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January 20, 2020 17:49
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| * using log directory ‘/private/var/folders/yc/53w8dbxx2hjg11_brr2pj5740000gn/T/RtmpWPpy1T/rcdk.Rcheck’ | |
| * using R version 3.6.0 (2019-04-26) | |
| * using platform: x86_64-apple-darwin15.6.0 (64-bit) | |
| * using session charset: UTF-8 | |
| * using options ‘--no-manual --as-cran’ | |
| * checking for file ‘rcdk/DESCRIPTION’ ... OK | |
| * this is package ‘rcdk’ version ‘3.4.9.2’ | |
| * checking package namespace information ... OK | |
| * checking package dependencies ... OK | |
| * checking if this is a source package ... OK | |
| * checking if there is a namespace ... OK | |
| * checking for executable files ... OK | |
| * checking for hidden files and directories ... OK | |
| * checking for portable file names ... OK | |
| * checking for sufficient/correct file permissions ... OK | |
| * checking serialization versions ... OK | |
| * checking whether package ‘rcdk’ can be installed ... OK | |
| * checking installed package size ... OK | |
| * checking package directory ... OK | |
| * checking for future file timestamps ... OK | |
| * checking ‘build’ directory ... OK | |
| * checking DESCRIPTION meta-information ... OK | |
| * checking top-level files ... OK | |
| * checking for left-over files ... OK | |
| * checking index information ... OK | |
| * checking package subdirectories ... OK | |
| * checking R files for non-ASCII characters ... OK | |
| * checking R files for syntax errors ... OK | |
| * checking whether the package can be loaded ... OK | |
| * checking whether the package can be loaded with stated dependencies ... OK | |
| * checking whether the package can be unloaded cleanly ... OK | |
| * checking whether the namespace can be loaded with stated dependencies ... OK | |
| * checking whether the namespace can be unloaded cleanly ... OK | |
| * checking dependencies in R code ... OK | |
| * checking S3 generic/method consistency ... OK | |
| * checking replacement functions ... OK | |
| * checking foreign function calls ... OK | |
| * checking R code for possible problems ... OK | |
| * checking Rd files ... OK | |
| * checking Rd metadata ... OK | |
| * checking Rd line widths ... OK | |
| * checking Rd cross-references ... OK | |
| * checking for missing documentation entries ... OK | |
| * checking for code/documentation mismatches ... OK | |
| * checking Rd \usage sections ... WARNING | |
| Undocumented arguments in documentation object 'copy.image.to.clipboard' | |
| ‘molecule’ ‘depictor’ | |
| Undocumented arguments in documentation object 'eval.atomic.desc' | |
| ‘molecule’ ‘which.desc’ ‘verbose’ | |
| Undocumented arguments in documentation object 'eval.desc' | |
| ‘molecules’ ‘which.desc’ ‘verbose’ | |
| Undocumented arguments in documentation object 'generate.formula' | |
| ‘mass’ ‘window’ ‘elements’ ‘validation’ ‘charge’ | |
| Undocumented arguments in documentation object 'generate.formula.iter' | |
| ‘mass’ ‘window’ ‘elements’ ‘validation’ ‘charge’ ‘as.string’ | |
| Undocumented arguments in documentation object 'get.alogp' | |
| ‘molecule’ | |
| Undocumented arguments in documentation object 'get.atomic.desc.names' | |
| ‘type’ | |
| Undocumented arguments in documentation object 'get.desc.names' | |
| ‘type’ | |
| Undocumented arguments in documentation object 'get.formula' | |
| ‘mf’ ‘charge’ | |
| Undocumented arguments in documentation object 'get.isotopes.pattern' | |
| ‘formula’ ‘minAbund’ | |
| Undocumented arguments in documentation object 'get.mcs' | |
| ‘mol1’ ‘mol2’ ‘as.molecule’ | |
| Undocumented arguments in documentation object 'get.mol2formula' | |
| ‘molecule’ ‘charge’ | |
| Undocumented arguments in documentation object 'get.tpsa' | |
| ‘molecule’ | |
| Undocumented arguments in documentation object 'get.volume' | |
| ‘molecule’ | |
| Undocumented arguments in documentation object 'get.xlogp' | |
| ‘molecule’ | |
| Undocumented arguments in documentation object 'isvalid.formula' | |
| ‘formula’ ‘rule’ | |
| Undocumented arguments in documentation object 'matches' | |
| ‘query’ ‘target’ ‘return.matches’ | |
| Undocumented arguments in documentation object 'set.charge.formula' | |
| ‘formula’ ‘charge’ | |
| Undocumented arguments in documentation object 'view.image.2d' | |
| ‘molecule’ ‘depictor’ | |
| Functions with \usage entries need to have the appropriate \alias | |
| entries, and all their arguments documented. | |
| The \usage entries must correspond to syntactically valid R code. | |
| See chapter ‘Writing R documentation files’ in the ‘Writing R | |
| Extensions’ manual. | |
| * checking Rd contents ... OK | |
| * checking for unstated dependencies in examples ... OK | |
| * checking contents of ‘data’ directory ... OK | |
| * checking data for non-ASCII characters ... OK | |
| * checking data for ASCII and uncompressed saves ... OK | |
| * checking line endings in Makefiles ... OK | |
| * checking for GNU extensions in Makefiles ... OK | |
| * checking include directives in Makefiles ... OK | |
| * checking installed files from ‘inst/doc’ ... OK | |
| * checking files in ‘vignettes’ ... OK | |
| * checking examples ... OK | |
| * checking for unstated dependencies in ‘tests’ ... OK | |
| * checking tests ... | |
| Running ‘doRUnit.R’ | |
| OK | |
| * checking for unstated dependencies in vignettes ... OK | |
| * checking package vignettes in ‘inst/doc’ ... OK | |
| * checking re-building of vignette outputs ... WARNING | |
| Error(s) in re-building vignettes: | |
| --- re-building ‘molform.Rmd’ using rmarkdown | |
| --- finished re-building ‘molform.Rmd’ | |
| --- re-building ‘using-rcdk.Rmd’ using rmarkdown | |
| ----------- FAILURE REPORT -------------- | |
| --- failure: length > 1 in coercion to logical --- | |
| --- srcref --- | |
| : | |
| --- package (from environment) --- | |
| rcdk | |
| --- call from context --- | |
| eval.desc(mols, descNames) | |
| --- call from argument --- | |
| length(vals) == 1 && is.na(vals) | |
| --- R stacktrace --- | |
| where 1: eval.desc(mols, descNames) | |
| where 2: eval(expr, envir, enclos) | |
| where 3: eval(expr, envir, enclos) | |
| where 4: withVisible(eval(expr, envir, enclos)) | |
| where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, | |
| error = eHandler, message = mHandler) | |
| where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, | |
| enclos)), warning = wHandler, error = eHandler, message = mHandler)) | |
| where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, | |
| envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))) | |
| where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, | |
| debug = debug, last = i == length(out), use_try = stop_on_error != | |
| 2L, keep_warning = keep_warning, keep_message = keep_message, | |
| output_handler = output_handler, include_timing = include_timing) | |
| where 9: evaluate::evaluate(...) | |
| where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), | |
| keep_message = !isFALSE(options$message), stop_on_error = if (options$error && | |
| options$include) 0L else 2L, output_handler = knit_handlers(options$render, | |
| options)) | |
| where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, | |
| keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), | |
| stop_on_error = if (options$error && options$include) 0L else 2L, | |
| output_handler = knit_handlers(options$render, options))) | |
| where 12: block_exec(params) | |
| where 13: call_block(x) | |
| where 14: process_group.block(group) | |
| where 15: process_group(group) | |
| where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), | |
| error = function(e) { | |
| setwd(wd) | |
| cat(res, sep = "\n", file = output %n% "") | |
| message("Quitting from lines ", paste(current_lines(i), | |
| collapse = "-"), " (", knit_concord$get("infile"), | |
| ") ") | |
| }) | |
| where 17: process_file(text, output) | |
| where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) | |
| where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), | |
| output_dir = getwd(), ...) | |
| where 20: vweave_rmarkdown(...) | |
| where 21: engine$weave(file, quiet = quiet, encoding = enc) | |
| where 22: doTryCatch(return(expr), name, parentenv, handler) | |
| where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]]) | |
| where 24: tryCatchList(expr, classes, parentenv, handlers) | |
| where 25: tryCatch({ | |
| engine$weave(file, quiet = quiet, encoding = enc) | |
| setwd(startdir) | |
| output <- find_vignette_product(name, by = "weave", engine = engine) | |
| if (!have.makefile && vignette_is_tex(output)) { | |
| texi2pdf(file = output, clean = FALSE, quiet = quiet) | |
| output <- find_vignette_product(name, by = "texi2pdf", | |
| engine = engine) | |
| } | |
| }, error = function(e) { | |
| OK <<- FALSE | |
| message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", | |
| file, conditionMessage(e))) | |
| }) | |
| where 26: tools:::.buildOneVignette("using-rcdk.Rmd", "/private/var/folders/yc/53w8dbxx2hjg11_brr2pj5740000gn/T/RtmpWPpy1T/rcdk.Rcheck/vign_test/rcdk", | |
| TRUE, FALSE, "using-rcdk", "UTF-8", "/var/folders/yc/53w8dbxx2hjg11_brr2pj5740000gn/T//RtmpgsaTPM/filef1d06a9d83ea.rds") | |
| --- value of length: 277 type: logical --- | |
| do.call..rbind...vals. | |
| C(Br)(Cl)(Cl)Cl FALSE | |
| ClC(F)(F)F FALSE | |
| C(Cl)(Cl)(Cl)Cl FALSE | |
| C(F)(F)(F)F FALSE | |
| BrC(Br)Br FALSE | |
| C(Cl)(F)F FALSE | |
| C(Cl)(Cl)F FALSE | |
| C(Cl)(Cl)Cl FALSE | |
| C(F)(F)F FALSE | |
| C(Br)Br FALSE | |
| C(Cl)Cl FALSE | |
| C(F)F FALSE | |
| C(I)I FALSE | |
| O=C FALSE | |
| C(=O)O FALSE | |
| CBr FALSE | |
| CCl FALSE | |
| CF FALSE | |
| CI FALSE | |
| CO FALSE | |
| CS FALSE | |
| C(C(F)(F)F)(Cl)(Cl)F FALSE | |
| C(C(F)(F)F)(F)(F)F FALSE | |
| C(C(Cl)Cl)(F)(F)F FALSE | |
| C(=C(Cl)Cl)Cl FALSE | |
| C(C=O)(Cl)(Cl)Cl FALSE | |
| C(C(Cl)(Cl)Cl)(Cl)Cl FALSE | |
| C(C(F)(F)F)(F)F FALSE | |
| C(C(Br)Br)(Br)Br FALSE | |
| C(CCl)(Cl)(Cl)Cl FALSE | |
| C(C(Cl)Cl)(Cl)Cl FALSE | |
| C=C(F)F FALSE | |
| C(C(F)F)(F)F FALSE | |
| C=CBr FALSE | |
| CC(=O)Cl FALSE | |
| CC(Cl)(Cl)Cl FALSE | |
| C(CCl)(Cl)Cl FALSE | |
| C=CF FALSE | |
| CC(F)(F)F FALSE | |
| CC(Br)Br FALSE | |
| C(CBr)Br FALSE | |
| C(C)(Cl)Cl FALSE | |
| C(CCl)Cl FALSE | |
| CC(F)F FALSE | |
| C(CF)F FALSE | |
| CC(=O)O FALSE | |
| COC=O FALSE | |
| CCBr FALSE | |
| CCCl FALSE | |
| CCF FALSE | |
| CCI FALSE | |
| COC FALSE | |
| CCO FALSE | |
| OCCO FALSE | |
| CSC FALSE | |
| CCS FALSE | |
| CSSC FALSE | |
| SCCS FALSE | |
| CC(=C)Cl FALSE | |
| C(C(CCl)Cl)Cl FALSE | |
| C(C(C)Cl)Cl FALSE | |
| CC(=O)C FALSE | |
| CCC=O FALSE | |
| CC1CO1 FALSE | |
| CCOC=O FALSE | |
| CC(=O)OC FALSE | |
| CCC(=O)O FALSE | |
| C(CC)Br FALSE | |
| CC(C)Cl FALSE | |
| CCCCl FALSE | |
| CC(C)I FALSE | |
| CCCI FALSE | |
| CC(C)O FALSE | |
| CCOC FALSE | |
| CCCO FALSE | |
| CC(O)CO FALSE | |
| C(CCO)O FALSE | |
| CC(C)S FALSE | |
| CCCS FALSE | |
| c1ccco1 FALSE | |
| c1cccs1 FALSE | |
| C1C=CCO1 FALSE | |
| CC(=C)C(=O)O FALSE | |
| C(C(CC)Cl)Cl FALSE | |
| CC(C(C)Cl)Cl FALSE | |
| C(=O)CCC FALSE | |
| CCC(=O)C FALSE | |
| CC(C)C=O FALSE | |
| O1CCCC1 FALSE | |
| CCCC(=O)O FALSE | |
| CCOC(=O)C FALSE | |
| CC(C)C(=O)O FALSE | |
| COC(=O)CC FALSE | |
| CCCOC=O FALSE | |
| S1CCCC1 FALSE | |
| C(CCC)Br FALSE | |
| CC(CC)Br FALSE | |
| CCCCCl FALSE | |
| CC(CC)Cl FALSE | |
| CC(C)(C)Cl FALSE | |
| CC(C)CCl FALSE | |
| CCCCO FALSE | |
| CC(CC)O FALSE | |
| CCOCC FALSE | |
| C(C(C)C)O FALSE | |
| CC(C)(C)O FALSE | |
| CCCOC FALSE | |
| OCCC(C)O FALSE | |
| OCCCCO FALSE | |
| CC(O)C(O)C FALSE | |
| C(C(CO)C)O FALSE | |
| CCCCS FALSE | |
| CCC(S)C FALSE | |
| CC(C)(C)S FALSE | |
| CC(C)CS FALSE | |
| CSCCC FALSE | |
| c1cc(sc1)C FALSE | |
| CC(C)C(=O)C FALSE | |
| CCCCC=O FALSE | |
| CCCC(=O)C FALSE | |
| CCC(=O)CC FALSE | |
| CCCCOC=O FALSE | |
| CC(CC)OC=O FALSE | |
| CC(C)(C)OC=O FALSE | |
| CCOC(=O)CC FALSE | |
| CC(C)COC=O FALSE | |
| CC(=O)OC(C)C FALSE | |
| CCCC(=O)OC FALSE | |
| CC(C)CC(=O)O FALSE | |
| CC(C)(C)C(=O)O FALSE | |
| CCCCC(=O)O FALSE | |
| CCCOC(=O)C FALSE | |
| CCCCCCl FALSE | |
| C(C(C)(C)C)O FALSE | |
| CCOC(C)C FALSE | |
| CCOCCC FALSE | |
| C(C(CC)C)O FALSE | |
| CC(CC)(C)O FALSE | |
| C(CC(C)C)O FALSE | |
| CC(C(C)C)O FALSE | |
| CCCCOC FALSE | |
| CCC(C)OC FALSE | |
| CC(C)(C)OC FALSE | |
| C(CCCC)O FALSE | |
| CC(CCC)O FALSE | |
| CCC(CC)O FALSE | |
| OCCCCCO FALSE | |
| CSCCCC FALSE | |
| CSC(C)(C)C FALSE | |
| CCCCCS FALSE | |
| c1(c(c(c(c(c1Cl)Cl)Cl)Cl)Cl)Cl FALSE | |
| c1(c(c(c(c(c1F)F)F)F)F)F FALSE | |
| c1cc(c(cc1Cl)Cl)Cl FALSE | |
| c1c(cccc1Cl)Cl FALSE | |
| c1(ccccc1Cl)Cl FALSE | |
| c1(ccc(cc1)Cl)Cl FALSE | |
| c1ccc(cc1O)Cl FALSE | |
| c1cccc(c1O)Cl FALSE | |
| c1cc(ccc1O)Cl FALSE | |
| c1(ccccc1)O FALSE | |
| c1(ccccc1O)O FALSE | |
| c1(cccc(c1)O)O FALSE | |
| c1cc(ccc1O)O FALSE | |
| C1CCC(=O)CC1 FALSE | |
| CC(=O)CC(=O)OCC FALSE | |
| CCOC(=O)C(=O)OCC FALSE | |
| C1CCC(CC1)O FALSE | |
| CC(=O)C(C)(C)C FALSE | |
| CC(C)C(=O)CC FALSE | |
| CCCCCC=O FALSE | |
| CC(=O)CCCC FALSE | |
| CCC(=O)CCC FALSE | |
| CC(=O)CC(C)C FALSE | |
| CC(=O)C(C)CC FALSE | |
| CC(=O)OCCCC FALSE | |
| CC(=O)OC(C)CC FALSE | |
| CC(=O)OC(C)(C)C FALSE | |
| CCCC(=O)OCC FALSE | |
| CCC(CC)C(=O)O FALSE | |
| CCOC(=O)C(C)C FALSE | |
| CCCCCC(=O)O FALSE | |
| CC(=O)OCC(C)C FALSE | |
| CCCCCOC=O FALSE | |
| CCCOC(=O)CC FALSE | |
| CCOCCCC FALSE | |
| CCOC(C)(C)C FALSE | |
| CC(C)OC(C)C FALSE | |
| CCC(CC)CO FALSE | |
| CCCCCCO FALSE | |
| CC(CCCC)O FALSE | |
| C(C(CCC)C)O FALSE | |
| CC(CC(C)C)O FALSE | |
| CCCCCOC FALSE | |
| OCCCCCCO FALSE | |
| CC(CC(C)O)(C)O FALSE | |
| CCCSCCC FALSE | |
| CCSC(C)(C)C FALSE | |
| CCCCCCS FALSE | |
| CCCSSCCC FALSE | |
| c1ccccc1C(Cl)(Cl)Cl FALSE | |
| c1(ccccc1)C(Cl)Cl FALSE | |
| c1ccccc1C(=O)O FALSE | |
| c1cc(ccc1O)C=O FALSE | |
| c1(ccccc1O)C=O FALSE | |
| c1ccccc1CCl FALSE | |
| c1(ccccc1)CO FALSE | |
| c1ccc(cc1O)C FALSE | |
| c1cccc(c1O)C FALSE | |
| c1cc(ccc1O)C FALSE | |
| CCOC(=O)CC(=O)OCC FALSE | |
| CC(C)C(=O)C(C)C FALSE | |
| CCCCCCC=O FALSE | |
| CC(=O)CCCCC FALSE | |
| CCCC(=O)CCC FALSE | |
| C1(CCCCC1)(C)O FALSE | |
| CC(=O)CCC(C)C FALSE | |
| CCCCOC(=O)CC FALSE | |
| CC(C)CC(=O)OCC FALSE | |
| CCCCCCC(=O)O FALSE | |
| CCCCCCOC=O FALSE | |
| CCCC(=O)OCCC FALSE | |
| CCCCCCCO FALSE | |
| CC(CCCCC)O FALSE | |
| C(CCCC(C)C)O FALSE | |
| CCCCCCCS FALSE | |
| c1cc(c(cc1C=O)OC)O FALSE | |
| c1cc(ccc1CC)O FALSE | |
| c1(c(cccc1C)O)C FALSE | |
| c1cc(cc(c1O)C)C FALSE | |
| c1c(ccc(c1O)C)C FALSE | |
| c1c(c(c(cc1)C)O)C FALSE | |
| c1(cc(ccc1C)O)C FALSE | |
| c1c(cc(cc1O)C)C FALSE | |
| CCOC(=O)C=CC(=O)OCC FALSE | |
| CCCCCCCC=O FALSE | |
| CCCCCCC(=O)C FALSE | |
| CCCCOC(=O)CCC FALSE | |
| CCCCCCCOC=O FALSE | |
| CCCCCCOC(=O)C FALSE | |
| CC(C)COC(=O)C(C)C FALSE | |
| CCC(C)OC(C)CC FALSE | |
| C(C(CCCC)CC)O FALSE | |
| C(CCCCCCC)O FALSE | |
| CC(CCCCCC)O FALSE | |
| CCCCCCCCS FALSE | |
| c1(ccccc1)C(=O)OCC FALSE | |
| c1cccc(c1)COCC FALSE | |
| C1(CC(=O)C=C(C1)C)(C)C FALSE | |
| CC(C)CC(=O)CC(C)C FALSE | |
| CCCCCCCC(=O)C FALSE | |
| CCCCC(=O)CCCC FALSE | |
| CCCCCCCOC(=O)C FALSE | |
| CCCCCCCCC(=O)O FALSE | |
| CCCCCCCCOC=O FALSE | |
| CC(C)CC(CC(C)C)O FALSE | |
| CCCCCCCCCO FALSE | |
| CCCCCCCC(C)O FALSE | |
| CCCCCCCCCS FALSE | |
| c1cccc(c1C(=O)OC)C(=O)OC FALSE | |
| CC=Cc1ccc(cc1)OC FALSE | |
| c1(ccc(cc1)C(C)(C)C)O FALSE | |
| CCCCCCCCCC(=O)O FALSE | |
| CC(C)CCOC(=O)CC(C)C FALSE | |
| CCCCCCCCOC(=O)C FALSE | |
| CCCCCCCCCCO FALSE | |
| CCCCCCCCCCS FALSE | |
| C=CC(=O)OCC(CCCC)CC FALSE | |
| CCCCCCCCCCC(=O)O FALSE | |
| CCCCCCCCCC(=O)OC FALSE | |
| CCCCCCCCCCCO FALSE | |
| c1cccc(c1C(=O)OCC)C(=O)OCC FALSE | |
| CCCCCCCCCCOC(=O)C FALSE | |
| CCCCCCCCCCCC(=O)O FALSE | |
| CCCCCCOCCCCCC FALSE | |
| CCCCCCCCCCCCC(=O)O FALSE | |
| c1cccc2c1C(=O)c3c(cccc3)C2=O FALSE | |
| c1cc(ccc1C(C)(C)CC(C)(C)C)O FALSE | |
| --- function from context --- | |
| function (molecules, which.desc, verbose = FALSE) | |
| { | |
| if (class(molecules) != "list") { | |
| jclassAttr <- attr(molecules, "jclass") | |
| if (jclassAttr != "org/openscience/cdk/interfaces/IAtomContainer") { | |
| stop("Must provide a list of molecule objects or a single molecule object") | |
| } | |
| molecules <- list(molecules) | |
| } | |
| else { | |
| jclassAttr <- lapply(molecules, attr, "jclass") | |
| if (any(jclassAttr != "org/openscience/cdk/interfaces/IAtomContainer")) { | |
| stop("molecule must be an IAtomContainer") | |
| } | |
| } | |
| dcob <- get.chem.object.builder() | |
| if (length(which.desc) == 1) { | |
| desc <- .jnew(which.desc) | |
| .jcall(desc, "V", "initialise", dcob) | |
| dnames <- .jcall(desc, "[Ljava/lang/String;", "getDescriptorNames") | |
| dnames <- gsub("-", ".", dnames) | |
| descvals <- lapply(molecules, function(a, b) { | |
| val <- tryCatch({ | |
| .jcall(b, "Lorg/openscience/cdk/qsar/DescriptorValue;", | |
| "calculate", a) | |
| }, warning = function(e) return(NA), error = function(e) return(NA)) | |
| }, b = desc) | |
| vals <- lapply(descvals, .get.desc.values, nexpected = length(dnames)) | |
| vals <- data.frame(do.call("rbind", vals)) | |
| names(vals) <- dnames | |
| return(vals) | |
| } | |
| else { | |
| counter <- 1 | |
| dl <- list() | |
| dnames <- c() | |
| for (desc in which.desc) { | |
| if (verbose) { | |
| cat("Processing ", gsub("org.openscience.cdk.qsar.descriptors.molecular.", | |
| "", desc), "\n") | |
| } | |
| desc <- .jnew(desc) | |
| .jcall(desc, "V", "initialise", dcob) | |
| dnames <- .jcall(desc, "[Ljava/lang/String;", "getDescriptorNames") | |
| dnames <- gsub("-", ".", dnames) | |
| descvals <- lapply(molecules, function(a, check) { | |
| val <- tryCatch({ | |
| .jcall(desc, "Lorg/openscience/cdk/qsar/DescriptorValue;", | |
| "calculate", a, check = check) | |
| }) | |
| }, check = FALSE) | |
| vals <- lapply(descvals, .get.desc.values, nexpected = length(dnames)) | |
| vals <- data.frame(do.call("rbind", vals)) | |
| if (length(vals) == 1 && is.na(vals)) { | |
| vals <- as.data.frame(matrix(NA, nrow = 1, ncol = length(dnames))) | |
| } | |
| names(vals) <- dnames | |
| dl[[counter]] <- vals | |
| counter <- counter + 1 | |
| } | |
| do.call("cbind", dl) | |
| } | |
| } | |
| <bytecode: 0x7f9999b0eb98> | |
| <environment: namespace:rcdk> | |
| --- function search by body --- | |
| Function eval.desc in namespace rcdk has this body. | |
| ----------- END OF FAILURE REPORT -------------- | |
| Fatal error: length > 1 in coercion to logical | |
| SUMMARY: processing the following file failed: | |
| ‘using-rcdk.Rmd’ | |
| Error: Vignette re-building failed. | |
| Execution halted | |
| * DONE | |
| Status: 2 WARNINGs | |
| See | |
| ‘/private/var/folders/yc/53w8dbxx2hjg11_brr2pj5740000gn/T/RtmpWPpy1T/rcdk.Rcheck/00check.log’ | |
| for details. | |
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