Created
August 20, 2018 09:41
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R package installation errors inside parallel make
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| root@7c782f3c2892:~# cat Makefile | |
| all: | |
| Rscript -e 'install.packages("getPass", type = "source")' | |
| root@7c782f3c2892:~# make | |
| Rscript -e 'install.packages("getPass", type = "source")' | |
| Installing package into '/usr/local/lib/R/site-library' | |
| (as 'lib' is unspecified) | |
| trying URL 'https://cloud.r-project.org/src/contrib/getPass_0.2-2.tar.gz' | |
| Content type 'application/x-gzip' length 252439 bytes (246 KB) | |
| ================================================== | |
| downloaded 246 KB | |
| * installing *source* package 'getPass' ... | |
| ** package 'getPass' successfully unpacked and MD5 sums checked | |
| ** libs | |
| make[1]: Entering directory '/tmp/RtmpdaoLvU/R.INSTALL2e1a472ebede/getPass/src' | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getPass_native.c -o getPass_native.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c readline_masked.c -o readline_masked.o | |
| g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o getPass.so getPass_native.o readline_masked.o -L/usr/lib/R/lib -lR | |
| make[1]: Leaving directory '/tmp/RtmpdaoLvU/R.INSTALL2e1a472ebede/getPass/src' | |
| installing to /usr/local/lib/R/site-library/getPass/libs | |
| ** R | |
| ** inst | |
| ** byte-compile and prepare package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| 'getPass.Rnw' | |
| ** testing if installed package can be loaded | |
| * DONE (getPass) | |
| The downloaded source packages are in | |
| '/tmp/RtmpG8hgcL/downloaded_packages' | |
| root@7c782f3c2892:~# make -j2 | |
| Rscript -e 'install.packages("getPass", type = "source")' | |
| Installing package into '/usr/local/lib/R/site-library' | |
| (as 'lib' is unspecified) | |
| trying URL 'https://cloud.r-project.org/src/contrib/getPass_0.2-2.tar.gz' | |
| Content type 'application/x-gzip' length 252439 bytes (246 KB) | |
| ================================================== | |
| downloaded 246 KB | |
| * installing *source* package 'getPass' ... | |
| ** package 'getPass' successfully unpacked and MD5 sums checked | |
| ** libs | |
| make[1]: Entering directory '/tmp/RtmpiyhZvZ/R.INSTALL2e436a8b454d/getPass/src' | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getPass_native.c -o getPass_native.o | |
| make[1]: *** read jobs pipe: No such file or directory. Stop. | |
| make[1]: *** Waiting for unfinished jobs.... | |
| make[1]: Leaving directory '/tmp/RtmpiyhZvZ/R.INSTALL2e436a8b454d/getPass/src' | |
| ERROR: compilation failed for package 'getPass' | |
| * removing '/usr/local/lib/R/site-library/getPass' | |
| * restoring previous '/usr/local/lib/R/site-library/getPass' | |
| The downloaded source packages are in | |
| '/tmp/RtmpVBb9Q3/downloaded_packages' | |
| Warning message: | |
| In install.packages("getPass", type = "source") : | |
| installation of package 'getPass' had non-zero exit status | |
| root@7c782f3c2892:~# | |
| root@7c782f3c2892:~# uname -a | |
| Linux 7c782f3c2892 4.9.93-linuxkit-aufs #1 SMP Wed Jun 6 16:55:56 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux | |
| root@7c782f3c2892:~# make --version | |
| GNU Make 4.1 | |
| Built for x86_64-pc-linux-gnu | |
| Copyright (C) 1988-2014 Free Software Foundation, Inc. | |
| License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> | |
| This is free software: you are free to change and redistribute it. | |
| There is NO WARRANTY, to the extent permitted by law. | |
| root@7c782f3c2892:~# Rscript -e 'devtools::session_info()' | |
| Session info ------------------------------------------------------------------ | |
| setting value | |
| version R version 3.4.4 (2018-03-15) | |
| system x86_64, linux-gnu | |
| ui X11 | |
| language (EN) | |
| collate C | |
| tz Europe/Amsterdam | |
| date 2018-08-20 | |
| Packages ---------------------------------------------------------------------- | |
| package * version date source | |
| base * 3.4.4 2018-04-21 local | |
| compiler 3.4.4 2018-04-21 local | |
| datasets * 3.4.4 2018-04-21 local | |
| devtools 1.13.6 2018-06-27 CRAN (R 3.4.4) | |
| digest 0.6.15 2018-01-28 CRAN (R 3.4.4) | |
| graphics * 3.4.4 2018-04-21 local | |
| grDevices * 3.4.4 2018-04-21 local | |
| memoise 1.1.0 2017-04-21 CRAN (R 3.4.4) | |
| methods 3.4.4 2018-04-21 local | |
| stats * 3.4.4 2018-04-21 local | |
| utils * 3.4.4 2018-04-21 local | |
| withr 2.1.2 2018-03-15 CRAN (R 3.4.4) | |
| root@7c782f3c2892:~# |
Long story short: For reasons I don't fully understand, prepending a + character before each Make recipe line that produces an install.packages call seems to usually be sufficient to fix this.
all:
+ Rscript -e 'install.packages("getPass", type = "source")'
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Same as above comment, in debug mode: