R devel - Jan 2018 - 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

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
>

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