Dear list,
(this is a follow up from a previous query)
Why does R CMD INSTALL write most of its messages to stderr? If it wrote to
stdout, then we could capture its output within an R session when calling
sink("stdout.txt", type="output")
install.packages("MASS", type="source")
sink()
As it stands, the stderr messages can't be captured via
sink/capture.output/suppressMessages within an R session. Interestingly, the
make output goes to stdout, but the R messages go to stderr:
# the 'make' output goes to stdout
$ R --vanilla CMD INSTALL -l /tmp MASS_7.3-14.tar.gz 2>/dev/null
gcc-4.2 -arch i386 -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include
-fPIC -g -O2 -c MASS.c -o MASS.o
gcc-4.2 -arch i386 -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include
-fPIC -g -O2 -c lqs.c -o lqs.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -o MASS.so MASS.o lqs.o -F/Library/Frameworks/R.framework/..
-framework R -Wl,-framework -Wl,CoreFoundation
gcc-4.2 -arch x86_64 -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-I/usr/local/include -fPIC -g -O2 -c MASS.c -o MASS.o
gcc-4.2 -arch x86_64 -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-I/usr/local/include -fPIC -g -O2 -c lqs.c -o lqs.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -o MASS.so MASS.o lqs.o -F/Library/Frameworks/R.framework/..
-framework R -Wl,-framework -Wl,CoreFoundation
# the R CMD INSTALL output goes to stderr
$ R --vanilla CMD INSTALL -l /tmp MASS_7.3-14.tar.gz >/dev/null
* installing *source* package MASS ...
** libs
*** arch - i386
installing to /private/tmp/MASS/libs/i386
*** arch - x86_64
installing to /private/tmp/MASS/libs/x86_64
** R
** data
** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (MASS)
$ R --vanilla CMD INSTALL -l /tmp MASS_7.3-14.tar.gz &>/dev/null
# no output
Why do I care? i'm writing some software which uses R behind the scenes, and
would like to suppress the messages that are produced by install.packages()
when R libraries are being installed.
So, will it be possible for R CMD INSTALL output be written to stdout in the
future?
kind regards,
Mark
-----------------------------------------------------
Mark Cowley, PhD
Pancreatic Cancer Program | Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia
-----------------------------------------------------
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
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