From r-devel at akersting.de  Fri Jan 26 08:56:22 2018
From: r-devel at akersting.de (Andreas Kersting)
Date: Fri, 26 Jan 2018 08:56:22 +0100
Subject: [Rd] utils::install.packages with quiet=TRUE fails for source
 packages on Windows
Message-ID: <12f4f428-a424-404b-eee4-e01af07758c3@akersting.de>

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



[Rd] utils::install.packages with quiet=TRUE fails for source packages on Windows
Andreas Kersting