote(paths), collapse=' '), ' ', server, ':', path, sep=''))
 system(cmd)
 system(cmd)
 system(paste(shQuote(gsexe), "-help > /dev/null"))
 system(cmd)
 system(cmd, invisible = TRUE)
 system(paste(program, '-where \"OGR_GEOMETRY=\'Polygon\'\" -f \"ESRI Shapefile\"', set.file.extension(outname, ".shp"), set.file.extension(tf, ".shp"), '-clipsrc',  y[j,1], y[j,2], y[j,3], y[j,4], '-skipfailures'), show.output.on.console = show.output.on.console)
 system(paste(program, '-where \"OGR_GEOMETRY=\'Linestring\'\" -f \"ESRI Shapefile\"', set.file.extension(outname, ".shp"), set.file.extension(tf, ".shp"), '-clipsrc',  y[j,1], y[j,2], y[j,3], y[j,4], '-skipfailures'), show.output.on.console = show.output.on.console)
 system(paste(program, shortPathName(normalizePath(filename(x))), set.file.extension(outname, ".tif"), '-te',  y[j,1], y[j,2], y[j,3], y[j,4]), show.output.on.console = show.output.on.console)
 system(paste(program, ' ', tf, extension, ' ', tf, '_ll.tif -dstnodata \"255\" -r near -ot \"Byte\" -tr ', pixsize, ' ', pixsize, sep=""), show.output.on.console = show.output.on.console)
 system(paste(program, ' ', tf, '.tif', ' -t_srs \"', proj4s, '\" ', tf, '_ll.tif -dstnodata \"255\" -r near -ot \"Byte\" -tr ', pixsize, ' ', pixsize, sep=""), show.output.on.console = show.output.on.console)
 system(paste(program, ' ', tf, extension, ' ', tf, '_ll.tif -dstnodata \"255\" -ot \"Byte\" -r near', ' -te ', bbox[1,1], ' ', bbox[2,1], ' ', bbox[1,2], ' ', bbox[2,2], ' -ts ', [email protected][1], ' ', [email protected][2], sep=""), show.output.on.console = show.output.on.console)
 system(paste(program, ' ', tf, '.tif', ' -t_srs \"', proj4s, '\" ', tf, '_ll.tif -dstnodata \"255\" -ot \"Byte\" -r near', ' -te ', bbox[1,1], ' ', bbox[2,1], ' ', bbox[1,2], ' ', bbox[2,2], ' -ts ', [email protected][1], ' ', [email protected][2], sep=""), show.output.on.console = show.output.on.console)
 system(paste(program, ' ', tf, extension, ' ', tf, '_ll.tif -dstnodata \"', NAflag, '\" -r ', resampling_method, ' -tr ', pixsize, ' ', pixsize, sep=""), show.output.on.console = show.output.on.console)
 system(paste(program, ' ', tf, '.tif', ' -t_srs \"', proj4s, '\" ', tf, '_ll.tif -dstnodata \"', NAflag, '\" -r ', resampling_method, ' -tr ', pixsize, ' ', pixsize, sep=""), show.output.on.console = show.output.on.console)
 system(paste(program, ' ', tf, extension, ' ', tf, '_ll.tif -dstnodata \"', NAflag, '\" -r ', resampling_method, ' -te ', bbox[1,1], ' ', bbox[2,1], ' ', bbox[1,2], ' ', bbox[2,2], ' -ts ', [email protected][1], ' ', [email protected][2], sep=""), show.output.on.console = show.output.on.console)
 system(paste(program, ' ', tf, '.tif', ' -t_srs \"', proj4s, '\" ', tf, '_ll.tif -dstnodata \"', NAflag, '\" -r ', resampling_method, ' -te ', bbox[1,1], ' ', bbox[2,1], ' ', bbox[1,2], ' ', bbox[2,2], ' -ts ', [email protected][1], ' ', [email protected][2], sep=""), show.output.on.console = show.output.on.console)
 system(paste0(gdalwarp, ' ', fname, ' ', out.fname[[i]], ' -t_srs \"', proj4string(dens), '\" -co \"COMPRESS=DEFLATE\" -r \"', resample.method, '\" -tr ', pixel.size, ' ', pixel.size,' -te ', paste(as.vector(dens@bbox), collapse=" ")))
 system(cmd)
 system(paste("tail -20 ",y,".log", sep=""))
 system(runme)
 system(paste("sendmail -t  <", tmp))
 system(paste("sendmail -t  <", tmp))
 system("curl 'http://localhost:54321'")
 system(paste0("open '", myFile, "'"))
 system(hiccmd)
 system("ls /usr/local/bin/", intern=TRUE)
 system(paste("/usr/local/bin/growlnotify -t 'R script info' -m '", textinfo, "' -a 'R'", sep=""))
 system(command, intern=intern, ignore.stdout=ignore.stdout, ignore.stderr=ignore.stderr)
 system(paste0("cd '", getwd(), "';rm *.gz;rm *.toc;rm *.tex;rm *.log"))
 system(cmd, intern = TRUE)
 system(sprintf('%s jar %s %s -input %s -output %s %s %s %s %s',
                 hadoop(henv), hadoop_streaming(henv), streaming_args, input, output,
                 mapper_arg, reducer_arg, files, cmdenv_arg),
         intern = TRUE)
 system(sprintf("chmod 775 %s", script), ignore.stderr = TRUE)
 system( .DFS_create_command(cmd, args, henv), ignore.stderr = TRUE )
 system( .DFS_create_command(cmd, args, henv), intern = TRUE, ignore.stderr = TRUE )
 system("whoami", intern = TRUE)
 system(command)
 system(sprintf("%s namenode -format", hadoop(henv)))
 system("hadoop version", intern = TRUE, ignore.stderr = TRUE)
 system( dfs_action_sh, intern = TRUE, ignore.stderr = TRUE )
 system('cd /tmp; latex -shell-escape z; display /tmp/z.png')
 system('nproc', intern=T)
 system('nproc', intern=T)
 system('nproc', intern=T)
 system(sprintf('curl -o "%s" "%s"', filename, url))
 system(sprintf('curl -o "%s" "%s"', filename, url))
 system(sprintf('curl -o "%s" "%s"', filename, url))
 system('nproc', intern=T)
 system('nproc', intern=T)
 system(paste("wc -l",file), intern=TRUE)
 system(paste("wc -l",file), intern=TRUE)
 system(paste(getOption("pdfviewer"), doc, "&"))
 system(paste(getOption("pager"), doc, "&"))
 system(paste(getOption("pdfviewer"), doc, "&"))
 system(paste("mkdir ", JSCPATH))
 system(paste("cp -r ", jscDIR,"* ", JSCPATH,"/",sep=""))
 system(paste("mkdir ", JSCPATH))
 system(paste("cp -r ", jscDIR,"* ", JSCPATH,"/",sep=""))
 system("uname",TRUE)
 system("whoami",TRUE)
 system(paste("open ", file))
 system(paste("cp ", ggg, " ", paste(basepath, path, Graphpath, gg, sep="") ,sep="") )
 system("mkdir Figures")
 system(cmd)
 system(command)
 system(paste(locale_util, "-a"), intern = TRUE)
 system(paste(shQuote(pandoc_path), "--version"),
                           intern = TRUE)
 system(paste(Sys.getenv("R_PDFVIEWER"),f,"&"))
 system(paste(shQuote(file.path(R.home("bin"), "R")),
               "CMD", "Rd2pdf", "--batch", if (!launch) "--no-preview", shQuote(path)),
         show.output.on.console = FALSE)
 system("cmd.exe", input = paste0('"C:/Program Files/7-Zip/7z.exe" e ', zipfiles[i], " -o\"", file.path(dest, regions[i])))
 system("cmd.exe", input = paste0("\"C:\\Program Files\\7-Zip\\7z.exe\" e ", Sys.glob(file.path(dirname(zipfiles[i]), paste0("NHDPlusV21_", regions[i],"_NHDPlusAttributes_*", ".7z"))), " -o\"", file.path(dest, regions[i])))
 system (sprintf ("echo '%s'", paste (...)))
 system ("wc --help", intern = TRUE)
 system(cmd)
 system(paste(shQuote(getOption("pdfviewer")), shQuote(ref)), 
              wait = FALSE)
 system(paste(shQuote(file.path(R.home("bin"), "R")),
             "CMD", "Rd2pdf", shQuote(path)))
 system(paste("open ", RasterPlotPath, sep="") )
 system(paste("cd", tmp, ";", "unzip", foodzip[1]))
 system(paste("cd", tmp, ";", "unzip", foodzip[2]))
 system(paste("cd", tmp, ";", "mv *.paj paj/"))
 system(str, wait=F, invisible=F)
 system(paste(cmd,fname),intern=TRUE)
 system("net localgroup",intern=TRUE)
 system(findeAdmin,intern=TRUE)
 system(
        paste0("runas /noprofile /user:",administrator," DOSBox0.74-win32-installer.exe"),
        invisible=FALSE,
        wait = FALSE)
 system("sudo -kS apt-get -y install build-essential autoconf automake",input=readline("Enter your password: "))
 system("sudo -kS apt-get -y install build-dep dosbox",input=readline("Enter your password: "))
 system(paste0("unzip -o ", destination_facets," -d /home/",user,"/facdos"))
 system(cmd, intern=!verbose)
 system(cmd)
 system(paste("R CMD check",cdir))
 system(paste("R CMD check",cdir))
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(paste0("\"pdftotext\" \"", i, "\""), wait = TRUE)
 system(paste("\"", pathToPdftotext, "\" \"", i, "\"", sep = ""), wait = TRUE)
 system(paste("pdftotext" , i, sep = " "), wait = TRUE)
 system(paste("pdftotext" , i, sep = " "), wait = TRUE)
 system("RCMD SHLIB mymod.c")
 system("RCMD SHLIB mymodff.f")
 system(update_packages_expression, wait = TRUE, intern = TRUE, show.output.on.console = TRUE)
 system(new_Rexe_path, wait = F)
 system(exe_path, wait = F)
 system("ipconfig", intern = TRUE)
 system("ifconfig", intern = TRUE)
 system(install_cmd, wait = wait,...)
 system("tasklist",intern = TRUE)
 system("shutdown -h now")
 system(call.prank)
 system(CALL)
 system(call)
 system(paste("./mb > execute", file))
 system(paste("mrbayes ", file, ".bayes", sep = ""))
 system(paste("mpirun", CALL))
 system(CALL)
 system(CALL)
 system(call.mafft, intern = FALSE, ignore.stdout = FALSE)
 system(call.mafft, intern = TRUE, ignore.stderr = FALSE)
 system(paste("mb > execute", file))
 system(paste("mrbayes ", file, ".bayes", sep = ""))
 system(call)
 system(call)
 system(paste(exec, " R2GBLOCK.fas -t=d", 
               " -b1=", b1,
               " -b2=", b2,
               " -b3=", b3,
               " -b4=", b4,
               " -b5=", b5, 
               sep = ""),
         )
 system (paste0("qstat -j ", jobid),
                 ignore.stdout = TRUE, ignore.stderr = TRUE,
                 intern = FALSE, wait = TRUE)
 system (paste0("qstat ", jobid),
                 ignore.stdout = TRUE, ignore.stderr = TRUE,
                 intern = FALSE, wait = TRUE)
 system(paste("icl",f))
 system(paste("wine","BLM1.EXE",run.name))
 system(paste("wine","BLM2.EXE",run.name))
 system(paste("wine","BLM3.EXE",run.name))
 system(paste("blm1",run.name))
 system(paste("blm2",run.name))
 system(paste("blm3",run.name))
 system(cmd)
 system("hdiutil mount JGR-1.6-SL.dmg")
 system("cp -r /Volumes/JGR-1.6-SL/JGR.app JGR-SL.app")
 system("hdiutil mount JGR.dmg")
 system("cp -r /Volumes/JGR/JGR.app JGR.app")
 system(paste("chmod 755 ", outfile))
 system(paste('msg *',s))
 system(paste0('osascript -e \'tell app "Finder" to display dialog "',s,'"\''))
 system("java -version")
 system(cmd,wait=FALSE)
 system('julia -e "println(1)"', intern = TRUE)
 system("which install_name_tool", intern = TRUE)
 system("which otool", intern = TRUE)
 system(paste(cmd.ot, " -L ", fn.JK.so, sep = ""),
                      intern = TRUE)
 system(paste0("xlsx2csv --delimiter=tab --dateformat=%m-%d-%y \"",
                file, "\" > ", csvfile))
 system(paste0("xelatex -interaction=batchmode ", temp_file, ".tex"))
 system("wmic desktopmonitor get screenwidth", 
                                 intern = TRUE)
 system("wmic desktopmonitor get screenheight", 
                                intern = TRUE)
 system(command, intern=TRUE)
 system(paste("security 2>&1 >/dev/null find-", type,"-password -gl ", label, " | grep '^password' | cut -c 12- | rev | cut -c 2- | rev", sep=""), intern=TRUE)
 system(paste("secret-tool lookup ", key_value_pairs, sep=""), intern=TRUE)
 system(paste(cmd, svm.options, train.filename[j], model.filename[j]), 
                  show.output.on.console = out)
 system(paste(cmd,svm.options, train.filename[j], model.filename[j]))
 system(paste(cmd, test.filename, model.filename[j], pred.filename[j]))
 system('lyx -version')
 system(cmd, ignore.stdout = TRUE)
 system(ffmpeg.cmd, ignore.stdout = TRUE)
 system(sprintf('%s %s.sty', kpsewhich(), name), intern = TRUE)
 system(cmd)
 system(paste('R CMD SHLIB', f), intern = TRUE)
 system(cmd)
 system("make integration-need", ignore.stdout = TRUE)
 system('make deps -C knitr-examples')
 system(command)
 system(sys.tt.call, ignore.stderr=TRUE, intern=TRUE)
 system(makeGit, intern = TRUE)
 system(messg1, intern = TRUE)
 system(messg2, intern = TRUE)
 system(cmd, intern = TRUE)
 system(cmd2, intern = TRUE)
 system(sprintf("ls -1 %s/*.kvh", dexample), intern=TRUE)
 system ( paste(Sys.getenv("COMSPEC")," /c ",cmd) , invisible =TRUE, intern=FALSE, ...)
 system(paste("gdalinfo ", filename, sep=""), intern=TRUE)
 system(paste("echo ", centerx, " ", centery, " | gdaltransform -s_srs EPSG:", centerepsg, " -t_srs EPSG:", lsepsg, 
                sep=""), intern=TRUE)
 system(paste("gdal_translate -projwin ", centerx - (lspixelsize[1]*widthx), " ", centery + (lspixelsize[2]*widthy), " ", centerx + (lspixelsize[1]*widthx), " ", centery - (lspixelsize[2]*widthy), " ", filename, " ", outname, sep=""), intern=TRUE)
 system(paste("Rscript -e 'library(parallel);library(LaplacesDemon);server_Listening(n=",CPUs,")'", sep=""), wait=FALSE)
 system(cmnd)
 system(cmd)
 system(command)
 system(sprintf("ttf2afm -o %s.afm %s.TTF", fn, 
                       file.path(Sys.getenv("windir"), "Fonts", fn)))
 system(sprintf("gzip %s.afm", fn))
 system(mycmd1)
 system(mycmd2)
 system(mycmd1,intern=TRUE)
 system(mycmd2,intern=TRUE)
 system(mycmd, wait=wait, intern=TRUE)
 system("prelis prelistmp.in prelistmp.out")
 system("mdfind -name ImageJ | grep 'ImageJ.app'", intern = TRUE)
 system(paste("cp -r", imagedir, temp))
 system(paste("java -Xmx", set.memory, "g -jar ",path.imagej,"ij.jar -ijpath ",path.imagej," ",exe,tempmacro," ", set.directory, sep = ""), wait = wait)
 system(paste("java -Xmx", set.memory, "g -jar ", path.imagej, "Contents/Resources/Java/ij.jar -ijpath ", path.imagej, " ", exe, tempmacro, " ", set.directory, sep = ""), wait = wait)
 system("killall java")
 system("python EMPA.py",wait=TRUE)
 system(paste("kill -9", pid))
 system('docker -v', intern = TRUE)
 system('docker info', intern = TRUE, ignore.stderr = TRUE)
 system(docker_build_cmd)
 system(docker_run_cmd)
 system('docker system prune --force')
 system('docker system prune --volumes --force')
 system('docker system prune --force')
 system('docker container prune --force')
 system(paste0("docker stop \"", container_name, "\""))
 system(paste0("docker rm -f \"", container_name, "\""))
 system('docker image prune --force')
 system(paste0("docker rmi -f \"", image_name, "\""))
 system(paste0("cmd.exe /c dir /B /S ", DL, "\\grass*.bat"), intern = T)
 system(paste0("cmd.exe /c TYPE \"", raw_GRASS[i], "\""), 
                              ignore.stdout = TRUE, intern = T)
 system(paste0(root_GRASS,"/bin/o-help.bat"))
 system(paste0("cmd.exe /c dir /B /S ",DL,"\\","saga_cmd.exe"),intern = TRUE)
 system(paste0("cmd.exe"," /c dir /B /S ",DL,"\\","otbcli.bat"),intern=TRUE)
 system(cmd)
 system(cmd)
 system(query, intern = TRUE)
 system(query, intern = TRUE)
 system(query, intern = TRUE)
 system(query, intern = TRUE)
 system(q, intern = TRUE)
 system(q, intern = TRUE)
 system(RNAfold.path, intern = TRUE, input = seq.string)
 system(paste("test -d", path), intern=FALSE)
 system(paste0("netstat -an | grep '[\\.:]", port, "' | wc -l"), intern = TRUE)
 system(query, intern = TRUE, ignore.stderr = TRUE)
 system(sprintf("echo 'source ~/%s; echo $PATH' | /bin/bash", profile_to_look_for), intern = TRUE)
 system(paste(wexe, s), intern = TRUE)
 system(paste0("tar -xvf ../",collectionname,".tgz"), intern=TRUE)
 system(paste0("tar -czf ../",collectionname,".tgz"," *"), intern = TRUE)
 system(paste(GB, " -", type, " -i ", i, " -f ", f,
 	" -o tabsep -F -", sep=""), intern=TRUE, invisible=invisible)
 system(paste(GB, " -", type, " -i ", i, " -f ", f,
 	" -o tabsep -F -", sep=""), intern=TRUE)
 system(paste(viewer, f, "&"))
 system(command)
 system("rm Tutorial.pdf")
 system("rm Tutorial.tex")
 system("rm Tutorial.log")
 system("rm Tutorial.aux")
 system("rm Tutorial.blg")
 system("rm Tutorial.bbl")
 system("rm Tutorial.toc")
 system(paste("cp ", MCpath, "Figures/Tutorial.Rnw ", MCpath, sep=""))
 system(paste("pdflatex", "Tutorial.tex"))
 system(paste("bibtex", "Tutorial"))
 system(paste("pdflatex", "Tutorial.tex"))
 system(paste("pdflatex", "Tutorial.tex"))
 system(paste("evince", "Tutorial.pdf&"))
 system("cp Tutorial.tex Tutorial.Rnw")
 system("rm Tutorial.tex")
 system(paste("rm *\\.aux", sep=""))
 system(paste("rm *\\.bbl", sep=""))
 system(paste("rm *\\.blg", sep=""))
 system(paste("rm *\\.eps", sep=""))
 system(paste("rm *\\.log", sep=""))
 system(paste("rm *\\.toc", sep=""))
 system(paste("rm Tutorial*-[A-Z]*\\.pdf", sep=""))
 system(cmd)
 system(cmd, wait = wait, ...)
 system("/Applications/RStudio.app/Contents/MacOS/pandoc/pandoc +RTS -K512m -RTS matrixpls-intro.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output matrixpls-intro.tex --template /Library/Frameworks/R.framework/Versions/3.3/Resources/library/rticles/rmarkdown/templates/jss_article/resources/template.tex --highlight-style tango --latex-engine /opt/local/bin/pdflatex --bibliography matrixpls-intro.bib --filter /Applications/RStudio.app/Contents/MacOS/pandoc/pandoc-citeproc")
 system(paste("java -jar", maxent,
      "-o", outdir,
      "-j", gridfolder,
      "-s", occurrencesites,
      "-e", backgroundsites,
      additionalargs,sep=" "),
            intern=TRUE,
            ignore.stdout = TRUE,
             show.output.on.console = FALSE,
            )
 system(paste("rm -f Lecture", i, "*", sep=""))
 system("rm -f CourseNotes.pdf")
 system("rm -f CourseNotes.tex")
 system("rm -f CourseNotes.log")
 system("rm -f CourseNotes.aux")
 system("rm -f CourseNotes.blg")
 system("rm -f *.pdf")
 system("rm -f *.eps")
 system("rm -f *.aux")
 system("rm -f *.log")
 system(paste("ex", Rnw, "-s +/alonefalse +:s/alonefalse/alonetrue +:x"))
 system(paste("ex", Rnw, "-s +/alonetrue +:s/alonetrue/alonefalse +:x"))
 system(paste("cp ~/Work/Tex/library/JarLib.bib ", UPpath_tmp, sep=""))
 system(paste("cp ", MCpath, "/rgl1.pdf ", UPpath_tmp, sep=""))
 system(paste("cp ", MCpath, "/rgl2.pdf ", UPpath_tmp, sep=""))
 system(paste("pdflatex", Tex))
 system(paste("bibtex", Bib))
 system(paste("pdflatex", Tex))
 system(paste("pdflatex", Tex))
 system(paste("evince", Pdf, "&"))
 system(paste("cp ~/Work/Tex/library/JarLib.bib ", UPpath_tmp, sep=""))
 system(paste("~/Library/TeXShop/bin/pdflatexc", Tex))
 system(paste("~/Library/TeXShop/bin/bibtexc", Bib))
 system(paste("~/Library/TeXShop/bin/pdflatexc", Tex))
 system(paste("~/Library/TeXShop/bin/pdflatexc", Tex))
 system(paste("open -a Preview", Pdf))
 system(paste("cp *.tex", MCpath))
 system(paste("cp *.pdf", MCpath))
 system(paste("cp ", MCpath, "Figures/CourseNotes.Rnw ", MCpath, sep=""))
 system(paste("cp ~/Work/Tex/library/JarLib.bib ", MCpath, "CourseNotes.bib", sep=""))
 system(paste("cp ~/Work/Tex/library/JarLib.bib ", MCpath, "Overview.bib", sep=""))
 system(paste("cp ~/Work/AManal/Tex/jss.cls " , MCpath, sep=""))
 system(paste("cp ~/Work/AManal/Tex/jss.bst " , MCpath, sep=""))
 system("pdflatex CourseNotes.tex")
 system("bibtex CourseNotes")
 system("pdflatex CourseNotes.tex")
 system("pdflatex CourseNotes.tex")
 system("xdg-open CourseNotes.pdf&")
 system("~/Library/TeXShop/bin/pdflatexc CourseNotes.tex")
 system("~/Library/TeXShop/bin/bibtexc CourseNotes")
 system("~/Library/TeXShop/bin/pdflatexc CourseNotes.tex")
 system("~/Library/TeXShop/bin/pdflatexc CourseNotes.tex")
 system("open -a Preview CourseNotes.pdf")
 system(paste("cp ", MCpath, "Figures/Overview.Rnw ", MCpath, sep=""))
 system("pdflatex Overview.tex")
 system("bibtex Overview")
 system("pdflatex Overview.tex")
 system("pdflatex Overview.tex")
 system("xdg-open Overview.pdf&")
 system("~/Library/TexShop/bin/pdflatexc article.tex")
 system("~/Library/TexShop/bin/bibtexc article")
 system("~/Library/TexShop/bin/pdflatexc article.tex")
 system("~/Library/TexShop/bin/pdflatexc article.tex")
 system("open -a Preview article.pdf")
 system(paste("bibtool -x ", MCpath, "CourseNotes.aux ", "-o ", MCpath, "CourseNotes.bib", sep=""))
 system(paste("bibtool -x ", MCpath, "Overview.aux ", "-o ", MCpath, "Overview.bib", sep=""))
 system(paste("cp ", MCpath, "CourseNotes.Rnw ", MCpath, "Figures", sep=""))
 system(paste("cp ", MCpath, "CourseNotes.tex ", MCpath, "CourseNotes.Rnw", sep=""))
 system(paste("cp ", MCpath, "Overview.Rnw ", MCpath, "Figures", sep=""))
 system(paste("cp ", MCpath, "Overview.tex ", MCpath, "Overview.Rnw", sep=""))
 system(paste("rm -f ", MCpath, "*\\.aux", sep=""))
 system(paste("rm -f ", MCpath, "*\\.bbl", sep=""))
 system(paste("rm -f ", MCpath, "*\\.blg", sep=""))
 system(paste("rm -f ", MCpath, "*\\.idx", sep=""))
 system(paste("rm -f ", MCpath, "*\\.toc", sep=""))
 system(paste("rm -f ", MCpath, "*\\.out", sep=""))
 system(paste("rm -f ", MCpath, "*\\.log", sep=""))
 system(paste("rm -f ", MCpath, "CourseNotes.tex", sep=""))
 system(paste("rm -f ", MCpath, "Overview.tex", sep=""))
 system(paste("rm -f ", MCpath, "jss.cls", sep=""))
 system(paste("rm -f ", MCpath, "jss.bst", sep=""))
 system(paste("rm -f ", MCpath, "Lecture[1-9]-[a-zA-z]*[.]pdf", sep=""))
 system(paste("cp ", MCpath, "CourseNotes.Rnw ", MCpath, "Figures", sep=""))
 system(paste("cp ", MCpath, "Overview.Rnw ", MCpath, "Figures", sep=""))
 system(paste("rm -f ", MCpath, "Overview.ps", sep=""))
 system(paste0('open ', paste0('"', file_out, '"')))
 system(paste("open ", raster_plot_path, sep = ""))
 system(paste(paste(paste(paste(paste(paste(paste(mdscan, len_motif,sep=" "),"-t", sep=" "), num_motif,sep=" "),"-b background.fa", sep=" "),"-r",sep=" "), num_motif,sep=" ") ,"-o res"))
 system(paste(paste(paste(call.mast,"memeout/meme.txt -d sequenciaEstudi.fa -text -mt",sep=" "), threshold, sep=" "), "-hit_list", sep=" "))
 system(paste(paste(paste(call.mast, "memeout/meme.txt -d sequenciaEstudi.fa -text -mt",sep=" "), threshold, sep=" "), "-hit_list", sep=" "))
 system(paste(paste(paste(paste(iicc$meme, " background.fa -oc memeout -dna -mod anr -w", sep =" "), len_motif,sep=" "), "-nmotifs", sep=" "),num_motif,sep=" "))
 system(paste(paste(paste(paste(paste(paste(paste(mdscan, len_motif,sep=" "),"-t", sep=" "), num_motif,sep=" "),"-b background.fa", sep=" "),"-r",sep=" "), num_motif,sep=" ") ,"-o res"))
 system(paste('which',executable), intern = TRUE)
 system(paste("./transfac2meme -bg bfile -pseudo 0.1 motif.dat>motif.meme"))
 system(paste(paste("./mast  motif.meme -d sequenciaEstudi.fa -text -mt", threshold, sep=" "), "-hit_list", sep=" "))
 system(paste("./transfac2meme -bg bfile -pseudo 0.1 motif.dat>motif.meme"))
 system(paste(paste("./mast  motif.meme -d sequenciaEstudi.fa -text -mt",threshold_final[i], sep=" "), "-hit_list", sep=" "))
 system(paste(paste(paste(paste(paste(call.meme,TF,sep=" "),"-oc memeout -dna -mod anr -w",sep=" "), len_motif,sep=" "), "-nmotifs", sep=" "),num_motif,sep=" "))
 system(paste(paste(paste(call.mast,"memeout/meme.txt -d sequenciaEstudi.fa -text -mt",sep=" "), threshold, sep=" "), "-hit_list", sep=" "))
 system(paste(paste("./mast  memeout/meme.txt -d sequenciaEstudi.fa -text -mt",threshold_final[i], sep=" "), "-hit_list", sep=" "))
 system(paste(paste(paste(paste(call.meme,filein,sep=" "),"-oc memeout -dna -mod anr -w", len_motif,sep=" "), "-nmotifs", sep=" "),num_motif,sep=" "))
 system(strtocall)
 system(paste(paste(paste(paste(call.meme,filein,sep=" "),"-oc memeout -dna -mod anr -w", len_motif,sep=" "), "-nmotifs", sep=" "),num_motif,sep=" "))
 system(strtocall)
 system(paste(getOption("pdfviewer"), doc, "&"))
 system(paste('mdb-tables -1', shQuote(i.file)), intern=TRUE)
 system(paste('mdb-schema -T', shQuote(i.dataset), shQuote(i.file)), intern=TRUE)
 system(paste('mdb-export -b strip', shQuote(i.file), shQuote(i.dataset), '>', filecsv))
 system("locale -a ", intern = TRUE)
 system(command, ignore.stdout = TRUE, ignore.stderr = TRUE)
 system(paste0("pdftops -eps ", f[i]))
 system(sprintf("blat -fastMap -out=blast8 %s %s %s", contigs, faFile, blatOutputFile))
 system(paste(sep=" ","zip", zipfile.name, filename.with.ext))
 system(paste(sep=" ","rm", filename.with.ext))
 system(paste(sep=" ","zip", zipfile.name, filename.with.ext))
 system(paste(sep=" ","rm", filename.with.ext))
 system(code)
 system(code[[x]])
 system(code[[x]])
 system(code[[x]])
 system(code[[x]])
 system(code[[x]])
 system(code[[x]])
 system(paste(javacommand), wait = TRUE)
 system( "_batch_pspp.bat" )
 system( p1 )
 system( cmd )
 system( cmd )
 system('prodigal -h', intern=TRUE)
 system('hmmscan -h', intern=TRUE)
 system('makeblastdb -help', intern=TRUE)
 system( cmd, intern=TRUE)
 system( command )
 system( cmd )
 system( command )
 system( command )
 system(paste("open", "microplot-lattice-ReporteRs-png.docx"))
 system(paste("open", x))
 system( cmd )
 system( cmd )
 system('muscle -version', intern = TRUE)
 system('cmalign -h', intern = TRUE)
 system(paste("evince ", UGpath, "/doc/MigClim_userGuide.pdf", sep=""))
 system(paste("open ", UGpath, "/doc/MigClim_userGuide.pdf", sep=""))
 system('mplus mplus2Dim.inp')
 system('mplus mplusSparse.inp')
 system('mplus mplusComplete.inp')
 system(paste("R CMD build --compact-vignettes=gs --resave-data ",name,sep=""),intern=TRUE)
 system(paste("R CMD build ",name,sep=""))
 system(paste("R CMD check ",checkflags," ",buildfn,sep=""))
 system(paste("R CMD build --compact-vignettes=gs --resave-data ",name,sep=""),intern=TRUE)
 system(paste("R CMD build ",name,sep=""))
 system(paste(cmd, file), wait = FALSE)
 system(muscleCommand)
 system(fastacmdCommand)
 system(fastacmdCommand)
 system(muscleCommand)
 system(muscleCommand)
 system(formatdbCommand)
 system(blastCommand )
 system(blastCommand )
 system(blastCommand )
 system(blastCommand)
 system(str, wait=F, invisible=F)
 system(lauchCommand)
 system(str, wait=T)
 system(str, wait=T)
 system(str, wait=T)
 system(str, wait=T)
 system(cmdstr)
 system(cmd,intern=TRUE)
 system(cmd,intern=TRUE)
 system(paste0(cmd, dataFormat),intern=TRUE)
 system(paste0("aria2c -x 3 --file-allocation=none ",paste(path$remotePath[which(names(path$remotePath)==opts$MODISserverOrder[hv[g]])],x[a],sep="/",collapse="")," -d ", dirname(destfile)))
 system(paste0(cmd,shQuote(x[i])),intern=TRUE)
 system(paste("mrtmosaic -i ",paraname," -o ",outDir,"/",TmpMosNam," -s '",SDSstringIntern$SDSstring,"'" ,sep=""))
 system(paste("resample -p ",paraname,sep=""))
 system(paste("gdalinfo ", HdfName,sep=""),intern=TRUE)
 system(paste("sdslist",HdfName,sep=" "),intern=TRUE)
 system(cmd1,intern=TRUE)
 system(cmd2,intern=TRUE)
 system(cmd)
 system(paste0("rmdir -p --ignore-fail-on-non-empty ", dirs[i]),intern=TRUE)
 system(paste0("rmdir -p --ignore-fail-on-non-empty ", orpath),intern=TRUE)
 system(cmd,intern=TRUE)
 system(paste0(cmd,correctPath(x[i],isFile=TRUE)), intern=TRUE)
 system(paste("which ", mrtpath, sep=""), intern=TRUE)
 system(cmdstr)
 system(paste("sudo -S ln -fs", file.path(MODIStsp_dir, "ExtData/Launcher/Bash/MODIStsp.sh"), bin_dir),
             input = readline("Enter your password: "))
 system(paste("sudo -S cp -f", file.path(MODIStsp_dir, "ExtData/Launcher/Bash/MODIStsp.desktop"),
                   file.path(desktop_dir, "MODIStsp.desktop")), input = readline("Enter your password: "))
 system(aria_string, intern = Sys.info()["sysname"] == "Windows")
 system(aria_string, intern = Sys.info()["sysname"] == "Windows")
 system(commandCharacter)
 system(command)
 system(paste("rm -f",files[i]))
 system(bat.file,wait=T)
 system(paste0("taskkill /F /PID ", correct.pid))
 system(paste0("kill ", correct.pid))
 system(paste0("ps ax | grep \"^", correct.pid, ".*mserver5\""), ignore.stdout=T)
 system(bat.file,wait=T)
 system(paste0("taskkill /F /PID ", correct.pid))
 system(paste0("kill ", correct.pid))
 system(paste0("ps ax | grep \"^", correct.pid, ".*mserver5\""), ignore.stdout=T)
 system("mp3splt -h", intern=TRUE)
 system(paste('mp3splt -Q -d', getwd(), filename, from, to, '-o temp16jp86mz2'))
 system(command=paste(player, tempname), wait=FALSE)
 system(command=paste(player, tempname), wait=FALSE)
 system(command="mp3splt -h", intern=TRUE)
 system(paste0("mp3splt -Q -d ", to, " ", recording, " ", surv.start[[x]], " ", surv.end[[x]], " -o ", filenames[x]))
 system("open Monograph_skeleton.docx")
 system("open Monograph_skeleton.html")
 system(paste("cp ",path,"/",orig[i],ext," ", dest.path,"/",alias[i],ext,sep=""))
 system(command)
 system("chmod +x batch.bat")
 system("chmod +x batch.bat")
 system(command, show.output.on.console = showOutput, invisible=(!showOutput), wait=TRUE)
 system(code)
 system(paste("mkfifo", fnam))
 system(cmd)
 system(cmd)
 system(cmd)
 system(cmd)
 system(cmd)
 system(cmd)
 system("xgettext -h", show.output.on.console = FALSE, ignore.stdout = TRUE)
 system(cmd)
 system(this@service, intern=FALSE,wait=TRUE )
 system(cmd)
 system(paste("ls ", res.file, sep=""), intern=T)
 system(paste("unzip -p",genoFile[marker[j]],rsidj),intern=TRUE)
 system(line,intern=TRUE)
 system(line,intern=TRUE)
 system(paste(Exec,
               " --Sample ", RDBinSampleFile,
               " --ChrFile ", RDBinChrSizeFile,
               " --samplename ", RDBinSampleFile,
               "  --window-size ", RDBinWindowSize,
               " --outputdirectory ", RDBinOut,
               sep = "")
 )
 system( cmd, wait=FALSE)
 system( cmd)
 system( bf, intern=intern, ...)
 system( paste( syscopy, f1, f2), show.output.on.console=FALSE)
 system( paste( syscopy, subbo( f1), subbo( f2)))
 system( paste( 'touch -m -t ', f1.mtime, subbo( f2)))
 system( paste( c( cmd, flags, pkg %&% postfix), collapse=' '), intern=intern)
 system(cmd, intern = TRUE, ignore.stderr=!Verbose)
 system(cmd,...)
 system(cmd)
 system('hostname',intern=TRUE)
 system('which texi2pdf')
 system('kpsewhich pdftex --version')
 system("which curl", ignore.stdout=TRUE)
 system("which gunzip", ignore.stdout=TRUE)
 system("which tar", ignore.stdout=TRUE)
 system("which perl", ignore.stdout=TRUE)
 system("curl -OL ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", ignore.stderr=TRUE, wait=TRUE)
 system("gunzip taxdump.tar.gz", ignore.stderr=TRUE, wait=TRUE)
 system("tar -xvf taxdump.tar", ignore.stderr=TRUE, wait=TRUE)
 system("perl -i -p -e's/[^\\w+^\\s+^\\d+^\\|+]//g' names.dmp")
 system("perl -i -p -e's/[^\\w+^\\s+^\\d+^\\|+]//g' nodes.dmp")
 system("which mv", ignore.stdout=TRUE)
 system("rm -rf /tmp/idx")
 system(paste("mv nodes.dmp", gb_path[["nodes"]], sep=" "))
 system(paste("mv names.dmp", gb_path[["names"]], sep=" "))
 system("which rm", ignore.stdout=TRUE)
 system(paste("rm -f", paste(cleanup, collapse=" "), sep=" "))
 system(paste('cdo seldate,', format(as.POSIXct(date.start.cut), '%Y-%m-%dT%H:%M'), ',',
              format(as.POSIXct(date.end.cut), '%Y-%m-%dT%H:%M'), ' ', file.names[i], ' ', file.cut, sep =''))
 system(cdoCmd)
 system(paste('cdo -O mergetime ', paste(file.names, collapse =' '), ' ', ofile, sep ='') )
 system(paste("if hash",cmd[dd],"2>/dev/null; then echo 'yes'; else echo 'no'; fi"),intern=T)
 system("top -l 1",intern=T)
 system("top -n 1 -b",intern=T)
 system(cmd,intern = TRUE, ignore.stderr = TRUE)
 system(paste0("mv ",new.filez[dd]," ",new.fnz[dd]))
 system(command,intern=TRUE)
 system(command,intern=TRUE)
 system("pandoc -s My_Analysis.html -o My_Analysis.pdf")
 system( "ruby multistagefca.rb" )
 system( "ruby multistagefca.rb" )
 system( "ruby multistagefca.rb" )
 system(cmd, intern = TRUE)
 system(cmd)
 system("clear")
 system( paste("open", file) )
 system(cmd)
 system(paste0("echo \"===== Starting MCMC test for ", name, ". =====\n\"", sep = ""))
 system('g++ add1p5.cpp -c -o add1p5.o')
 system('g++ add1p5b.cpp -c -o add1p5b.o')
 system(ssdSHLIBcmd, ignore.stdout = !showCompilerOutput, ignore.stderr = !showCompilerOutput, show.output.on.console = showCompilerOutput)
 system(ssdSHLIBcmd, ignore.stdout = !showCompilerOutput, ignore.stderr = !showCompilerOutput)
 system(dryRunCmd, intern = TRUE)
 system(dryRunCmd, intern = TRUE)
 system(SHLIBcmd, ignore.stdout = !showCompilerOutput, ignore.stderr = !showCompilerOutput, show.output.on.console = showCompilerOutput)
 system(SHLIBcmd, ignore.stdout = !showCompilerOutput, ignore.stderr = !showCompilerOutput)
 system(paste("pdftk", filepath, "cat 2-end output", tf, "; mv -f", tf, filepath))
 system(paste("ssh -q calvin.seml.astrazeneca.net \"cd $(pwd); module unload psn && module load psn && sumo",file.path, "\""))
 system(paste0(cmd1, cmd2, cmd, "\""), ...)
 system(cmd, ...)
 system("rm optim.debug bandwidth.out optim.out")
 system("/bin/rm Allegro.07.pdf")
 system("./modelMEE")
 system("./modelMEE.exe")
 system("./modelMEE")
 system("./modelMEE.exe")
 system(cmd)
 system(paste("mv", destfile, destpath))
 system("unzip", intern=TRUE, invisible=TRUE)
 system("unzip", intern = TRUE)
 system(zipCmd[2], invisible = TRUE)
 system(zipCmd[2])
 system(zipCmd[1], invisible=TRUE)
 system(zipCmd[1])
 system(z)
 system(z)
 system(z)
 system(z)
 system('java', ignore.stdout=TRUE, ignore.stderr=TRUE)
 system(command, intern=TRUE)
 system(cmd)
 system(cmd)
 system(cmdline)
 system(paste("mx", x, y))
 system(paste("mx < ", x, "> ", y))
 system("sw_vers -productVersion", intern=TRUE)
 system(paste0("sh ", script.name))
 system(paste0(script.name))
 system(command = myCommand)
 system(command = myCommand)
 system(string, intern=TRUE)
 system("gzip -d muenchen.osm.gz")
 system(request, ...)
 system(paste0(
      osrm_path, "osrm-routed ", map_name), wait = F)
 system("pkill osrm-routed")
 system(paste(shQuote(normalizePath(oxcal_path)), option_file))
 system("ping -c3 www.google.com", intern=T)
 system("nproc", intern=T)
 system("sysctl -n hw.ncpu", intern=T)
 system(paste(fullCmd, "| grep \\;"), intern=T)
 system(paste("cd", msdir, ";", "gcc -o ms ms.c streec.c rand1.c -lm"))
 system(paste("python2", pySc, inFn))
 system("which travis", intern = TRUE)
 system("travis encrypt GITHUB_PAT=$GITHUB_PAT --add env.global", ...)
 system("travis encrypt GITHUB_PAT=$GITHUB_PAT", ...)
 system(paste("echo ${#", key, "}", sep = ""), intern = TRUE)
 system(paste(
    "set -e

    # config
    git config --global user.email \"", email, "\"
    git config --global user.name \"", name, "\"

    # deploy
    git init      # resets the repo in the website folder
    git add .     # add all files
    git commit -m \"Travis build: $TRAVIS_BUILD_NUMBER\"
    # push the above commit and force it on the 'gh-pages' branch
    # since it's coming from a \"new\" repo, this is the master branch

    echo \"Attempting a silent push to '", repo, "@", push_branch, "'\"
    git push --force --quiet \"https://${", token_key, "}@github.com/", repo, ".git\" master:", push_branch, " > /dev/null 2>&1
    "
    , sep = ""
  ))
 system("git config --get remote.origin.url", intern = TRUE)
 system(paste("gunzip", "-c", filename), intern = TRUE)
 system(fullCmd)
 system(paste("R --vanilla CMD build", file.path(dir, "sashimi")))
 system(paste(svn, "propget", "svn:ignore"), intern = TRUE)
 system(paste(svn, "propset", "svn:ignore", shQuote(ignores), "."), intern = TRUE)
 system("git rev-list --all --objects", intern = TRUE)
 system("git branch", intern = TRUE)
 system("git branch -a | grep remotes | grep -v HEAD | grep -v master",
                        intern = TRUE)
 system(paste("git branch --track",
                   gsub(".*/", "", branch),
                   branch), ignore.stdout = TRUE, ignore.stderr = TRUE)
 system(cmd, ignore.stdout = TRUE, ignore.stderr = TRUE)
 system("git reflog expire --expire=now --all")
 system("git gc --prune=now")
 system("git gc --aggressive --prune=now")
 system(paste(Sys.getenv("R_BROWSER"), dir))
 system(w)
 system(paste(shQuote(file.path(R.home("bin"), 
                    "R")), "CMD", "Rd2pdf", shQuote(path)))
 system('pdflatex -version', intern = T)
 system(paste(shQuote('open'), shQuote(f)), wait = FALSE, ignore.stderr = TRUE)
 system(paste(shQuote('/usr/bin/xdg-open'), shQuote(f)), #nolint
                   wait = FALSE,
                   ignore.stdout = TRUE)
 system(cmd, intern = TRUE)
 system(sprintf('%s %s stat %s >/dev/null 2>&1', agent, host, qs(path)))
 system(cmd)
 system(sprintf("swig -r %s", ifile))
 system(sprintf("cd %s ; gcc -O2 -D__USE_BSD -D__USE_GNU -std=c99 -c -fpic %s.c %s_wrap.c -I/usr/local/lib64/R/include -lm ",
 		splitPath(ifile)$dir, base, base))
 system(sprintf("cd %s ; gcc -shared %s.o %s_wrap.o -o %s.so", splitPath(ifile)$dir, base, base, base))
 system("egrep '^MemFree:' /proc/meminfo", intern = TRUE)
 system("egrep '^Cached:' /proc/meminfo", intern = TRUE)
 system("egrep '^Inactive:' /proc/meminfo", intern = TRUE)
 system("egrep '^Buffers:' /proc/meminfo", intern = TRUE)
 system("wmic OS get FreePhysicalMemory /Value", intern=TRUE)
 system("vm_stat | grep 'Pages free'", intern = TRUE)
 system("vm_stat | grep 'Pages inactive'", intern = TRUE)
 system("vm_stat | grep 'Pages speculative'", intern = TRUE)
 system("vm_stat | grep 'Pages purgeable'", intern = TRUE)
 system("vmstat -s | grep 'free memory'", intern = TRUE)
 system("vmstat -s | grep 'inactive memory'", intern = TRUE)
 system("vmstat -s | grep 'buffer memory'", intern = TRUE)
 system("vmstat -s | grep 'swap cache'", intern = TRUE)
 system("egrep '^MemFree:' /proc/meminfo", intern = TRUE)
 system("egrep '^Cached:' /proc/meminfo", intern = TRUE)
 system("egrep '^Inactive:' /proc/meminfo", intern = TRUE)
 system("egrep '^Buffers:' /proc/meminfo", intern = TRUE)
 system("wmic OS get FreePhysicalMemory /Value", intern=TRUE)
 system("vm_stat | grep 'Pages free'", intern = TRUE)
 system("vm_stat | grep 'Pages inactive'", intern = TRUE)
 system("vm_stat | grep 'Pages speculative'", intern = TRUE)
 system("vm_stat | grep 'Pages purgeable'", intern = TRUE)
 system("vmstat -s | grep 'free memory'", intern = TRUE)
 system("vmstat -s | grep 'inactive memory'", intern = TRUE)
 system("vmstat -s | grep 'buffer memory'", intern = TRUE)
 system("vmstat -s | grep 'swap cache'", intern = TRUE)
 system(command, intern = T)
 system(command, intern = T)
 system("git commit -a -m 'update website'")
 system("git push")
 system(cmd, wait=wait)
 system(cmd)
 system(tosend)
 system(tosend)
 system("screen -ls",intern=T)
 system("screen -ls",intern=T)
 system(cmd)
 system(cmd, intern = TRUE)
 system(cmd, wait=FALSE, invisible=FALSE)
 system(cmd, wait=FALSE, invisible=FALSE)
 system(cmd, intern = TRUE)
 system(cmd, intern=TRUE, ignore.stderr=TRUE)
 system(cmd, intern = TRUE)
 system(paste(shQuote(bibtex), shQuote(base)))
 system(cmd)
 system(cmd, intern = TRUE)
 system(cmd, intern = TRUE)
 system(cmd, wait=FALSE, invisible=FALSE)
 system(cmd, wait=FALSE, invisible=FALSE)
 system(cmd, intern = TRUE)
 system(cmd)
 system(cmd, wait=FALSE, invisible=FALSE)
 system(sprintf(uncompress, oldname, pdfname))
 system(paste0("java -Xss4m -jar \"", active_search_path, "\"",
                  " -sif=\"", pin_path,"\"",
                  " -sig=../input_for_search.txt",
                  " -method=", search_method,
                  use_all_positives,
                  " -saTemp0=", saTemp0,
                  " -saTemp1=", saTemp1,
                  " -saIter=", format(saIter, scientific = F),
                  " -saInitProb=", saInitProbs[i],
                  " -gaPop=", gaPop,
                  " -gaIter=", gaIter,
                  " -gaThread=", gaThread,
                  " -gaMut=", gaMut,
                  " -grMaxDepth=", grMaxDepth,
                  " -grSearchDepth=", grSearchDepth,
                  " -grOverlap=", grOverlap,
                  " -grSubNum=", grSubNum))
 system( paste( wineStr, pbat.get(), " ", "killme.txt", sep="" ) )
 system( paste( pbat.get(), commandfile ), intern=TRUE )
 system( paste( pbat.get(), i, case.aa[i], case.Aa[i], case.AA[i], control.aa[i], control.Aa[i], control.AA[i], replicates, statistic, method ) )
 system(paste("open",pdffilename,sep = " "))
 system("mpiexec", intern = TRUE)
 system("which mpiexec", intern = TRUE)
 system("which mpirun", intern = TRUE)
 system("which orterun", intern = TRUE)
 system(cmd, intern = TRUE, ignore.stdout = FALSE,
                  ignore.stderr = FALSE, wait = TRUE)
 system(cmd, intern = TRUE, ignore.stdout = FALSE,
                  ignore.stderr = FALSE, wait = FALSE)
 system(cmd.pid, intern = TRUE)
 system(cmd)
 system(cmd)
 system(cmd, intern = TRUE)
 system(cmd, intern = TRUE)
 system(cmd, intern = TRUE)
 system(paste0(exec, " -V"),
                               intern = TRUE, wait = FALSE,
                               show.output.on.console = FALSE)
 system(paste0(exec, " -V"),
                               intern = TRUE, wait = FALSE)
 system(cmd, intern = intern, wait = wait)
 system(cmd, intern = intern, wait = wait)
 system("whoami", intern=TRUE)
 system("./00_make.sh", intern = TRUE, ignore.stderr = TRUE)
 system("which install_name_tool", intern = TRUE)
 system("which otool", intern = TRUE)
 system(paste(cmd.ot, " -L ", fn.pbdZMQ.so, sep = ""),
                        intern = TRUE)
 system(cmd)
 system(cmd)
 system(paste(cmd.ot, " -L ", fn.pbdZMQ.so, sep = ""),
                        intern = TRUE)
 system(paste(cmd.ot, " -L ", fn.libzmq.dylib, sep = ""),
                        intern = TRUE)
 system(cmd)
 system(paste(cmd.ot, " -L ", fn.libzmq.dylib, sep = ""),
                        intern = TRUE)
 system("which otool", intern = TRUE)
 system(paste(cmd.ot, " -L ", fn.so, sep = ""), intern = TRUE)
 system("which install_name_tool", intern = TRUE)
 system(cmd)
 system(cmd,wait=FALSE)
 system(cmd,intern=TRUE)
 system(paste("cscript //NoLogo", fname), minimized=TRUE)
 system(paste("cscript //NoLogo", fname), minimized = TRUE)
 system( paste( "open", fname ) )
 system( paste( "xdg-open", fname ) )
 system( paste( "gnome-open", fname ) )
 system(cmd,wait=FALSE)
 system(command, intern=TRUE)
 system(cmd, wait=FALSE, invisible=FALSE)
 system("R CMD Rd2pdf --pdf ../PCAmixdata")
 system("R CMD build ../PCAmixdata")
 system("R CMD check --as-cran ../PCAmixdata")
 system(command1)
 system(command2)
 system(paste("rm -f ", path,"*.tmp", sep = ""))
 system(paste("echo 'Alignment has been trimmed to ", perc,"%' >> ",path,"PdPDB.log", sep = ""))
 system(paste("echo 'Drop option was ", dropsReplicate,"!' >> ",path,"PdPDB.log", sep = ""))
 system(paste("echo 'You recovered an old job' >> ",path,"PdPDB.log", sep = ""))
 system(paste("echo 'n is now tuned to ", n,"' >> ",path,"PdPDB.log", sep = ""))
 system(paste("echo ' ' >> ",path,"PdPDB.log", sep = ""))
 system(paste("echo 'PdPDB exited gracefully...!!!' >> ",path,"PdPDB.log", sep = ""))
 system(cmd)
 system(cmd, intern=TRUE)
 system(cmd, intern=TRUE)
 system(paste("rm cop.",jk,".id=",id,".Rdata",sep=""))
 system(paste("rm cop.",jk,".id=",id,".Rdata",sep=""))
 system(paste("gpsbabel -",type," -i ", i, " -f ", f, 
        " -o gpx -F -", sep = ""), intern = TRUE, invisible = TRUE)
 system(paste("gpsbabel -",type," -i gpx -f ",gpx," -o garmin -F ",f,sep=""))
 system(paste("gpsbabel -",type," -i gpx -f ",gpx," -o garmin -F ",f,sep=""))
 system(paste("gpsbabel -w -i ",i," -f ",f," -o gpx -F -", sep = ""), intern = TRUE, invisible = TRUE)
 system(paste("gpsbabel -t -i ",i," -f ",f," -o gpx -F -", sep = ""), intern = TRUE, invisible = TRUE)
 system(paste(shQuote(path), '--play-and-exit','play_tmp.wav'),ignore.stderr=TRUE)
 system(paste(shellrun,"call \"./NLME7.exe\"",bootargs,nlmeargs,"1> err1.txt 2> err2.txt"),wait=TRUE,invisible=TRUE)
 system(cmd.line2,invisible=FALSE,wait=TRUE)
 system(paste ("open ",pdfname, sep=""))
 system(paste ("xdg-open ",pdfname, sep=""))
 system(paste(shellrun,"call \"./NLME7.exe\" ",
                       simargs,nlmeargs,"1> err1.txt 2> err2.txt"),wait=TRUE,invisible=TRUE)
 system("open test.pdf")
 system(CALL, wait = TRUE)
 system(CALL, wait = TRUE)
 system(os$cmd, intern = ! verbose)
 system(paste(R, "CMD build simpleTest"))
 system(paste(R, "CMD check simpleTest_1.0.tar.gz"))
 system(cmd, intern=interactive())
 system(sysCmd, intern = T)
 system(paste(gdalwarp, " ", tf, ".tif", " -t_srs \"", CRS, "\" ", tf, "_ll.tif -dstnodata \"", NAflag, "\" ", " -r ", method, sep=""), show.output.on.console = show.output.on.console)
 system(paste(gdalwarp, ' ', tf, '.tif', ' -t_srs \"', CRS, '\" ', tf, '_ll.tif -dstnodata \"', NAflag, '\" -r near', sep=""), show.output.on.console = show.output.on.console)
 system(paste(gdalwarp, ' ', tf, '.tif', ' -t_srs \"', CRS, '\" ', tf, '_ll.tif -dstnodata \"', NAflag, '\" -r bilinear', sep=""), show.output.on.console = show.output.on.console)
 system(paste(convert, ' ', raster_name, ' -matte -transparent "#FFFFFF" ', raster_name, sep=""))
 system(paste(convert, ' ', legend.file, ' -matte -transparent "#FFFFFF" ', legend.file, sep=""))
 system(paste("open ", utils::shortPathName(normalizePath(paste(getwd(), "/", file.name, sep=""))), sep=""))
 system(paste("open ", normalizePath(paste(getwd(), "/", file.name, sep="")), sep=""))
 system(paste("xdg-open ", normalizePath(paste(getwd(), "/", file.name, sep="")), sep=""))
 system(paste(convert, ' ', raster_name, ' -matte -transparent "#FFFFFF" ', raster_name, sep=""))
 system(convert,  show.output.on.console = FALSE, intern = TRUE)
 system(convert,  show.output.on.console = FALSE, intern = TRUE)
 system(convert,  show.output.on.console = FALSE, intern = TRUE)
 system("git status")
 system("git add *")
 system(sprintf("git commit -q -m 'Pushed from %s'", build_link))
 system(paste("git pull", repo, "gh-pages"))
 system(paste("git push -q", repo, "gh-pages"))
 system(paste(system("which tar", intern=TRUE), "xzfv", tarFilename))
 system("which tar", intern=TRUE)
 system("which tar", intern=TRUE)
 system(paste("rm", tarFilename))
 system(cmd, intern = TRUE)
 system(cmd)
 system(cmd)
 system(cmdMake)
 system("cwb-s-decode -h", intern = FALSE, ignore.stderr =  TRUE)
 system(paste(cmd, collapse = " "), intern = TRUE)
 system(sprintf(self$as.cmd(.cqi_perl[["attribute_size"]]), corpus, attribute), intern=TRUE)
 system(
          sprintf(self$as.cmd(.cqi_perl[["lexicon_size"]]), corpus, pAttribute),
          intern=TRUE
        )
 system(
          sprintf(self$as.cmd(.cqi_perl[["cpos2struc"]]), corpus, pAttribute, paste(as.character(cpos), collapse=",")),
          intern=TRUE)
 system(
        sprintf(self$as.cmd(.cqi_perl[["cpos2str"]]), corpus, pAttribute, paste(as.character(cpos), collapse=",")),
        intern=TRUE
      )
 system(
          sprintf(self$as.cmd(.cqi_perl[["cpos2id"]]), corpus, pAttribute, paste(as.character(cpos), collapse=",")),
          intern=TRUE)
 system(
          sprintf(self$as.cmd(.cqi_perl[["struc2cpos"]]), corpus, sAttribute, struc),
          intern=TRUE)
 system(
        sprintf(self$as.cmd(.cqi_perl[["id2str"]]), corpus, pAttribute, paste(as.character(id), collapse=",")),
        intern=TRUE
      )
 system(
        sprintf(
          self$as.cmd(.cqi_perl[["struc2str"]]), corpus, sAttribute, paste(as.character(struc), collapse=",")),
        intern=TRUE
      )
 system(
          sprintf(self$as.cmd(.cqi_perl[["regex2id"]]), corpus, pAttribute, regex),
          intern=TRUE
        )
 system(
          sprintf(self$as.cmd(.cqi_perl[["str2id"]]), corpus, pAttribute, paste('"', str, '"', sep="", collapse=",")),
          intern=TRUE
        )
 system(
          sprintf(self$as.cmd(.cqi_perl[["id2freq"]]), corpus, pAttribute, paste(id, collapse=",")),
          intern=TRUE
        )
 system(
          sprintf(self$as.cmd(.cqi_perl[["id2cpos"]]), corpus, pAttribute, paste(id, collapse=",")),
          intern=TRUE
        )
 system(cqpCmd, intern=TRUE)
 system(paste(cmd, collapse = " "))
 system(cwbEncodeCmd)
 system(cwbEncodeCmd)
 system(cwbMakeCmd)
 system(cmd, intern = TRUE)
 system(paste(cmd, collapse = " "))
 system("cwb-s-decode -h", intern = FALSE, ignore.stderr =  TRUE)
 system("cwb-encode -h", intern = FALSE, ignore.stderr =  TRUE)
 system("cwb-lexdecode -h", intern = FALSE, ignore.stderr =  TRUE)
 system("cwb-regedit -h", intern = FALSE, ignore.stderr = TRUE)
 system(paste(Sys.getenv("R_BROWSER"), polyglotDirectory))
 system(paste(jags, "< ", cmd.file ," > /dev/null"),
                      ignore.stderr = quiet)
 system("R CMD SHLIB two_comp_oral_CL.c")
 system("R CMD SHLIB HCV_ode.c")
 system("R CMD SHLIB one_comp_oral_CL.c")
 system("R CMD SHLIB tmdd_qss_one_target.c")
 system("R CMD SHLIB one_comp_oral_CL.c")
 system(paste(mscall," > ms.out"))
 system(command)
 system(command)
 system(command)
 system(command)
 system(command)
 system(command)
 system('wmic OS get FreePhysicalMemory /Value', intern=TRUE)
 system(command)
 system("tput lines", intern = TRUE)
 system(paste(exec, '--help'), intern=TRUE)
 system(cmdstr)
 system(paste(sep=" ", "rm ", efile))
 system(paste(sep=" ", "chmod +x",  pfile))
 system(pfile)
 system("rm tmp.out")
 system(paste('Rscript', file.path('src', analysis.script)))
 system(cmddb, ignore.stdout = TRUE)
 system(cmddb)
 system(cmdpsi, ignore.stdout = TRUE)
 system(cmdpsi)
 system(cmd, intern=TRUE, ignore.stderr = TRUE)
 system("where python.exe", intern = TRUE, 
               ignore.stdout = FALSE, ignore.stderr = TRUE)
 system(quote('python -c "import sys;import os;sys.stdout.write(os.path.dirname(sys.executable))"'), intern=TRUE)
 system(action, wait = FALSE, ignore.stderr = TRUE)
 system(paste(Sys.getenv("R_BROWSER"), y))
 system(paste0(tempdir(), "/curl http://curl.haxx.se/ca/cacert.pem -o " , 
            tempdir() , "/curl-ca-bundle.crt"))
 system(cmd1)
 system(cmd2, intern = TRUE)
 system(cmd3, intern = TRUE)
 system(cmdEM)
 system(cmd4, intern = TRUE)
 system(cmd5, intern = TRUE)
 system(cmd6, intern = TRUE)
 system( paste0( "cd ", project.dir , " && " , gitpath , " init" ) )
 system( paste0( "cd ", project.dir , " && " , gitpath , " add \\." ) )
 system( paste0( "cd ", project.dir , " && " , gitpath , 
            " commit -m \"Initial commit\"" ) )
 system( paste0( "cd ", project.dir , " && " , gitpath, 
            " remote add origin https://github.com/", github.user, "/", repo, ".git") )
 system("qcollectiongenerator qtbase.qhcp -o qtbase.qhc")
 system(paste("scp yandell@simon:", file.path(dirpath, "Phase31.RData"), " ", run, sep = ""))
 system(paste("rm -f", file.path(run, "Phase31.RData")))
 system(paste("scp yandell@simon:",
               file.path(dirpath, "phase2data", paste("perm.", cross.index, "_1.RData", sep = "")),
               " ", run, sep = ""))
 system(paste("scp yandell@simon:",
               file.path(dirpath2, paste("perm.", cross.index, "_1.RData", sep = "")),
               " ", run, sep = ""))
 system(paste("scp yandell@simon:", file.path(dirpath, "phase2data", "Phase1.RData"),
             " ", run, sep = ""))
 system(paste("rm -f", file.path(run, "Phase1.RData")))
 system(paste("ln -s", file.path(null.dir, "quantiles.csv"), "."))
 system(paste("ln -s", trait.mlratio, trait.file))
 system(paste("mkdir", run))
 system(paste("mkdir ", run, "/shared", sep = ""))
 system("rm -f Trait.RData")
 system(paste("mv *.RData ", run, "/shared", sep = ""))
 system(paste("sed -e 's/TISSUE/", tissue, "/' < ../params.txt > ", run, "/params.txt", sep = ""))
 system(paste("cp -r ", run, "~/soar/rundata/stage_qtlhot"))
 system(paste("cd ~/soar/rundata/stage_qtlhot; ./stage.pl --input", run))
 system("df ./",intern=T)
 system("fsutil volume diskfree c:",intern=T)
 system(paste(findstr,cpstr))
 system("locate bin/admb | grep bin/admb$",intern=TRUE)
 system("admb",intern=TRUE)
 system("./testversion --version",intern=TRUE)
 system("admb",intern=TRUE)
 system(paste("admb",args,fn," 2>",paste(fn,".cout",sep="")),
 			intern=TRUE)
 system(paste("rm --force", files[k]))
 system(paste("rm --force", res$bayesx.prg$file.dir))
 system(command)
 system(command)
 system(command)
 system(command)
 system(command)
 system(paste(jags.call, "jagsscript.txt"))
 system("which OpenBUGS", TRUE)
 system("which OpenBUGS", TRUE)
 system(paste("which ", x, sep=""), intern=TRUE)
 system(paste("locate ", x, " | grep bin/", x, "$", sep=""), intern=TRUE)
 system(paste(WINEPATH, "-w", x), intern=TRUE)
 system(paste(WINEPATH, " \"", x, "\"", sep=""), intern=TRUE)
 system(bugsCall,invisible=FALSE)
 system(bugsCall)
 system(paste("which ", x, sep=""), intern=TRUE)
 system(paste("locate ", x, " | grep bin/", x, "$", sep=""), intern=TRUE)
 system(paste(WINEPATH, "-w", x), intern=TRUE)
 system(paste(WINEPATH, " \"", x, "\"", sep=""), intern=TRUE)
 system(bugsCall)
 system(paste("pdflatex",out),ignore.stdout=TRUE)
 system(paste("pdflatex",out),ignore.stdout=TRUE)
 system(paste0("open \"",sub("\\.tex$","\\.pdf",out),"\""),wait=FALSE)
 system(paste0("xdg-open '",sub("\\.tex$","\\.pdf",out),"'"))
 system(paste0("open '",normalizePath(out),"'"),wait=FALSE)
 system(paste(exefile,extras),intern=intern)
 system(command, intern=Intern)
 system(command)
 system(command,intern=Intern)
 system(command,intern=Intern)
 system(command,intern=Intern)
 system(command,intern=Intern)
 system("spline_selex -maxfn 0 -nohess")
 system("./spline_selex -maxfn 0 -nohess")
 system(paste("touch",log.file),ignore.stderr=TRUE)
 system("hostname",intern=TRUE)
 system("hostname",intern=TRUE)
 system(paste0(Sys.which("R"), " -e \"install.packages('radiant', repos = 'https://radiant-rstats.github.io/minicran', type = '", type, "'); update.packages(lib.loc = .libPaths()[1], repos = 'https://radiant-rstats.github.io/minicran', ask = FALSE, type = '", type, "'); pkgs <- new.packages(lib.loc = .libPaths()[1], repos = 'https://radiant-rstats.github.io/minicran', type = '", type, "', ask = FALSE); if (length(pkgs) > 0) install.packages(pkgs, repos = 'https://radiant-rstats.github.io/minicran', type = '", type, "')\""))
 system(paste0("R CMD INSTALL --build ", f))
 system(paste0(Sys.which("R"), " -e \"source('radiant/build/build_mac.R')\""))
 system("git add --all .")
 system(paste0("git commit -m '",mess,"'"))
 system("git push")
 system("git add --all .")
 system(paste0("git commit -m '",mess,"'"))
 system("git push")
 system(paste0("R CMD INSTALL --build ", f))
 system("where zip", intern = TRUE)
 system("where 7z", intern = TRUE)
 system("tr < temp.dm.m.csv -s ':' | tr ':' ',' > temp.dm.m.split.csv")
 system("rm temp.*.csv")
 system(cmd)
 system(cmd)
 system(cmd)
 system("mencoder")
 system(txt)
 system(paste("grep \"\\examples\" -A 10000 ", path, "/", files[i], sep=""))
 system(cmd)
 system(paste("grep [eE][rR][rR][oO][rR] ", dir, "/",  pkgs[i],
 		     ".Rcheck/", f, sep=""))
 system(paste("mkdir ", dir))
 system(paste("rm ", dir, "/*tar.gz*", sep=""))
 system(paste("(cd ", dir, "; wget ", URL, PKGS[i], ")", sep=""))
 system(command)
 system(cmd, intern = TRUE)
 system(cmd, intern=TRUE)
 system(paste(cmd, Sys.getpid()))
 system(paste("oowriter", ofile), wait = FALSE)
 system(sprintf('R -q --vanilla -e "%s"', r_expr), wait=F, intern=F)
 system("ipconfig", intern = TRUE)
 system("ifconfig", intern = TRUE)
 system(runcommand)
 system(paste("host",host), intern=TRUE,
                          ignore.stdout=FALSE, ignore.stderr=FALSE,wait=TRUE)
 system("which OpenBUGS", TRUE)
 system("which OpenBUGS", TRUE)
 system("which OpenBUGS", TRUE)
 system(command)
 system(cmd)
 system(cmd)
 system(cmd)
 system("java -version",ignore.stderr = TRUE)
 system("defaults read org.R-project.R NSAppSleepDisabled", 
                  intern=TRUE, ignore.stderr=TRUE)
 system("defaults delete org.R-project.R NSAppSleepDisabled", ignore.stderr=TRUE)
 system("defaults write org.R-project.R NSAppSleepDisabled -bool YES")
 system("defaults write org.R-project.R NSAppSleepDisabled -bool NO")
 system(paste("open -a Preview", shQuote(file)))
 system(paste(shQuote(getOption("pdfviewer")), shQuote(file)), wait=FALSE)
 system("defaults read -g AppleLocale", intern=TRUE)
 system( cmd, intern = TRUE )
 system(paste("sudo dpkg -i", debfile))
 system(paste("sudo dpkg --purge", debpkg))
 system( cmd )
 system( paste(R, "CMD build", pkg_path) )
 system(cmd)
 system(cmd, intern = !showOutput)
 system(cmd,
                                          ignore.stderr = TRUE,
                                          intern = TRUE)
 system(paste0("egrep -r -q \"\\.(C|Fortran)\\(\" ", deb[i, "Package"], "/R/*"))
 system(cmd)
 system("gsl-config --cflags", intern = TRUE)
 system("gsl-config --libs"  , intern = TRUE)
 system(paste0(cmd, " --version 2>&1"), intern=TRUE)
 system(paste0(cmd, " --version"), intern=TRUE)
 system(paste0(cmd, " --print-prog-name=ld"),
                              intern=TRUE)
 system(paste0(file.path(R.home("bin"), "R"),
                                  " CMD config ", rConfigParam), intern=TRUE)
 system(paste0(cmd, " --version 2>&1"), intern=TRUE)
 system(paste0(cmd, " --version"), intern=TRUE)
 system(paste0(cmd, " --print-prog-name=ld"),
                              intern=TRUE)
 system(paste0(file.path(R.home("bin"), "R"),
                                    " CMD config ", rConfigParam), intern=TRUE)
 system("redis-server /tmp/redis.conf --port 7777 --slaveof localhost 6379", wait=FALSE)
 system("make auth.so")
 system(sprintf('%s CMD build %s %s', Rbin(), build.opts, pkg))
 system(sprintf('%s CMD INSTALL %s %s ', Rbin(), install.opts, res))
 system(sprintf('%s CMD check %s %s', Rbin(), res, check.opts))
 system(...)
 system(paste0("doxygen -g ", doxyFileName))
 system(paste("doxygen", doxyFileName))
 system(paste0(arduino," --upload ",bcfile," --port /dev/",uport))
 system(paste0("rm ",bcfile))
 system(paste0('java ', paste0(names(jarOpt), jarOpt, collapse = ' '))
             ,ignore.stdout = TRUE, ignore.stderr = TRUE, wait = FALSE)
 system(paste0('java ', paste0(names(jarOpt), jarOpt, collapse = ' ')), wait = FALSE, 
             invisible = invisible)
 system(cmd,intern=TRUE)
 system(paste(command, address[i]))
 system(paste("grep input ", fname, ".tex", sep = ""), intern = TRUE)
 system(paste("grep includegraphics ", fname, ".tex", sep = ""), intern = TRUE)
 system(paste("grep bibliograph ", fname, ".tex", sep = ""), intern = TRUE)
 system(paste("grep -l ", Rtab[i,2], " ", tables, "/*.R", sep = ""), intern = TRUE)
 system(paste("grep -l ", Rfig[i,2], " ", figures, "/*.R", sep = ""), intern = TRUE)
 system(paste("grep source", Rfiles[i]), ignore.stdout = TRUE)
 system(paste("grep source", Rfiles[i]), intern = TRUE)
 system(paste("grep load", Rfiles[i]), ignore.stdout = TRUE)
 system(paste("grep load", Rfiles[i]), intern = TRUE)
 system(paste("grep -l save ", paste(Rlist, collapse = " ")), intern = TRUE)
 system(paste("grep -l", rda, paste(Slist, collapse = " ")), ignore.stdout = TRUE)
 system(paste("grep -l", rda, paste(Slist, collapse = " ")), intern = TRUE)
 system(paste("tar cz -f ", fname, ".R.tar.gz ", paste(Rfiles, collapse = " "),sep = ""))
 system(paste("pbcopy < ",tmp.file.name))
 system(paste("pbcopy < ",tmp.file.name))
 system(paste("pbcopy < ",tmp.file.name))
 system("which gs",intern=TRUE)
 system("echo q|latex tmptmp.tex;dvips tmptmp.dvi")
 system(paste("convert",jpgname,gifname))
 system(paste(gsexe, "-help > /dev/null"))
 system(cmd)
 system(paste(gsexe, "-help > /dev/null"))
 system(cmd)
 system("which pnmcrop",intern=TRUE)
 system(paste("mv ",ppmname," tmptmp.ppm; pnmcrop tmptmp.ppm > ",ppmname,"; rm tmptmp.ppm"))
 system(latex)
 system(paste(cmd," &"))
 system(view)
 system(dvipdf)
 system(cmd)
 system(paste("pbcopy < ",tmp.file.name))
 system(paste("pbcopy < ",tmp.file.name))
 system(paste("pbcopy < ",tmp.file.name))
 system("echo q | latex tmptmp.tex; dvips -E tmptmp.dvi")
 system(paste("convert tmptmp.ps ",jpgname))
 system(paste("convert tmptmp.ps tmptmp.ppm; pnmcrop tmptmp.ppm > ",ppmname))
 system("rm tmptmp.tex tmptmp.aux tmptmp.log tmptmp.ppm tmptmp.dvi tmptmp.ps")
 system(paste("diff ",workname.sys," ",get("tmp.file.name",envir=revive.sys)
 ," | grep \"^[0-9]\" > ",get("tmp.file.name",envir=revive.sys)
 ))
 system(paste(browser.sys,fname),wait=FALSE)
 system(paste(options()$browser,fname),wait=FALSE)
 system("which firefox",TRUE)
 system(paste("firefox",fname),wait=FALSE)
 system("which mozilla",TRUE)
 system(paste("mozilla",fname),wait=FALSE)
 system("which epiphany",TRUE)
 system(paste("epiphany",fname),wait=FALSE)
 system(cmd)
 system(paste("convert",jpgname,gifname))
 system(paste("convert",jpgname,gifname))
 system("which convert",TRUE,TRUE)
 system("which dvips",TRUE,TRUE)
 system(paste("pbcopy < ",get("tmp.file.name",envir=revive.sys)
 ))
 system(paste(browser.sys,fname),wait=FALSE)
 system(paste("convert",jpgname,gifname))
 system("convert -density 90 -trim remoter-hex.pdf -quality 100 -flatten -sharpen 0x1.0 remoter-hex.png")
 system(full, intern = TRUE, ignore.stderr = quiet)
 system(paste0("git rev-parse --verify HEAD"), intern = TRUE)
 system(paste0("git rev-parse --abbrev-ref HEAD"),
    intern = TRUE)
 system(paste0("git log --format=%B -n 1 ", git_commit),
                        intern = TRUE)
 system(syscomm)
 system(tmp)
 system(action)
 system(paste0(tempdir(), "/curl http://curl.haxx.se/ca/cacert.pem -o " , 
            tempdir() , "/curl-ca-bundle.crt"))
 system(cmd1)
 system( paste0( "cd ", project.dir , " && " , gitpath , " init" ) )
 system( paste0( "cd ", project.dir , " && " , gitpath , " add \\." ) )
 system( paste0( "cd ", project.dir , " && " , gitpath , 
        " commit -m \"Initial commit\"" ) )
 system( paste0( "cd ", project.dir , " && " , gitpath, 
        " remote add origin https://github.com:", github.user, "/", repo, ".git") )
 system(action)
 system(action)
 system(paste0(rpath, " --quiet --vanilla -e \"do.call(install.packages,list('",
                            pkg, "',lib='", libPath, "',dependencies=FALSE,repos='", repos,
                            "'))\""), wait = TRUE)
 system(paste0(rpath, " --quiet --vanilla -e \"install.packages('", pkg,
                              "',lib='", libPath,
                              "',dependencies=FALSE,repos=NULL,type='source')\""), wait = TRUE)
 system(paste(rpath, syscall), wait = TRUE)
 system(robocopy, intern = TRUE)
 system(rsync, intern = TRUE)
 system(EQScmd, intern = FALSE, ignore.stderr = TRUE, wait = TRUE, input = NULL)
 system(line)
 system(line)
 system(line)
 system("stty -echo")
 system("stty echo")
 system(cmd)
 system(cmd)
 system(cmd)
 system(paste(shQuote(file.path(R.home("bin"), "R")), 
               "CMD", "Rd2pdf", 
               shQuote(path)))
 system(paste("java -jar ",system.file("java", "RFrEAK-0.2-8.jar", package = "RFreak")," --edit-schedule='",load,"' --save-edited-schedule='",saveTo,"'",sep=""))
 system(subst(runAsy, filename))
 system(convert)
 system("uname",intern=TRUE)
 system('gnuplot -V', intern = TRUE, ignore.stderr = T)
 system('xprop -name "Gnuplot (window id : "' %s% windowid %s% '")" WM_STATE 1', intern =TRUE)
 system('echo $DISPLAY')
 system('xprop -name "Gnuplot (window id : "' %s% windowid %s% '")" _NET_WM_PID', intern =TRUE)
 system('kill ' %s% pid, intern =TRUE)
 system('xprop -name "Gnuplot (window id : "' %s% windowid %s% '")" WM_STATE 1', intern =TRUE)
 system("cp Web/extra-zoomplot2.png Web/extra-axisscale3.png")
 system("cp Figures/graph-pkgdep.png Web/")
 system("rm Web/interactgrid-latticevps1.png")
 system("rm Web/interactgrid-latticeleaves1.png")
 system("cp Figures/maps-brazilraster.png Web/")
 system("dot -Kneato grpkgs.dot -Tps -Gsize='8,8' -Gmargin=0 > organisation-graphicslevels.ps")
 system("epstopdf Figures/threed-3dproj.eps")
 system("convert Figures/threed-3dproj.pdf Web/threed-3dproj.png")
 system("epstopdf Figures/threed-3dvp.eps")
 system("convert Figures/threed-3dvp.pdf Web/threed-3dvp.png")
 system("cp Figures/threed-rglpersp.png Web/")
 system("cp Figures/contour3d.png Web/threed-contour3d.png")
 system(paste("g.dirseps.exe -g",
            shQuote(Sys.getenv("GISRC"))), intern=TRUE)
 system(paste("g.dirseps.exe -g",
            shQuote(gisDbase)), intern=TRUE)
 system(paste(paste("g.gisenv", get("addEXE", envir=.GRASS_CACHE), sep=""),
        shQuote(paste("set=GISDBASE=", gisDbase))))
 system(paste(paste("g.gisenv", get("addEXE", envir=.GRASS_CACHE), sep=""),
        shQuote(paste("set=GISDBASE", gisDbase, sep="="))))
 system(paste(paste("g.gisenv", get("addEXE", envir=.GRASS_CACHE), sep=""),
        shQuote(paste("set=LOCATION_NAME", location, sep="="))))
 system(paste(paste("g.gisenv", get("addEXE", envir=.GRASS_CACHE), sep=""),
        shQuote(paste("set=MAPSET", mapset, sep="="))))
 system(paste(paste("g.gisenv", get("addEXE", envir=.GRASS_CACHE), sep=""),
        shQuote("set=GRASS_GUI=text")))
 system(paste("g.version", get("addEXE", envir=.GRASS_CACHE),
                       sep=""),  intern=TRUE)
 system(paste("cygpath -w", gtmpfl1, sep=" "),
                          intern=TRUE)
 system(paste("cygpath -w", gtmpfl1, sep=" "), intern=TRUE)
 system(paste("cygpath -w", gtmpfl1, sep=" "), 
 			intern=TRUE)
 system(paste("cygpath -w", gtmpfl1, sep=" "), intern=TRUE)
 system(cmd0, intern=TRUE)
 system(syscmd, intern=intern, ignore.stderr=ignore.stderr,
                ignore.stdout=Sys_ignore.stdout, wait=Sys_wait, input=Sys_input)
 system(syscmd, intern=intern, ignore.stderr=ignore.stderr,
                ignore.stdout=Sys_ignore.stdout, wait=Sys_wait, input=Sys_input,
                show.output.on.console=Sys_show.output.on.console, 
                minimized=Sys_minimized, invisible=Sys_invisible)
 system(texto, ignore.stderr = TRUE)
 system("gretlcli -e -v -b -t", intern = T,ignore.stderr =T)
 system(texto, ignore.stderr = TRUE, intern = TRUE)
 system(texto,intern = TRUE,ignore.stdout =TRUE,ignore.stderr=TRUE)
 system(paste("open", path))
 system('which xclip', intern=T)
 system('which xsel', intern=T)
 system(paste("taskkill /F /PID", process.pid), wait=F)
 system("R CMD BATCH infile.R outfile.R", wait=F)
 system(sprintf('"%s" --app=%s', chrome, appUrl))
 system(paste("ping -n 1", site_url))
 system(glue::glue('"{compil32}" /cc "{iss_file}"'))
 system(paste("pdflatex",filetopdf), intern=TRUE)
 system(paste("xelatex",filetopdf), intern=TRUE)
 system(paste("bibtex",filetopdf), intern=TRUE)
 system(paste("pdflatex",filetopdf), intern=TRUE)
 system(paste("pdflatex",filetopdf), intern=TRUE)
 system(paste("dsymutil ", file, sep=''))
 system(x, ...)
 system(paste0(javaExe, ' -classpath ', file.path(find.package('RJSDMX'), 'java', 'SDMX.jar'), ' it.bancaditalia.oss.sdmx.helper.SDMXHelper'), wait=FALSE)
 system(paste(Sys.getenv("R_PDFVIEWER"), f, "&"))
 system(command, wait = FALSE)
 system(cmd)
 system("mapshaper --version 2>&1", intern = TRUE)
 system(paste(MarkPath," i=mxxx.tmp"," o=",release.out,sep="" ),
            invisible = invisible)
 system(paste(dQuote(MarkViewer),release.out),invisible=FALSE)
 system(paste(markpath, " i=",inputfile," o=", outfile,
 								 " v=",vcvfile, " r=",resfile, " threads=", threads,sep = ""),ignore.stdout=TRUE,ignore.stderr=TRUE)
 system(paste(markpath, " i=",inputfile," o=", outfile,
 								 " v=",vcvfile, " r=",resfile, " threads=", threads,sep = ""),ignore.stderr=ignore.stderr)
 system(paste(markpath, " i=",inputfile," o=", outfile,
 								 " v=",vcvfile, " r=",resfile, " threads=", threads,sep = ""),invisible=TRUE,ignore.stderr=ignore.stderr)
 system(paste("mark i=",inputfile," o=", outfile,
            " v=", vcvfile," r=",resfile, " threads=", threads,sep = ""),ignore.stderr=ignore.stderr)
 system(paste(shQuote(MarkViewer),paste(model$output,".out",sep="")),invisible=FALSE,wait=FALSE)
 system(paste(MarkViewer,paste(model$output,".out",sep="")),wait=FALSE)
 system(paste(shQuote(MarkViewer),paste(model$output,".inp",sep="")),invisible=FALSE,wait=FALSE)
 system(paste(MarkViewer,paste(model$output,".inp",sep="")),wait=FALSE)
 system(command)
 system(paste(shQuote(pandoc_path), "--version"),
                           intern = TRUE)
 system(paste(locale_util, "-a"), intern = TRUE)
 system(paste0("PATH=\"", sanitized_path, "\" /usr/bin/which ", program),
             intern = TRUE)
 system(cmd, intern = intern, wait = wait, ...)
 system(command, intern = TRUE)
 system(cmd, wait=FALSE)
 system(cmd)
 system(curlCall, intern=TRUE, ignore.stderr=TRUE)
 system(paste(pdfcrop, "--pdftexcmd", pdftex, f, f, "1>/dev/null 2>&1"),
           intern=FALSE)
 system("lamnodes C -c -n", TRUE)
 system(paste("ls", logfile),TRUE,ignore.stderr=TRUE)
 system(paste("rm", logfile))
 system(paste("ls", logfile),TRUE,ignore.stderr=TRUE)
 system(paste("tail -",nlines," ", logfile,sep=""))
 system("lamnodes",TRUE,ignore.stderr=TRUE)
 system("sysctl hw.ncpu",TRUE,ignore.stderr=TRUE)
 system("lamnodes",TRUE,ignore.stderr = TRUE)
 system("lamboot -H",ignore.stderr = TRUE)
 system(sprintf("dot -Tpdf -o %s %s", tmp.pdf, tmp.dot))
 system(comm)
 system(command = 'pdflatex --version', intern = T)
 system('pdflatex -version', intern = T)
 system(command = my.c, show.output.on.console = F)
 system(command = my.c)
 system("ls *.xml", intern=TRUE)
 system(paste0("aria2c -c -x2 ", ntLtsFileUrl, " -d ", getNlDir("dirNlTiles"), " -o ", getNlTileZipLclNameVIIRS(nlYearMonth, tileNum)))
 system(paste0("aria2c -c -x2 ", ntLtsFileUrl, " -d ", getNlDir("dirNlTiles"), " -o ", getNlTileZipLclNameOLS(nlYear)))
 system(command)
 system('wgrib2', intern = TRUE)
 system(paste0("wgrib2 ", grib.file, " -inv -"), intern = TRUE)
 system(paste0("wgrib2 ", grib.file, " -grid"), intern = TRUE)
 system('wgrib', intern = TRUE)
 system(paste0("wgrib ", grib.file, " -s"), intern = TRUE)
 system('wgrib2', intern = TRUE)
 system(wg2.str, intern = TRUE)
 system('wgrib', intern = TRUE)
 system(wg.str, ignore.stderr = TRUE)
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system("source ~/Downloads/test.sh")
 system(paste("R CMD INSTALL",ll.string," RObsDat"))
 system(cmd)
 system(paste(extractor, "-v"))
 system(paste(extractor, "-enc UTF-8 -nopgbrk", ..., pdf, txt, sep = " "), wait = TRUE)
 system(paste(extractor, "-enc UTF-8 -nopgbrk", ..., pdf, txt, sep = " "), wait = TRUE)
 system(make)
 system("touch outfile")
 system("touch outancestors")
 system("touch outmixture")
 system("touch outcategories")
 system(paste(path,"/seqboot",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/clique",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/restml",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outfile")
 system(paste(path,"/gendist",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outfile")
 system(paste(path,"/restdist",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/kitsch",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outfile")
 system(paste(path,"/gendist",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/dolpenny",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/dollop",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/penny",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/mix",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/pars",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/fitch",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/dnainvar",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/dnacomp",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outfile")
 system(paste(path,"/protdist",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/protpars",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/",exe,sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/consense",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/dnapenny",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outfile")
 system(paste(path,"/dnadist",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outfile")
 system(paste(path,"/treedist",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outfile")
 system(paste(path,"/threshml",sep=""),input=oo,show.output.on.console=(!quiet))
 system(paste("rm",fs[i],sep=" "),show.output.on.console=FALSE)
 system(paste("rm",fs[i],sep=" "))
 system(paste("cp ",path,"/src/linkmac ",path,"/exe/linkmac",sep=""))
 system(paste("chmod +x ",path,"/exe/linkmac",sep=""))
 system(paste("cd ",path,"/exe/\n./linkmac",sep=""))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/neighbor",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/dnapars",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outfile")
 system(paste(path,"/contml",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outfile")
 system(paste(path,"/contml",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outtree")
 system("touch outfile")
 system(paste(path,"/",exe,sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outfile")
 system(paste(path,"/contrast",sep=""),input=oo,show.output.on.console=(!quiet))
 system("touch outfile")
 system(paste(path,"/contrast",sep=""),input=oo,show.output.on.console=(!quiet))
 system("git log --pretty=format:'%h' -n 1",intern=TRUE)
 system(paste("createdb", tempdb))
 system(paste("dropdb", tempdb))
 system(paste("createdb", tempdb))
 system(paste("dropdb", tempdb))
 system(paste("dropdb", tempdb))
 system(paste("createdb", tempdb))
 system(paste("dropdb", tempdb))
 system(paste("psql beancounter -c \"create table timetest ( d1", tt, ")\" >/dev/null"))
 system("psql beancounter -c \"insert into timetest values( \'now\' )\" >/dev/null")
 system("psql beancounter -c \"drop table timetest\" >/dev/null")
 system(paste("createdb", tempdb))
 system(paste("dropdb", tempdb))
 system(paste("createdb", tempdb))
 system(paste("dropdb", tempdb))
 system(py.call, invisible = TRUE, minimize = TRUE, wait = wait)
 system("find /Applications -name 'QGIS.app'", intern = TRUE)
 system(cmd, intern = TRUE, ignore.stderr = TRUE)
 system(cmd, intern = TRUE, ignore.stderr = TRUE)
 system("bash -c 'type -p quantlib-config'", ignore.stderr=TRUE, intern=TRUE)
 system(paste(qc, "--cflags"), intern = TRUE)
 system(paste(qc, "--libs"),   intern = TRUE)
 system(command = comnd, ignore.stderr = TRUE, intern = TRUE)
 system(shQuote(file.path(raven.path, "Raven"), type = "cmd"), ignore.stderr = TRUE, intern = TRUE)
 system(file.path(raven.path, "Raven"), ignore.stderr = TRUE, intern = TRUE)
 system("open Raven.app", ignore.stderr = TRUE, intern = TRUE)
 system(command = comnd, ignore.stderr = TRUE, intern = TRUE)
 system(cmd)
 system(content, intern=TRUE)
 system(cmd)
 system(paste0("cd ", gsub(" ", "\\ ", getwd(), fixed=TRUE)))
 system(paste(paste0("ffmpeg -r ", fps, " -i ", name, "/", name, "_%04d.jpg -sameq -r ", fps," -b:v 5000K ",  paste0(name, "/", name, ".avi"))))
 system( command, intern=intern,
            show.output.on.console=show.output.on.console, 
            invisible=invisible, ...)
 system( command, intern=intern, ignore.stderr = TRUE, ...)
 system( command, intern=intern, ...)
 system(paste(shQuote(ssfile), infile), show.output.on.console=verbose)
 system("systeminfo /FO csv", intern=TRUE, wait=TRUE)
 system(command)
 system('ps -Ao"pid"', intern = TRUE)
 system('ps -Ao"args"', intern = TRUE)
 system('ps -Ao"%p"', intern = TRUE)
 system('ps -Ao"%a"', intern = TRUE)
 system(paste("file --mime-type", tmpF), intern = TRUE)
 system("tasklist /v /fo csv", intern = TRUE)
 system('ps -Ao"pid"', intern = TRUE)
 system('ps -Ao"args"', intern = TRUE)
 system('ps -Ao"%p"', intern = TRUE)
 system('ps -Ao"%a"', intern = TRUE)
 system(EQScmd, intern = FALSE, ignore.stderr = TRUE, 
        wait = TRUE, input = NULL)
 system(paste("dsymutil ", file, sep=''))
 system(fn, wait=wait, ...)
 system(cmd, wait=wait, ...)
 system('grep "##@" *.r *.R > comments.lis')
 system('sinfo', ignore.stdout = TRUE, ignore.stderr = TRUE)
 system('sinfo', ignore.stdout = TRUE, ignore.stderr = TRUE)
 system(paste(rscript_path, "--vanilla local_run.R"))
 system("sbatch submit.sh")
 system(
        paste('test -z "$(squeue -hn', slr_job$jobname, '2>/dev/null)"'),
        ignore.stderr = TRUE)
 system(srun)
 system('squeue', ignore.stdout = TRUE)
 system('squeue', ignore.stdout = TRUE)
 system(paste("scancel -n", slr_job$jobname))
 system(paste("squeue -n", slr_job$jobname), intern = TRUE)
 system(paste(bin, configPath),
           wait=FALSE, ignore.stdout=!isTRUE(getOption("verbose")))
 system(cmd)
 system("R CMD INSTALL ~/src/R/rstpm2")
 system(cmd)
 system(cmd, ignore.stdout = T, ignore.stderr = F)
 system("source $FREESURFER_HOME/SetUpFreeSurfer.sh && cd $SUBJECTS_DIR && cp $FREESURFER_HOME/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh $PWD && source kvlQuantifyHippocampalSubfieldSegmentations.sh")
 system("source $FREESURFER_HOME/SetUpFreeSurfer.sh && cd $SUBJECTS_DIR && cp $FREESURFER_HOME/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh $PWD && source kvlQuantifyHippocampalSubfieldSegmentations.sh", ignore.stdout=T, ignore.stderr=F)
 system(cmd)
 system(cmd, ignore.stdout = T, ignore.stderr = F)
 system(paste(MRTpath, '/mrtmosaic -i ', MRTpath, '/TmpMosaic.prm -s "',bands_subset,'" -o ',getwd(), '/',filename, sep=""))
 system(paste(MRTpath, '/mrtmosaic -i ', MRTpath, '/TmpMosaic.prm -o ',getwd(), '/',filename, sep=""))
 system(paste(MRTpath, '/resample -p ',getwd(),'/','tmp.prm', sep=''))
 system(paste("awk -f", gscript, path, " > ", gfile))
 system(paste("awk -f", rscript, repunits, " > ", rfile))
 system(paste("cat ", makeconfFile," | grep  \"^CXX =\" "),
                         intern=TRUE)
 system("printf '\n'")
 system(wrapper, intern=TRUE)
 system(command, intern=FALSE)
 system(paste('xgrid -job delete -id ', jobnum[s], sep=''), intern=TRUE)
 system(paste('xgrid -job delete -id ', jobnum, sep=''), intern=TRUE)
 system('xgrid 2>&1', intern=TRUE)
 system("sysctl -n kern.osrelease", intern=TRUE)
 system('expect -c "# exp_internal 1" -c "spawn xgrid -job list" -c"expect {Password:  { send \r\n; interact }eof { exit }}" 2>&1', intern=TRUE)
 system(paste('uuencode -m -o "', encodefile, '" "', scriptfile, '" script.R', sep=""), intern=TRUE, wait=TRUE)
 system(paste('cat "', encodefile, '" >> "', artfile, '"', sep=""), intern=TRUE, wait=TRUE)
 system(paste('cp "', rankscript, '" "', artfile, '"', sep=""))
 system(paste('chmod 755 "', artfile, '"', sep=""), intern=TRUE)
 system(paste('"', artfile, '"', sep=""), intern=TRUE)
 system(paste('xgrid -job attributes -id ', jobnum[s], sep=''), intern=TRUE)
 system(paste('xgrid -job results -id ', jobnum[s], sep=''))
 system(paste('xgrid -job attributes -id ', jobnum[s], sep=''), intern=TRUE)
 system(paste('xgrid -job results -id ', jobnum[s], ' -out "', directory, if(jags) '/sim.', if(jags) s, '"', sep=''), intern=TRUE)
 system(paste('xgrid -job delete -id ', jobnum[s], sep=''), intern=TRUE)
 system(paste('xgrid -job attributes -id ', jobnum, sep=''), intern=TRUE)
 system(paste('xgrid -job results -id ', jobnum, sep=''))
 system(paste('xgrid -job attributes -id ', jobnum, sep=''), intern=TRUE)
 system(paste('xgrid -job results -id ', jobnum, ' -out "', directory, '"', sep=''), intern=TRUE)
 system(paste('xgrid -job delete -id ', jobnum, sep=''), intern=TRUE)
 system(paste("xgrid -job wait -id ", j, " 2>&1 > waitfile.txt", sep=""), intern=FALSE, wait=FALSE)
 system(paste("xgrid -job wait -id ", j, sep=""), intern=TRUE, wait=TRUE)
 system(paste('which ', paths[i], ' 2>&1', sep=""), intern=TRUE)
 system('where jags',intern=TRUE)
 system("ls -l Robjects.Rsave | awk '{print $5}'", intern=TRUE)
 system('( ./starter.sh 2>&3 | tee .starterout.txt) 3>&2 | tee starteroutput.txt', intern=FALSE, wait=TRUE)
 system(paste("kill ", pid, sep=""))
 system('( ./starter.sh 2>&3 | tee .starterout.txt) 3>&2 | tee starteroutput.txt', intern=FALSE, wait=TRUE)
 system(paste("kill ", pid, sep=""))
 system(paste(shQuote(jags), if(!batch.jags) " <", " sim.1/script.cmd 2>&1", sep=""), intern=TRUE, wait=TRUE, ignore.stderr=FALSE)
 system(paste(shQuote(jags), if(!batch.jags) " <", " sim.", s, "/script.cmd > sim.", s, "/jagsoutput.txt 2>&1", sep=""), intern=TRUE, wait=TRUE)
 system(command, intern=FALSE, wait=FALSE)
 system('TASKLIST', intern=TRUE)
 system('TASKLIST', intern=TRUE)
 system('./scriptlauncher.sh 1', wait=TRUE, intern=FALSE)
 system(paste('taskkill /F /PID ', pid, sep=''), intern=TRUE)
 system(paste('kill ', pid, sep=''), ignore.stderr=TRUE)
 system('TASKLIST', intern=TRUE)
 system('TASKLIST', intern=TRUE)
 system(paste('./scriptlauncher.sh ', s, sep=''), wait=TRUE, intern=FALSE)
 system(paste('taskkill /F /PID ', k, sep=''), intern=TRUE)
 system(paste('kill ', pid[s], sep=''), ignore.stderr=TRUE)
 system('( ./starter.sh 2>&3 | tee .starterout.txt) 3>&2 | tee starteroutput.txt', intern=FALSE, wait=TRUE)
 system(paste("kill ", pid, sep=""))
 system('/bin/ps', intern=TRUE, ignore.stderr=TRUE)
 system(sprintf("cat %s", fh))
 system(cmd, wait=FALSE)
 system(start, intern=TRUE)
 system(cmd, wait=FALSE)
 system(cmd)
 system(cmd, intern=FALSE)
 system(cmd, intern=TRUE)
 system(cmd, intern=FALSE)
 system(cmd, intern=TRUE)
 system("subst", intern=TRUE)
 system("net use", intern=TRUE)
 system(cmd, ...)
 system("open .")
 system("xdg-open . &")
 system(paste(merlinDir,"merlin -d  ",datFN," -p  ",pedFN," -m  ",mapFN,"  -x NA --best --horizontal --prefix ",outFN.prefix,sep=""))
 system(paste0("grep -f snps2out.txt -w ",
                  filename,
                  " >HaploDataSubset.haps"))
 system(paste(path2Plink,
                             "--noweb --file",
                             plinkbasefile,
                             "--make-rel square --out RelMat",
                             sep=" "))
 system("rm RelMat.log RelMat.rel RelMat.rel.id")
 system(paste(path2Plink, "--noweb --tfile",
                             plinkbasefile,
                             "--make-rel square --out RelMat",
                             sep=" "))
 system("rm RelMat.log RelMat.rel RelMat.rel.id")
 system(paste(path2Plink,
                         "--noweb --bfile",
                         plinkbasefile,
                         "--make-rel square --out RelMat",
                         sep=" "))
 system("rm RelMat.log RelMat.rel RelMat.rel.id")
 system(command)
 system('rm -rf RWebLogo/build/RWebLogo_1.0.3.tar.gz')
 system('R CMD BUILD RWebLogo')
 system('mv RWebLogo_1.0.3.tar.gz RWebLogo/build/RWebLogo_1.0.3.tar.gz')
 system('R CMD INSTALL RWebLogo/build/RWebLogo_1.0.3.tar.gz')
 system(systemcommand)
 system("python -m pip install sympy")
 system("python -m pip install sympy")
 system(cmd, ignore.stdout=!RxODE.verbose,
                                    ignore.stderr=!RxODE.verbose)
 system(paste('cdo -s griddes', filein, '2> /dev/null'), intern = TRUE)
 system(paste0("cdo -s ", work_piece[['remap']], ",", 
                      common_grid_name, 
                      " -selname,", namevar, " ", filecopy, " ", filein, 
                      " 2>/dev/null", sep = ""))
 system(paste('cdo showmon ', filein, 
                         ' 2>/dev/null'), intern = TRUE)
 system(paste('cdo showyear ', filein, 
                          ' 2>/dev/null'), intern = TRUE)
 system(paste0("cdo -s -sellonlatbox,", if (lonmin > lonmax) {
                                                     "0,360,"
                                                   } else {
                                                     paste0(lonmin, ",", lonmax, ",")
                                                   }, latmin, ",", latmax,
                   " -", work_piece[['remap']], ",", common_grid_name, 
                   " ", filein2, " ", filein, " 2>/dev/null", sep = ""))
 system(paste0("cdo -s ", work_piece[['remap']], ",", common_grid_name, 
                     " ", mask_file, " ", mask_file_remap, " 2>/dev/null", sep = ""))
 system(paste0("cdo -s ", sellonlatbox, "remap", method, ",", grid, " ", tmp_file, " ", tmp_file2))
 system(paste("convert -rotate 90 -loop 10 -delay 50 ", 
        fileout[(jexp - 1) * nobs + jobs], ".png ", fileout[(jexp - 
          1) * nobs + jobs], ".gif", sep = ""))
 system(rcmd)
 system(paste(shell, script.file, sep=" "))
 system(command, intern=intern)
 system(system.str)
 system("stty -echo", ignore.stdout=TRUE, ignore.stderr=TRUE)
 system("stty echo", ignore.stdout=TRUE, ignore.stderr=TRUE)
 system(cmd, intern=TRUE)
 system(cmd, intern=TRUE)
 system(paste(get.sccv, ' "', pkg.dir.path, '"', sep=''), intern=TRUE)
 system(paste("diff -bw", shQuote(a), shQuote(b)))
 system(cmd)
 system(cmd)
 system(cmd, intern=TRUE, ignore.stdout=TRUE, ignore.stderr=FALSE)
 system(cmd, intern=TRUE, ignore.stdout=TRUE, ignore.stderr=FALSE)
 system(strdotcall, intern=TRUE, ignore.stderr=TRUE)
 system(strevincecall, intern=FALSE, wait=FALSE, ignore.stderr=TRUE)
 system(strdotcall, intern=TRUE, ignore.stderr=TRUE)
 system(strevincecall, intern=TRUE, ignore.stderr=TRUE)
 system(strdotcall, intern=TRUE, ignore.stderr=TRUE)
 system(strevincecall, intern=TRUE, ignore.stderr=TRUE)
 system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE)
 system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = FALSE)
 system(cmd, intern = TRUE, invisible = TRUE)
 system(cmd, intern = TRUE)
 system(paste(exename, command),ignore.stderr = TRUE)
 system(paste(exe, command, sep=" "), ignore.stderr = TRUE)
 system(paste(exe, "-v"), ignore.stderr = TRUE)
 system(paste(exe, "-d", file), ignore.stderr = TRUE)
 system(paste(exe, file), ignore.stderr = TRUE)
 system(paste(shQuote(exe), "-d", shQuote(file, type = "cmd"), sep = " "), ignore.stderr = TRUE)
 system(paste(shQuote(exe), shQuote(file, type = "cmd"), sep = " "), ignore.stderr = TRUE)
 system(paste("file --mime-type", tmpF), intern = TRUE)
 system(cmd)
 system(EQScmd, intern = FALSE, ignore.stderr = TRUE, 
        wait = TRUE, input = NULL)
 system(cmd)
 system("pbcopy", ignore.stderr = TRUE)
 system("xclip -version", ignore.stderr = TRUE)
 system("mkdir makeImapTempDir", ignore.stderr =TRUE)
 system(paste("mv ",dir,"*Dot* makeImapTempDir/",sep=""), ignore.stderr =TRUE)
 system(paste("mv ",dir,fname.root,".tif makeImapTempDir/", sep=""), ignore.stderr =TRUE)
 system("rm -r makeImapTempDir", ignore.stderr =TRUE)
 system(paste("convert ",dir,fname.ps," -size 800x1100 -resize ",resize," ",dir,fname.png,sep=""))
 system(paste("kolourpaint ", dir,fname.png," &", sep=""))
 system(paste("mspaint ", dir,fname.png," &", sep=""))
 system(paste(img.prog, " ", dir, fname.png, " &", sep=""))
 system(paste("convert ",dir,fname.Dot.ps," -size 800x1100 -resize ",resize," ",dir,fname.Dot.png,sep=""))
 system(paste("convert ",dir,fname.Dot.png, " ", dir,fname.Dot.tif,sep=""))
 system(paste("kolourpaint ", dir,fname.Dot.png," &", sep=""))
 system(paste("mspaint ", dir,fname.Dot.png," &", sep=""))
 system(paste(img.prog, " ", dir, fname.Dot.png, " &", sep=""))
 system(paste("convert ",dir,fname.ps," -size 800x1100 -resize ",resize," ",dir,fname.png,sep=""))
 system(paste("convert ",dir,fname.png, " ", dir,fname.tif,sep=""))
 system(paste("kolourpaint ", dir,fname.png," &", sep=""))
 system(paste("mspaint ", dir,fname.png," &", sep=""))
 system(paste(img.prog, " ", dir, fname.png, " &", sep=""))
 system(cmd)
 system(cmd)
 system(cmd)
 system(cmd)
 system(paste('dotter',sf1,sf2),wait=FALSE)
 system(paste(clustal.path, " -outfile=", tmp ," -infile=", protseq.file, sep = ""))
 system(paste('gzip -d -c ',file,' | grep -c "^', chr.name, '\t"', sep = ''), intern = TRUE)
 system(paste('gzip -d -c', file, '| wc'), intern = TRUE)
 system(paste(paste('grep -c "^', chr.name, '\t"', sep = ''), file, sep = ' '), intern = TRUE)
 system(paste('wc', file), intern = TRUE)
 system("find /sys/ -iname tty\\* 2>/dev/null",intern=T)
 system('make -q')
 system('make')
 system(command)
 system(command, wait = TRUE)
 system(paste(paste0("pdflatex -output-directory=", dirname(t.file)),
             t.file))
 system(paste(getOption("pdfviewer"), p.file),  wait=FALSE)
 system(paste0(...), intern=intern)
 system(paste("ldd", so), intern=TRUE)
 system(cmd, intern = !usefile)
 system(paste(ps.cmd,"m",process), intern = TRUE)
 system(cmd, intern=TRUE, ignore.stderr=TRUE)
 system(paste(cmd,"> /dev/null"))
 system(paste("unzip -oq", i))
 system(paste("gzip", paste(tmp.state, "SGP_LONG_Data.txt", sep="_")))
 system(paste("gzip", paste0(tmp.state, "_SGP_LONG_Data_", final.year, ".txt")))
 system(paste("gzip", paste(tmp.state, "SGP_WIDE_Data.txt", sep="_")))
 system(paste("gzip", paste(tmp.state, "SGP_INSTRUCTOR_Data.txt", sep="_")))
 system(paste("gzip", paste(file.label, "txt", sep=".")))
 system(paste("gzip", paste(file.label, "txt", sep=".")))
 system(paste0("pdflatex -interaction=batchmode student_report_", i, "_", j, ".tex"), ignore.stdout = TRUE)
 system(paste0("pdflatex -interaction=batchmode school_catalog_", i, "_", j, ".tex"), ignore.stdout = TRUE)
 system(paste0("pdflatex -interaction=batchmode school_catalog_", i, "_", j, ".tex"), ignore.stdout = TRUE)
 system(paste("du -s", file.path(sgPlot.folder, year_folder, district_folder, school_folder)), intern=TRUE)
 system(paste("tar cfz", paste0(school_folder, ".tar.gz"), school_folder, sep=" "))
 system(paste0("pdflatex -interaction=batchmode student_report_", i, "_", j, "_", k, ".tex"), ignore.stdout = TRUE)
 system(paste0("pdflatex -interaction=batchmode instructor_catalog_", i, "_", j, "_", k, ".tex"), ignore.stdout = TRUE)
 system(paste0("pdflatex -interaction=batchmode instructor_catalog_", i, "_", j, "_", k, ".tex"), ignore.stdout = TRUE)
 system(paste("du -s", file.path(sgPlot.folder, year_folder, district_folder, school_folder, instructor_folder)), intern=TRUE)
 system(paste("tar cfz", paste0(instructor_folder, ".tar.gz"), instructor_folder, sep=" "))
 system(command,intern=T)
 system('clear')
 system('wmic logicaldisk get Caption', intern=T)
 system('wmic logicaldisk get VolumeName', intern=T)
 system(command)
 system(paste(locale_util, "-a"), intern = TRUE)
 system(paste(shQuote(pandoc_path), "--version"),
                           intern = TRUE)
 system(paste0("chmod +x ", bashReference))
 system(paste0("chmod +x ", shortcut_reference))
 system(paste("mplus.exe ",mplus,".inp",sep=""), wait = TRUE)
 system(paste0("subst ",virD, " ", out_dir), intern=T)
 system(paste0("subst ",virD," /D"), intern =T)
 system(cmd)
 system(paste(getOption("pdfviewer"), doc, "&"))
 system("R CMD check --as-cran simcausal_0.5.0.tar.gz")
 system("R CMD SHLIB clotka.c")
 system("R CMD SHLIB clotka.c")
 system(cmd, intern = TRUE)
 system("where plink", intern = TRUE)
 system("which plink", intern = TRUE)
 system(cmd1)
 system(cmd2)
 system("which plink")
 system(paste("pdfcrop --pdftexcmd pdftex", f, f, "1>/dev/null 2>&1"),
           intern=FALSE)
 system(paste("pdfcrop --pdftexcmd pdftex", f, f, "1>/dev/null 2>&1"))
 system(crop)
 system(embedFonts)
 system( "noharm_analysis.bat" , show.output.on.console = F  )
 system( "analysis.bat"  )
 system(paste(path.conquest,"\\" , conquest.name , ".exe ", name,".cqc",sep=""),
 					show.output.on.console = show.conquestoutput , invisible = FALSE)
 system(cmd, wait = FALSE)
 system(sprintf("%s -colmodel=%s -clustfile=%s %s %s %d",
                       vcluster, colmodel, clustfile, control,
                       datfile, k),
               intern = TRUE)
 system(sprintf("%s -c %s %s -O %s %s %s",
                       gmeans, k,
                       if(!is.null(start)) paste("-i f", initfile) else "",
                       tmp, control, datfile),
               intern = TRUE)
 system(paste(viewer, file, sep=" "))
 system(paste(viewer, file, sep=" "))
 system(Rcmd)
 system(paste("grep -l 'proc.time()' ", workDir, "/*.Rout | wc -l",
                                       sep = ""), intern = TRUE)
 system(paste("grep -l 'Execution halted' ", workDir, "/*.Rout | wc -l",
                                       sep = ""), intern = TRUE)
 system(cmd, wait = FALSE, input = "")
 system(cmd, wait = FALSE)
 system(cmd, wait = FALSE, input = "")
 system(cmd, wait = FALSE)
 system(paste("ps v", Sys.getpid()), intern = TRUE)
 system(command)
 system("cp Examples/regForColorPlot.pdf Plate1.pdf; mv Plate1.pdf Chambers-color*")
 system("cp Examples/regForColorPlot.R Chambers-color*")
 system(cmd)
 system(cmd)
 system(cmd)
 system(cmd)
 system(command=paste("qpdf --check ",fileName,sep=""))
 system("solar", input = c("load pedigree dat.ped", 
    "load phenotypes dat.phe",
    "trait trait1",
    "covariate age age^2 SEX trait2",
    "polygenic",
    "quit"))
 system("solar", input = cmd, intern = result, 
      ignore.stdout = ignore.stdout, ignore.stderr = ignore.stderr)
 system(paste("open", r_helpfile_location))
 system(scpcmd)
 system(cmd)
 system("awk '/MemFree/ {print $2}' /proc/meminfo", intern=TRUE)
 system(cmd, intern = TRUE)
 system(cmd, intern = TRUE)
 system(cmd, intern = TRUE, ignore.stderr = TRUE)
 system(cmd, intern = TRUE, ignore.stderr = TRUE, ignore.stdout = TRUE)
 system(getOption("spant.tqn_cmd"),
                                       intern = TRUE, ignore.stderr = TRUE)
 system(getOption("spant.tqn_cmd"),
                                       intern = TRUE, ignore.stderr = TRUE)
 system(cmd, intern = TRUE)
 system("sudo modprobe ifb")
 system("sudo ip link set dev ifb0 up")
 system("sudo tc qdisc add dev eth0 ingress")
 system("sudo tc filter add dev eth0 parent ffff: protocol ip u32 match u32 0 0 flowid 1:1 action mirred egress redirect dev ifb0")
 system("sudo ifconfig ifb0 192.168.1.23 netmask 255.255.255.0 up")
 system("sudo tc qdisc del dev ifb0 root")
 system("sudo tc qdisc del dev eth0 handle ffff: ingress")
 system("sudo ifconfig ifb0 down")
 system(cmd)
 system(cmd)
 system(cmd)
 system(cmd, intern = TRUE)
 system(paste(executablepath, 'ss/satscan.prm'), wait = TRUE)
 system("cd ./pli-R-v0.0.3-2007-07-25/zeta-function/ && make")
 system("cd ./pli-R-v0.0.3-2007-07-25/exponential-integral/ && make")
 system("cd ./pli-R-v0.0.3-2007-07-25/ && \
            gcc -lm discpowerexp.c -o discpowerexp && \
            chmod +x discpowerexp")
 system("cd ./pli-R-v0.0.3-2007-07-25/zeta-function/ && rm zeta_func zeta_func.o")
 system("cd ./pli-R-v0.0.3-2007-07-25/exponential-integral/ && rm exp_int exp_int.o")
 system("cd ./pli-R-v0.0.3-2007-07-25/ && rm discpowerexp")
 system("cd ./pli-R-v0.0.3-2007-07-25/zeta-function/ && make")
 system("cd ./pli-R-v0.0.3-2007-07-25/exponential-integral/ && make")
 system("cd ./pli-R-v0.0.3-2007-07-25/ && \
            gcc discpowerexp.c -lm -o discpowerexp && \
            chmod +x discpowerexp")
 system("cd ./pli-R-v0.0.3-2007-07-25/zeta-function/ && rm zeta_func zeta_func.o")
 system("cd ./pli-R-v0.0.3-2007-07-25/exponential-integral/ && rm exp_int exp_int.o")
 system("cd ./pli-R-v0.0.3-2007-07-25/ && rm discpowerexp")
 system(zeta.command,intern=TRUE)
 system(discpowerexp.command,intern=TRUE)
 system(ei.command,intern=TRUE)
 system(sprintf("dd if=%s of=%s bs=512*512*2 skip=%d count=1", data_file, tmp_file, frame - 1),
         ignore.stderr = TRUE)
 system(paste('mkdir -p ', path.debug, sep = ''))
 system(paste('mkdir -p ', path.debug, sep = ''))
 system(paste('mkdir -p ', path.debug, sep = ''))
 system(paste('mkdir -p ', path.file, sep = ''))
 system("hostname", intern = TRUE)
 system("whoami", intern = TRUE)
 system("whoami", intern = TRUE)
 system(paste("g.dirseps.exe -g",
            shQuote(Sys.getenv("WINGISRC"))), intern=TRUE)
 system(paste("g.dirseps.exe -g",
            shQuote(gisDbase)), intern=TRUE)
 system(paste(paste("g.gisenv", get("addEXE", envir=.GRASS_CACHE), sep=""),
        shQuote(paste("set=GISDBASE=", gisDbase))))
 system(paste(paste("g.gisenv", get("addEXE", envir=.GRASS_CACHE), sep=""),
        shQuote(paste("set=GISDBASE", gisDbase, sep="="))))
 system(paste(paste("g.gisenv", get("addEXE", envir=.GRASS_CACHE), sep=""),
        shQuote(paste("set=LOCATION_NAME", location, sep="="))))
 system(paste(paste("g.gisenv", get("addEXE", envir=.GRASS_CACHE), sep=""),
        shQuote(paste("set=MAPSET", mapset, sep="="))))
 system(paste(paste("g.gisenv", get("addEXE", envir=.GRASS_CACHE), sep=""),
        shQuote("set=GRASS_GUI=text")))
 system(paste("g.version", get("addEXE", envir=.GRASS_CACHE),
        sep=""),  intern=TRUE)
 system(paste("cygpath -w", gtmpfl1, sep=" "), intern=TRUE)
 system(paste("cygpath -w", gtmpfl1, sep=" "), intern=TRUE)
 system(cmd, intern=TRUE)
 system(cmd, 
 		intern=TRUE, ignore.stderr=ignore.stderr)
 system(paste("cygpath -w", gtmpfl1, sep=" "), intern=TRUE)
 system(paste("cygpath -w", gtmpfl1, sep=" "), 
 			intern=TRUE)
 system(paste("cygpath -w", gtmpfl1, sep=" "), intern=TRUE)
 system(paste("cygpath -w", gisrc, sep=" "), intern=TRUE)
 system(paste("cygpath -w",
                    paste(Sys.getenv("GISBASE"), "scripts", sep="/")),
                    intern=TRUE)
 system(cmd0, intern=TRUE)
 system(syscmd, intern=intern, ignore.stderr=ignore.stderr,
                ignore.stdout=Sys_ignore.stdout, wait=Sys_wait, input=Sys_input)
 system(syscmd, intern=intern, ignore.stderr=ignore.stderr,
                ignore.stdout=Sys_ignore.stdout, wait=Sys_wait, input=Sys_input,
                show.output.on.console=Sys_show.output.on.console, 
                minimized=Sys_minimized, invisible=Sys_invisible)
 system(td)
 system(paste("zip \"",zf,"\" \"",fname,"\"",sep=""))
 system(paste("rm \"",fname,"\"",sep=""))
 system(cmd)
 system(unixcmdstring)
 system(paste(bin, "-noest"), ignore.stdout = TRUE)
 system(paste(bin, "-noest"), show.output.on.console = FALSE, invisible = TRUE, ignore.stdout = TRUE)
 system(paste0("cd ", pastef(sc, it, type), ";", paste0(bin, " "),
           ss_em_options, " ", admb_options), ignore.stdout = ignore.stdout, ...)
 system(paste0(paste0(bin, " "), ss_em_options, admb_options),
          invisible = TRUE, ignore.stdout = ignore.stdout,
               show.output.on.console = show.output.on.console, ...)
 system(paste(ss_bin, "-nohess"), show.output.on.console = FALSE,
           ignore.stdout=TRUE)
 system('wmic logicaldisk get caption', intern = TRUE)
 system('wmic logicaldisk get caption', intern = TRUE)
 system('wmic logicaldisk get caption', intern = TRUE)
 system('wmic logicaldisk get caption', intern = TRUE)
 system(command, intern=intern)
 system(paste0('chmod -R 777 ', tempdir(),'/MiddleFork04.ssn'))
 system(command = system_command)
 system(command = system_command)
 system(command = system_command)
 system(paste( "pdflatex --interaction=nonstopmode", shQuote(tex.temp.file)),  show.output.on.console = FALSE )
 system(cmd)
 system(paste('pdftotext -q -enc "ASCII7" "',x[i],'"',sep=""))
 system(command=command, intern=TRUE)
 system(command=command, intern=TRUE)
 system(command=command)
 system(paste(plink," --allow-no-sex --bfile ",trainbed," --assoc --pfilter ",maxal," --maf ",maf," --hwe ",hwe," --geno ",geno," --out ",fout,sep=""))
 system(paste(plink," --recodeA --bfile ",trainbed," --extract ",fout,".",qua,"assoc --out ",fout,sep=""))
 system(paste(plink," --bfile ",trainbed," --extract ",fout,".",qua,"assoc --freq --allow-no-sex --out ",fout,sep=""))
 system(paste(plink," --allow-no-sex --bfile ",trainbed," --logistic --covar ",fout,".cov --hide-covar --pfilter ",maxal," --maf ",maf," --hwe ",hwe," --geno ",geno," --out ",fout,sep=""))
 system(paste(plink," --recodeA --bfile ",trainbed," --extract ",fout,".assoc.logistic --out ",fout,sep=""))
 system(paste(plink," --bfile ",trainbed," --extract ",fout,".assoc.logistic --freq --allow-no-sex --out ",fout,sep=""))
 system(paste(plink," --allow-no-sex --bfile ",trainbed," --linear --covar ",fout,".cov --hide-covar --pfilter ",maxal," --maf ",maf," --hwe ",hwe," --geno ",geno," --out ",fout,sep=""))
 system(paste(plink," --recodeA --bfile ",trainbed," --extract ",fout,".assoc.linear --out ",fout,sep=""))
 system(paste(plink," --bfile ",trainbed," --extract ",fout,".assoc.linear --freq --allow-no-sex --out ",fout,sep=""))
 system(paste(plink," --out ",fout," --bfile ",trainbed," --score ",fout,".score",sep=""))
 system(paste(plink," --out ",trainfout," --bfile ",trainbed," --recodeA --recode-allele ",fout,".list --extract ",fout,".frq",sep=""))
 system(paste(plink," --out ",testfout," --bfile ",testbed," --recodeA --recode-allele ",fout,".list --extract ",fout,".frq",sep=""))
 system(cmd, ignore.stderr = TRUE)
 system("mapshaper --version")
 system(cmd)
 system(cmd)
 system(paste("CLUMPP", param.file))
 system(phase.cmd)
 system(mafft.cmd, intern = FALSE)
 system(genepop.cmd, intern = F, ignore.stdout = !show.output, wait = T, 
           ignore.stderr = T, show.output.on.console = F, minimized = F, 
           invisible = T
    )
 system(genepop.cmd, intern = F, ignore.stdout = !show.output, wait = T, 
           ignore.stderr = T)
 system(cmd.line, intern = F)
 system(paste(shQuote('open'), shQuote(f)), wait = FALSE, ignore.stderr = TRUE)
 system(paste(shQuote('/usr/bin/xdg-open'), shQuote(f)), #nolint
             wait = FALSE,
             ignore.stdout = TRUE)
 system(sys_call, ...)
 system(paste('rm', fn.gz))
 system(paste('bgzip', fn))
 system(paste('tabix -p vcf', fn.gz))
 system(paste("/usr/bin/xdg-open", outfile_path), wait = FALSE, ignore.stdout = TRUE)
 system(paste("open", outfile_path), wait = FALSE, ignore.stderr = TRUE)
 system(paste(Sys.getenv('R_PDFVIEWER'), f, '&'))
 system(paste("osascript", cmd, ">", tfile), wait = TRUE,
 		intern = FALSE, ignore.stderr = TRUE)
 system(msg, intern = TRUE, ignore.stderr = TRUE)
 system(msg)
 system(paste("osascript", cmd), intern = TRUE, wait = TRUE)
 system(cmd, intern = TRUE)
 system(paste(msg, fields, default), intern = TRUE)
 system(cmd, ignore.stdout = TRUE, ignore.stderr = TRUE, wait = TRUE)
 system(msg)
 system(msg)
 system(paste("zenity --question --text=\"Continue?\"",
 			"--ok-label=\"OK\" --cancel-label=\"Cancel\" --title=\"Confirm\""))
 system(paste("osascript", cmd, ">", tfile), wait = TRUE,
 		intern = FALSE, ignore.stderr = TRUE)
 system(msg, intern = TRUE)
 system(paste("osascript", cmd, ">", tfile), wait = TRUE,
 		intern = FALSE, ignore.stderr = TRUE)
 system(msg, intern = TRUE)
 system(paste("osascript", cmd, ">", tfile), wait = TRUE,
 		intern = FALSE, ignore.stderr = TRUE)
 system(msg, intern = TRUE)
 system(sprintf("open %s", shQuote(tmp)))
 system(paste("\"", IDE, "\"", sep = ""), wait = FALSE)
 system(cmd, intern = TRUE, wait = TRUE)
 system(cmd, intern = TRUE)
 system(cmds[i], ignore.stdout = TRUE,
          ignore.stderr = TRUE, wait = wait, minimized = FALSE,
          invisible = FALSE, show.output.on.console = FALSE)
 system(cmds[i], ignore.stdout = TRUE,
          ignore.stderr = TRUE, wait = wait)
 system("which edit", intern = TRUE)
 system("which gedit", intern = TRUE)
 system("which kate",
          intern = TRUE)
 system(shQuote(paste(path.package("SWATmodel"),libarch,swatbin, sep = "/")))
 system(shQuote(paste(path.package("SWATmodel"),libarch,swatbin, sep = "/")))
 system(shQuote(paste(path.package("SWATmodel"),libarch,swatbin, sep = "/")))
 system(git_clone)
 system("git checkout -f DESCRIPTION")
 system("git checkout master")
 system("git checkout -f DESCRIPTION")
 system(cmd, ...)
 system(paste("plink --script ",pre,"plinkScript.txt",sep=""))
 system(paste("java -jar ",#-Xmx5g
                         shQuote(paste(sort(path.package()[grep("synbreed", path.package())])[1], "/java/beagle.21Jan17.6cc.jar", sep="")),
                         # caution with more than one pacakge with names synbreed*, assume synbreed to be the first one
                         " gtgl=beagle/run", pre, "_input.vcf out=beagle/run", pre, "_out gprobs=true nthreads=", cores, mapfile, sep=""),
                         intern=!showBeagleOutput)
 system(paste("ls"),intern=TRUE)
 system(paste("mkdir ASReml"))
 system("asreml -ns1000 Model.as",TRUE)
 system("asreml -p Model.pin")
 system(paste('mv Model.asr ','ASReml/Model_rep',i,'_fold',ii,'.asr',sep=''))
 system(paste('mv Model.sln ','ASReml/Model_rep',i,'_fold',ii,'.sln',sep=''))
 system(paste('mv Model.vvp ','ASReml/Model_rep',i,'_fold',ii,'.vvp',sep=''))
 system(paste('mv Model.yht ','ASReml/Model_rep',i,'_fold',ii,'.vht',sep=''))
 system(paste('mv Model.pvc ','ASReml/Model_rep',i,'_fold',ii,'.pvc',sep=''))
 system(paste("ls"),intern=TRUE)
 system(paste("mkdir BRR"))
 system(paste("ls"),intern=TRUE)
 system(paste("mkdir BL"))
 system(cmd, input = text_vector, intern = TRUE, ignore.stderr = TRUE)
 system(paste(Sys.getenv("R_PDFVIEWER"), f, "&"))
 system(cmd, intern = TRUE)
 system(cmd, intern = TRUE)
 system(cmd, intern = FALSE)
 system(cmd, intern = FALSE)
 system(cmd, intern = FALSE)
 system("./phylocom bladj > phyloout.txt")
 system(cmd)
 system(cmd)
 system(sprintf("mysql %s %s -e 'CREATE DATABASE IF NOT EXISTS col';",
                 cl("-u ", user), cl("-p ", pwd)))
 system(sprintf("mysql %s %s col < %s", cl("-u ", user), cl("-p ", pwd),
                 path))
 system(paste("rm ",getwd(),"/define.function",sep=""))
 system(paste("rm ",getwd(),"/define.metric",sep=""))
 system("cat /etc/issue",
 		intern = TRUE, ignore.stderr = TRUE)
 system(paste('java',
                 paste('-Xmx', .mem, sep = ''),
                 '-jar',
                 paste(.mitcr.path, 'mitcr.jar', sep = ''),
                 args.str))
 system(cmd)
 system(cmd)
 system(cmd)
 system("bash -c 'which touch'", ignore.stdout = TRUE)
 system(paste0("bash -c 'sleep 1;", command, "'"), wait = FALSE)
 system("pdflatex -interaction=batchmode Report.tex")
 system("biber --onlylog Report")
 system("pdflatex -interaction=batchmode Report.tex")
 system("pdflatex -halt-on-error -interaction=batchmode article-for-min-bib.tex",
           intern = TRUE)
 system("biber article-for-min-bib",
           intern = TRUE)
 system("pdflatex -halt-on-error -interaction=batchmode article-for-min-bib.tex", 
           intern = TRUE)
 system("bibexport -o extracted.bib myarticle.aux")
 system(paste("pdflatex -draftmode", latex_file),
         show.output.on.console = FALSE,
         ignore.stderr = TRUE)
 system(paste("pdflatex -draftmode", latex_file),
         show.output.on.console = FALSE, 
         ignore.stderr = TRUE)
 system(paste("pdflatex -interaction=batchmode", latex_file))
 system(paste("pdftotext -layout", gsub("\\.tex$", ".pdf", latex_file)))
 system(paste0("pdftotext -layout ", file.pdf))
 system('mpm --list-package-names',intern = TRUE)
 system('tlmgr list --only-installed',intern = TRUE)
 system(sprintf("%s -synctex=1 -interaction=%s --halt-on-error %s",engine,interaction_mode,temp_file),...)
 system(sprintf('tlmgr list --only-installed %s | grep installed',pkg),intern=TRUE)
 system(paste(shQuote(getOption("pdfviewer")), 
                        shQuote(tmp)), wait = FALSE)
 system("sysctl -n hw.ncpu", intern=TRUE)
 system("nproc", intern=TRUE)
 system(
    paste(
      shQuote(tex_cmd), "-interaction=batchmode",
      "-output-directory", test_work_dir,
      graph_file
    ), intern = TRUE
  )
 system(
    paste(
      # Force the command to be executed through bash
      "bash -c ", shQuote(command_line)
    ),
    intern = TRUE, ignore.stderr = TRUE
  )
 system(
    paste(
      shQuote(gs_cmd), "-dNOPAUSE", "-sDEVICE=pdfwrite",
      paste0("-sOUTPUTFILE=", test_output),
      "-dBATCH", paste(shQuote(graph_files), collapse = " ")
    ),
    intern = TRUE, ignore.stderr = TRUE
  )
 system(
    paste(
      shQuote(convert_cmd),
      paste(shQuote(graph_files), collapse = " "),
      diff_output
    ),
    intern = TRUE, ignore.stderr = TRUE
  )
 system("bash -c 'which convert'", intern = TRUE, ignore.stderr = TRUE)
 system(latexCmd)
 system(latexCmd, intern = TRUE, ignore.stderr = TRUE)
 system("zdump")
 system(paste("zdump ", finCenter[k], sep=" "), intern=TRUE)
 system(paste("zdump -v", finCenter[k], sep=" "), intern=TRUE)
 system(paste("R --vanilla < ",name,".R",sep=""))
 system(cmd,intern=FALSE,ignore.stdout=FALSE,ignore.stderr=TRUE)
 system(cmd,intern=TRUE,ignore.stdout=FALSE,ignore.stderr=TRUE)
 system(cmd,intern=TRUE,ignore.stdout=FALSE,ignore.stderr=TRUE)
 system("open .")
 system("R CMD check --as-cran tmlenet_0.0.9.tar.gz")
 system(paste(pl, tf1, ">", tf2))
 system("ipconfig", intern = TRUE)
 system("ifconfig", intern = TRUE)
 system(paste0(libavpath, " -loglevel quiet -r 10 -i ",
                         path,"/images/images%d.png -b:v 1000k ",
                         path,"/",name,".mp4"))
 system(paste(pythonpath," ",path,'/tmp.py',sep=''))
 system(paste(Sys.getenv("COMSPEC"),"/c \"", cmd, "\""), ...)
 system(cmd,...)
 system(command, TRUE)
 system(runCmd)
 system(runCmd)
 system(runCmd)
 system(paste(rsync, " -a -v ", sshFlag,
    path.expand(vdbConn$path), "/* ",
    user, ip, webConn$serverDir, "/", webConn$name,
    sep = ""
  ), intern = TRUE, ignore.stderr = FALSE, ignore.stdout = FALSE)
 system(paste(rsync, " -a -v ", sshFlag,
    file.path(pkgPath, "trelliscopeViewer/*"), " ",
    user, ip, webConn$serverDir, "/", webConn$name,
    sep = ""
  ), intern = TRUE, ignore.stderr = FALSE, ignore.stdout = FALSE)
 system(paste(sshString, sshQuote, "sudo chown -R shiny ", webConn$serverDir, sshQuote, sep = ""), intern = TRUE, ignore.stderr = FALSE, ignore.stdout = FALSE)
 system(paste(rsync, "-avh", ll, newDatDir))
 system(command)
 system(command)
 system(paste("sleep", sleep))
 system(paste("sleep", sleep))
 system(paste("xpdf ",.libPaths()[i],"/TSTutorial/doc/Tutorial.pdf&",sep=""))
 system(paste("xpdf ",.libPaths()[i],"/TSTutorial/doc/Stationary.pdf&",sep=""))
 system("pdfLatex LatexTest.tex",intern=T)
 system("pdflatex LatexTest.tex",intern=T)
 system(paste("pdflatex ",session["report"]@contRep$name,".tex",sep=""))
 system(paste("xpdf ",session["report"]@contRep$name,".pdf&",sep=""))
 system(paste("pdflatex ",session["report"]@contRep$name,".tex",sep=""))
 system(paste("xpdf ",session["report"]@contRep$name,".pdf&",sep=""))
 system(paste(shQuote(TTH), tth.control(...)),
                input = x, intern = TRUE, ignore.stderr = TRUE)
 system(paste(shQuote(TTM), tth.control(...)),
      input = x, intern = TRUE, ignore.stderr = TRUE)
 system(paste(player, ..., object))
 system(paste0("rm -rf ",file.path(projectDir,locationName,dateString,"fp-data/run")))
 system(paste0("sshpass -p 'TjSDBkAu' ssh  [email protected] ls -l -h /log/",logFiles),intern = TRUE)
 system( paste0("sshpass -p 'TjSDBkAu'  scp '[email protected]:/log/",logFiles,"' ",logFolder,"/. " ),wait = TRUE)
 system(paste0("sshpass -p 'TjSDBkAu' ssh  [email protected] ls -h /log/dataflash"),intern = TRUE)
 system(paste0("sshpass -p 'TjSDBkAu' ssh  [email protected] cat /log/dataflash/LASTLOG.TXT"),intern = TRUE)
 system(paste0("sshpass -p 'TjSDBkAu' ssh  [email protected] ls -l -h /log/dataflash"),intern = TRUE)
 system( paste0("sshpass -p 'TjSDBkAu'  scp -P 22 [email protected]:/log/dataflash/*.BIN ",logFolder,"/. " ),wait=TRUE)
 system(paste0("sshpass -p 'TjSDBkAu' ssh  [email protected] ls -l -h /log/dataflash/",unlist(strsplit(lastlog, "\r")[[1]]),".BIN"),intern = TRUE)
 system( paste0("sshpass -p 'TjSDBkAu'  scp -P 22 [email protected]:/log/dataflash/",unlist(strsplit(lastlog, "\r")[[1]]),".BIN ",logFolder,"/. " ),wait=TRUE)
 system( paste0("sshpass -p 'TjSDBkAu'  scp -P 22 [email protected]:/log/dataflash/",logFiles,".BIN ",logFolder,"/. " ),wait=TRUE)
 system("ls", intern=TRUE)
 system(str_c("rm -rf ", file))
 system("mkdir tmp")
 system(xelatexCmd)
 system(str_c("biber ", filename))
 system(xelatexCmd)
 system("mkdir tmp")
 system(pandocCmd)
 system(xelatexCmd)
 system(str_c("biber ", filename))
 system(xelatexCmd)
 system("ls", intern=TRUE)
 system(str_c("mv ", file, " ./tmp/", file))
 system(paste0("open 'https://cran.r-project.org/package=", p, "'"))
 system(intern = TRUE, "osascript -e 'tell application \"Finder\" to get the POSIX path of (target of front window as alias)'")
 system(cmd, intern=TRUE)
 system(intern = TRUE, "osascript -e 'tell application \"Finder\" to get the POSIX path of (target of front window as alias)'")
 system(paste(opener, shQuote(filepath)))
 system(intern = TRUE, "osascript -e 'tell application \"Finder\" to get the POSIX path of (selection as alias)'")
 system(paste0("open ", file))
 system(paste0("dot -Tpdf -O ", shQuote(file)))
 system(command, intern=FALSE,ignore.stderr=TRUE)
 system("uuidgen",intern=TRUE)
 system(executable.string,intern=TRUE)
 system("sync")
 system(paste("rm ", filename, sep=" "),intern=TRUE)
 system(paste0('"', pdfLatexPath, '/pdflatex" "',
                               paste0(rnwPath, '/', fileName, '.tex'), '" ',
                               '-output-directory "', rnwPath, '"'),
                        intern=TRUE)
 system(paste0('"', pdfLatexPath, '/pdflatex" "',
                               paste0(rnwPath, '/', fileName, '.tex'), '" ',
                               '-output-directory "', rnwPath, '"'),
                        intern=TRUE)
 system(command)
 system(command)
 system(command)
 system(command)
 system(command)
 system(command)
 system(cmd.prot,
                                   ignore.stderr = FALSE,
                                   ignore.stdout = FALSE)
 system(cmd.hetatm,
                                     ignore.stderr = FALSE,
                                     ignore.stdout = FALSE)
 system("freesasa --version",
                              ignore.stderr = FALSE,
                              ignore.stdout = FALSE)
 system(fcmd)
 system(paste("sox", x, " -t wavpcm", filout, "rate", samp.rate * 1000), ignore.stdout = FALSE, intern = TRUE)
 system(paste("sox", x, "-t wavpcm", filout), ignore.stdout = FALSE, intern = TRUE)
 system("./cthresh.maxloglik")
 system("rm cthresh.maxloglik.out cthresh.maxloglik.data cthresh.maxloglik.start"
 				)
 system(comm,ignore.stderr=TRUE,ignore.stdout=TRUE)
 system(comm,ignore.stderr=TRUE)
 system(comm)
 system(comm)
 system("id -un", intern = TRUE)
 system("whoami", intern = TRUE, show.output.on.console = FALSE)
 system("id -P", intern = TRUE)
 system("osascript -e \"long user name of (system info)\"",
                     intern = TRUE)
 system("git config --global user.name", intern = TRUE)
 system(
        paste0("wmic useraccount where name=\"", username,
               "\" get fullname"),
        intern = TRUE
      )
 system("getent passwd $(whoami)", intern = TRUE)
 system("git config --global user.name", intern = TRUE)
 system("git config --global user.email", intern = TRUE)
 system("query user", intern=TRUE)
 system(paste(func, wavFiles[1], paste('-od=', normalizePath(fromLibasspDir), sep = '')), intern=T)
 system(paste(func, wavFiles[1], '-hp=4000', paste('-od=', normalizePath(fromLibasspDir), sep = '')))
 system(paste('spectrum', wavFiles[1], '-t=CEP', paste('-od=', normalizePath(fromLibasspDir), sep = '')))
 system(paste('spectrum', wavFiles[1], '-t=CSS', paste('-od=', normalizePath(fromLibasspDir), sep = '')))
 system(paste('spectrum', wavFiles[1], '-t=DFT', paste('-od=', normalizePath(fromLibasspDir), sep = '')))
 system(paste('f0_ksv', wavFiles[1], paste('-od=', normalizePath(fromLibasspDir), sep = '')))
 system(paste('f0_mhs', wavFiles[1], paste('-od=', normalizePath(fromLibasspDir), sep = '')))
 system(paste('spectrum', wavFiles[1], '-t=LPS', paste('-od=', normalizePath(fromLibasspDir), sep = '')))
 system(cmd)
 system(CMD, intern = TRUE)
 system(command)
 system(command, ignore.stdout = !verbose)
 system(command)
 system(paste(x13.bin, file.path(tdir, "Testairline")), intern = TRUE)
 system(command, intern=TRUE,wait=TRUE)
 system(command, wait=FALSE, minimized=TRUE)
 system(command, intern=FALSE, wait=TRUE, minimized=TRUE)
 system(command, FALSE)
 system(command, wait=FALSE, minimized=TRUE)
 system(command, intern=FALSE, wait=TRUE, minimized=TRUE)
 system(command, FALSE)
 system(ffmpeg_local[i])
 system(convert_local[i])
 system(ffmpeg_local[i])
 system(convert_local[i])
 system(paste("mkdir -p ", PLOT_PATH, "/PC", sep=""))
 system("which convert", ignore.stdout=TRUE, ignore.stderr=TRUE)
 system(paste("convert ", paste(paste(plotNames, ".png", sep=""), collapse=" "), " ", PLOT_PATH, "/PC.", job, ".pdf", sep=""))
 system(paste("mkdir -p ", PLOT_DIR, sep=""))
 system(getDims, intern=TRUE)
 system(paste("grep 'Removing first' ", PCA_NORMALIZE_OUT_FILE, " | awk '{print $3}'", sep=""), intern=TRUE)
 system(sprintf(cmd, tmp), wait = TRUE)
 system(sprintf('mkdir -p -m %s %s',mode,x))
 system(cmd, intern=T)
 system(cmd, intern=T)
 system("julia < ./juliaTest.jl", wait = FALSE)
 system("julia < ./juliaTestLines.jl", wait = FALSE)
 ::
 ::
 ::
 system(paste("head -n5 ", datafile))
 system(cmd, ignore.stdout = TRUE, ignore.stderr = TRUE)
 system(paste("dolphin", x@root, "&"))
 system(cmd, show.output.on.console = FALSE, invisible = TRUE,
 			intern = FALSE)
 system(cmd, ignore.stdout = TRUE, ignore.stderr = TRUE,
 			intern = FALSE)
 system("unzip", intern = TRUE)
 system(cmd, invisible = TRUE, intern = TRUE)
 system(cmd, intern = TRUE)
 system(cmd)
 system(cmd, wait = FALSE, ignore.stdout = TRUE, ignore.stderr = TRUE)
 system(cmd, wait = FALSE, ignore.stdout = TRUE, ignore.stderr = TRUE)
 system(paste(pgmPath, cmdline), wait = wait, ignore.stdout = TRUE,
 			ignore.stderr = TRUE)
 system(paste(shQuote(getOption("pdfviewer")), shQuote(manual)),
 				wait = FALSE)
 system(paste('"', Asoft, '"', sep = ""), wait = FALSE)
 system(cmd , intern = TRUE)
 system(cmd, intern = TRUE)