Andreas Kersting
2018-Jan-26 07:56 UTC
[Rd] utils::install.packages with quiet=TRUE fails for source packages on Windows
Hi, Installing a source package on Windows using utils::install.packages() with quiet=TRUE fails, while it works with the default quiet = FALSE. The problem seems to be caused by the fact that when quiet = TRUE, stdout and stderr are set to FALSE when calling "R CMD INSTALL" with base::system2() here: https://github.com/wch/r-source/blob/tags/R-3-4-3/src/library/utils/R/packages2.R#L660-L661.> trace(base::system2, quote(print(ls.str())))Tracing function "system2" in package "base" [1] "system2"> utils::install.packages("partDF_1.0.0.9001.tar.gz", repos = NULL, lib= tempdir(), quiet = TRUE) Tracing system2(cmd0, args, env = env, stdout = output, stderr = output) on entry args : chr [1:5] "CMD" "INSTALL" "-l" "\"C:\\Users\\askers\\AppData\\Local\\Temp\\RtmpoRb97l\"" ... command : chr "C:/PROGRA~1/R/R-34~1.3/bin/x64/R" env : chr(0) input : NULL invisible : logi TRUE minimized : logi FALSE stderr : logi FALSE stdin : chr "" stdout : logi FALSE wait : logi TRUE Warning messages: 1: running command '"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" CMD INSTALL -l "C:\Users\askers\AppData\Local\Temp\RtmpoRb97l" "partDF_1.0.0.9001.tar.gz"' had status 1 2: In utils::install.packages("partDF_1.0.0.9001.tar.gz", repos = NULL, : installation of package 'partDF_1.0.0.9001.tar.gz' had non-zero exit status> utils::install.packages("partDF_1.0.0.9001.tar.gz", repos = NULL, lib= tempdir(), quiet = FALSE) Tracing system2(cmd0, args, env = env, stdout = output, stderr = output) on entry args : chr [1:5] "CMD" "INSTALL" "-l" "\"C:\\Users\\askers\\AppData\\Local\\Temp\\RtmpoRb97l\"" ... command : chr "C:/PROGRA~1/R/R-34~1.3/bin/x64/R" env : chr(0) input : NULL invisible : logi TRUE minimized : logi FALSE stderr : chr "" stdin : chr "" stdout : chr "" wait : logi TRUE * installing *source* package 'partDF' ... ** libs c:/Rtools/mingw_64/bin/gcc -I"C:/PROGRA~1/R/R-34~1.3/include" -DNDEBUG -O2 -Wall -std=gnu99 -mtune=generic -c partDF.c -o partDF.o c:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o partDF.dll tmp.def partDF.o -LC:/PROGRA~1/R/R-34~1.3/bin/x64 -lR installing to C:/Users/askers/AppData/Local/Temp/RtmpoRb97l/partDF/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'partDF' finding HTML links ... done anti_glob html partDF html read_partDF html write_partDF html ** building package indices ** testing if installed package can be loaded * DONE (partDF) In R CMD INSTALL> sessionInfo()R version 3.4.3 (2017-11-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252 [4] LC_NUMERIC=C LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_3.4.3 tools_3.4.3 yaml_2.1.16 This problem is also there when installing source packages from CRAN:> utils::install.packages("mvtnorm", lib = tempdir(), quiet = TRUE)There is a binary version available but the source version is later: binary source needs_compilation mvtnorm 1.0-6 1.0-7 TRUE Do you want to install from sources the package which needs compilation? y/n: y installing the source package 'mvtnorm' Tracing system2(cmd0, args, env = env, stdout = outfile, stderr = outfile) on entry args : Named chr [1:5] "CMD" "INSTALL" "-l" "\"C:\\Users\\askers\\AppData\\Local\\Temp\\RtmpoRb97l\"" ... command : chr "C:/PROGRA~1/R/R-34~1.3/bin/x64/R" env : chr(0) input : NULL invisible : logi TRUE minimized : logi FALSE stderr : logi FALSE stdin : chr "" stdout : logi FALSE wait : logi TRUE Warning messages: 1: running command '"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" CMD INSTALL -l "C:\Users\askers\AppData\Local\Temp\RtmpoRb97l" C:\Users\askers\AppData\Local\Temp\RtmpoRb97l/downloaded_packages/mvtnorm_1.0-7.tar.gz' had status 1 2: In utils::install.packages("mvtnorm", lib = tempdir(), quiet = TRUE) : installation of package 'mvtnorm' had non-zero exit status I do not encounter this problem on my Linux machine. Andreas
Andreas Kersting
2018-Jan-26 08:17 UTC
[Rd] utils::install.packages with quiet=TRUE fails for source packages on Windows
Just noticed that this problem only occurs from within RStudio (v1.1.414). Any ideas why? Am 26.01.2018 um 08:56 schrieb Andreas Kersting:> Hi, > > Installing a source package on Windows using utils::install.packages() > with quiet=TRUE fails, while it works with the default quiet = FALSE. > The problem seems to be caused by the fact that when quiet = TRUE, > stdout and stderr are set to FALSE when calling "R CMD INSTALL" with > base::system2() here: > https://github.com/wch/r-source/blob/tags/R-3-4-3/src/library/utils/R/packages2.R#L660-L661. > > >> trace(base::system2, quote(print(ls.str()))) > Tracing function "system2" in package "base" > [1] "system2" > > >> utils::install.packages("partDF_1.0.0.9001.tar.gz", repos = NULL, lib > = tempdir(), quiet = TRUE) > Tracing system2(cmd0, args, env = env, stdout = output, stderr = output) > on entry > args :? chr [1:5] "CMD" "INSTALL" "-l" > "\"C:\\Users\\askers\\AppData\\Local\\Temp\\RtmpoRb97l\"" ... > command :? chr "C:/PROGRA~1/R/R-34~1.3/bin/x64/R" > env :? chr(0) > input :? NULL > invisible :? logi TRUE > minimized :? logi FALSE > stderr :? logi FALSE > stdin :? chr "" > stdout :? logi FALSE > wait :? logi TRUE > Warning messages: > 1: running command '"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" CMD INSTALL -l > "C:\Users\askers\AppData\Local\Temp\RtmpoRb97l" > "partDF_1.0.0.9001.tar.gz"' had status 1 > 2: In utils::install.packages("partDF_1.0.0.9001.tar.gz", repos = NULL,? : > ? installation of package 'partDF_1.0.0.9001.tar.gz' had non-zero exit > status > > >> utils::install.packages("partDF_1.0.0.9001.tar.gz", repos = NULL, lib > = tempdir(), quiet = FALSE) > Tracing system2(cmd0, args, env = env, stdout = output, stderr = output) > on entry > args :? chr [1:5] "CMD" "INSTALL" "-l" > "\"C:\\Users\\askers\\AppData\\Local\\Temp\\RtmpoRb97l\"" ... > command :? chr "C:/PROGRA~1/R/R-34~1.3/bin/x64/R" > env :? chr(0) > input :? NULL > invisible :? logi TRUE > minimized :? logi FALSE > stderr :? chr "" > stdin :? chr "" > stdout :? chr "" > wait :? logi TRUE > * installing *source* package 'partDF' ... > ** libs > c:/Rtools/mingw_64/bin/gcc? -I"C:/PROGRA~1/R/R-34~1.3/include" -DNDEBUG > ?????? -O2 -Wall? -std=gnu99 -mtune=generic -c partDF.c -o partDF.o > c:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o partDF.dll > tmp.def partDF.o -LC:/PROGRA~1/R/R-34~1.3/bin/x64 -lR > installing to C:/Users/askers/AppData/Local/Temp/RtmpoRb97l/partDF/libs/x64 > ** R > ** inst > ** byte-compile and prepare package for lazy loading > ** help > *** installing help indices > ? converting help for package 'partDF' > ??? finding HTML links ... done > ??? anti_glob?????????????????????????????? html > ??? partDF????????????????????????????????? html > ??? read_partDF???????????????????????????? html > ??? write_partDF??????????????????????????? html > ** building package indices > ** testing if installed package can be loaded > * DONE (partDF) > In R CMD INSTALL > > >> sessionInfo() > R version 3.4.3 (2017-11-30) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows >= 8 x64 (build 9200) > > Matrix products: default > > locale: > [1] LC_COLLATE=German_Germany.1252? LC_CTYPE=German_Germany.1252 > LC_MONETARY=German_Germany.1252 > [4] LC_NUMERIC=C??????????????????? LC_TIME=German_Germany.1252 > > attached base packages: > [1] stats???? graphics? grDevices utils???? datasets? methods?? base > > loaded via a namespace (and not attached): > [1] compiler_3.4.3 tools_3.4.3??? yaml_2.1.16 > > > This problem is also there when installing source packages from CRAN: > >> utils::install.packages("mvtnorm", lib = tempdir(), quiet = TRUE) > > ? There is a binary version available but the source version is later: > ??????? binary source needs_compilation > mvtnorm? 1.0-6? 1.0-7????????????? TRUE > > Do you want to install from sources the package which needs compilation? > y/n: y > installing the source package 'mvtnorm' > > Tracing system2(cmd0, args, env = env, stdout = outfile, stderr = > outfile) on entry > args :? Named chr [1:5] "CMD" "INSTALL" "-l" > "\"C:\\Users\\askers\\AppData\\Local\\Temp\\RtmpoRb97l\"" ... > command :? chr "C:/PROGRA~1/R/R-34~1.3/bin/x64/R" > env :? chr(0) > input :? NULL > invisible :? logi TRUE > minimized :? logi FALSE > stderr :? logi FALSE > stdin :? chr "" > stdout :? logi FALSE > wait :? logi TRUE > Warning messages: > 1: running command '"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" CMD INSTALL -l > "C:\Users\askers\AppData\Local\Temp\RtmpoRb97l" > C:\Users\askers\AppData\Local\Temp\RtmpoRb97l/downloaded_packages/mvtnorm_1.0-7.tar.gz' > had status 1 > 2: In utils::install.packages("mvtnorm", lib = tempdir(), quiet = TRUE) : > ? installation of package 'mvtnorm' had non-zero exit status > > > > I do not encounter this problem on my Linux machine. > > Andreas > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
peter dalgaard
2018-Jan-26 10:15 UTC
[Rd] utils::install.packages with quiet=TRUE fails for source packages on Windows
The obvious guess would be that Rstudio is attempting something like redirecting output and getting itself confused. However, it is pretty clearly Their Problem, no? Rstudio has their own support infrastructure. -pd> On 26 Jan 2018, at 09:17 , Andreas Kersting <r-devel at akersting.de> wrote: > > Just noticed that this problem only occurs from within RStudio (v1.1.414). Any ideas why? > > Am 26.01.2018 um 08:56 schrieb Andreas Kersting: >> Hi, >> Installing a source package on Windows using utils::install.packages() with quiet=TRUE fails, while it works with the default quiet = FALSE. The problem seems to be caused by the fact that when quiet = TRUE, stdout and stderr are set to FALSE when calling "R CMD INSTALL" with base::system2() here: https://github.com/wch/r-source/blob/tags/R-3-4-3/src/library/utils/R/packages2.R#L660-L661. >>> trace(base::system2, quote(print(ls.str()))) >> Tracing function "system2" in package "base" >> [1] "system2" >>> utils::install.packages("partDF_1.0.0.9001.tar.gz", repos = NULL, lib >> = tempdir(), quiet = TRUE) >> Tracing system2(cmd0, args, env = env, stdout = output, stderr = output) on entry >> args : chr [1:5] "CMD" "INSTALL" "-l" "\"C:\\Users\\askers\\AppData\\Local\\Temp\\RtmpoRb97l\"" ... >> command : chr "C:/PROGRA~1/R/R-34~1.3/bin/x64/R" >> env : chr(0) >> input : NULL >> invisible : logi TRUE >> minimized : logi FALSE >> stderr : logi FALSE >> stdin : chr "" >> stdout : logi FALSE >> wait : logi TRUE >> Warning messages: >> 1: running command '"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" CMD INSTALL -l "C:\Users\askers\AppData\Local\Temp\RtmpoRb97l" "partDF_1.0.0.9001.tar.gz"' had status 1 >> 2: In utils::install.packages("partDF_1.0.0.9001.tar.gz", repos = NULL, : >> installation of package 'partDF_1.0.0.9001.tar.gz' had non-zero exit status >>> utils::install.packages("partDF_1.0.0.9001.tar.gz", repos = NULL, lib >> = tempdir(), quiet = FALSE) >> Tracing system2(cmd0, args, env = env, stdout = output, stderr = output) on entry >> args : chr [1:5] "CMD" "INSTALL" "-l" "\"C:\\Users\\askers\\AppData\\Local\\Temp\\RtmpoRb97l\"" ... >> command : chr "C:/PROGRA~1/R/R-34~1.3/bin/x64/R" >> env : chr(0) >> input : NULL >> invisible : logi TRUE >> minimized : logi FALSE >> stderr : chr "" >> stdin : chr "" >> stdout : chr "" >> wait : logi TRUE >> * installing *source* package 'partDF' ... >> ** libs >> c:/Rtools/mingw_64/bin/gcc -I"C:/PROGRA~1/R/R-34~1.3/include" -DNDEBUG -O2 -Wall -std=gnu99 -mtune=generic -c partDF.c -o partDF.o >> c:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o partDF.dll tmp.def partDF.o -LC:/PROGRA~1/R/R-34~1.3/bin/x64 -lR >> installing to C:/Users/askers/AppData/Local/Temp/RtmpoRb97l/partDF/libs/x64 >> ** R >> ** inst >> ** byte-compile and prepare package for lazy loading >> ** help >> *** installing help indices >> converting help for package 'partDF' >> finding HTML links ... done >> anti_glob html >> partDF html >> read_partDF html >> write_partDF html >> ** building package indices >> ** testing if installed package can be loaded >> * DONE (partDF) >> In R CMD INSTALL >>> sessionInfo() >> R version 3.4.3 (2017-11-30) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> Running under: Windows >= 8 x64 (build 9200) >> Matrix products: default >> locale: >> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252 >> [4] LC_NUMERIC=C LC_TIME=German_Germany.1252 >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> loaded via a namespace (and not attached): >> [1] compiler_3.4.3 tools_3.4.3 yaml_2.1.16 >> This problem is also there when installing source packages from CRAN: >>> utils::install.packages("mvtnorm", lib = tempdir(), quiet = TRUE) >> There is a binary version available but the source version is later: >> binary source needs_compilation >> mvtnorm 1.0-6 1.0-7 TRUE >> Do you want to install from sources the package which needs compilation? >> y/n: y >> installing the source package 'mvtnorm' >> Tracing system2(cmd0, args, env = env, stdout = outfile, stderr = outfile) on entry >> args : Named chr [1:5] "CMD" "INSTALL" "-l" "\"C:\\Users\\askers\\AppData\\Local\\Temp\\RtmpoRb97l\"" ... >> command : chr "C:/PROGRA~1/R/R-34~1.3/bin/x64/R" >> env : chr(0) >> input : NULL >> invisible : logi TRUE >> minimized : logi FALSE >> stderr : logi FALSE >> stdin : chr "" >> stdout : logi FALSE >> wait : logi TRUE >> Warning messages: >> 1: running command '"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" CMD INSTALL -l "C:\Users\askers\AppData\Local\Temp\RtmpoRb97l" C:\Users\askers\AppData\Local\Temp\RtmpoRb97l/downloaded_packages/mvtnorm_1.0-7.tar.gz' had status 1 >> 2: In utils::install.packages("mvtnorm", lib = tempdir(), quiet = TRUE) : >> installation of package 'mvtnorm' had non-zero exit status >> I do not encounter this problem on my Linux machine. >> Andreas >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel-- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com