Unable to install cli from source on Windows 4.2 (and binary install causes other source installations to fail) #494

cpsievert · 2022-07-11T15:21:07Z

> remotes::install_github("r-lib/cli")
Downloading GitHub repo r-lib/cli@HEAD
Installing 1 packages: glue
Installing package into ‘C:/Users/cpsievert/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/glue_1.6.2.zip'
Content type 'application/zip' length 162214 bytes (158 KB)
downloaded 158 KB

package ‘glue’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\cpsievert\AppData\Local\Temp\Rtmp0ErltS\downloaded_packages
Running `R CMD build`...
* checking for file 'C:\Users\cpsievert\AppData\Local\Temp\Rtmp0ErltS\remotes14d445844e46\r-lib-cli-e92e517/DESCRIPTION' ... OK
* preparing 'cli':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'cli_3.3.0.9000.tar.gz'
Installing package into ‘C:/Users/cpsievert/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
* installing *source* package 'cli' ...
** using staged installation
** libs
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ansi.c -o ansi.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c cleancall.c -o cleancall.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c diff.c -o diff.o
diff.c: In function 'clic_diff_chr':
diff.c:104:3: warning: 'sn' may be used uninitialized in this function [-Wmaybe-uninitialized]
  104 |   SET_VECTOR_ELT(result, 0, allocVector(INTSXP, sn));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c errors.c -o errors.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c md5.c -o md5.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c progress-altrep.c -o progress-altrep.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c progress.c -o progress.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sha256.c -o sha256.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c thread.c -o thread.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c tty.c -o tty.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c utf8.c -o utf8.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c utils.c -o utils.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c win-utf8.c -o win-utf8.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c winfiles.c -o winfiles.o
gcc -shared -s -static-libgcc -o cli.dll tmp.def ansi.o cleancall.o diff.o errors.o init.o md5.o progress-altrep.o progress.o sha256.o thread.o tty.o utf8.o utils.o win-utf8.o winfiles.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~2/R/R-42~1.1/bin/x64 -lR
installing to C:/Users/cpsievert/AppData/Local/R/win-library/4.2/00LOCK-cli/00new/cli/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
ERROR: loading failed
* removing 'C:/Users/cpsievert/AppData/Local/R/win-library/4.2/cli'
Warning message:
In i.p(...) :
  installation of package ‘C:/Users/CPSIEV~1/AppData/Local/Temp/Rtmp0ErltS/file14d42af8c6a/cli_3.3.0.9000.tar.gz’ had non-zero exit status

Also, more problematically, installing the current {cli} binary on CRAN causes other type="source" installations to fail with the same error:

> install.packages("cli")
Installing package into ‘C:/Users/cpsievert/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/cli_3.3.0.zip'
Content type 'application/zip' length 1221213 bytes (1.2 MB)
downloaded 1.2 MB

package ‘cli’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\cpsievert\AppData\Local\Temp\Rtmp0ErltS\downloaded_packages

> install.packages("rlang", type = "source")
Installing package into ‘C:/Users/cpsievert/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/rlang_1.0.3.tar.gz'
Content type 'application/x-gzip' length 740744 bytes (723 KB)
downloaded 723 KB

* installing *source* package 'rlang' ...
** package 'rlang' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c capture.c -o capture.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c internal.c -o internal.o
g++  -std=gnu++11 -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rlang-rcc.cpp -o rlang-rcc.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rlang.c -o rlang.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c version.c -o version.o
g++ -shared -s -static-libgcc -o rlang.dll tmp.def capture.o internal.o rlang-rcc.o rlang.o version.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~2/R/R-42~1.1/bin/x64 -lR
installing to C:/Users/cpsievert/AppData/Local/R/win-library/4.2/00LOCK-rlang/00new/rlang/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
ERROR: loading failed
* removing 'C:/Users/cpsievert/AppData/Local/R/win-library/4.2/rlang'
* restoring previous 'C:/Users/cpsievert/AppData/Local/R/win-library/4.2/rlang'
Warning in install.packages :
  installation of package ‘rlang’ had non-zero exit status

The downloaded source packages are in
	‘C:\Users\cpsievert\AppData\Local\Temp\Rtmp0ErltS\downloaded_packages’

And after remove.packages("cli"), it succeeds:

> install.packages("rlang", type = "source")
Installing package into ‘C:/Users/cpsievert/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/rlang_1.0.3.tar.gz'
Content type 'application/x-gzip' length 740744 bytes (723 KB)
downloaded 723 KB

* installing *source* package 'rlang' ...
** package 'rlang' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c capture.c -o capture.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c internal.c -o internal.o
g++  -std=gnu++11 -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rlang-rcc.cpp -o rlang-rcc.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rlang.c -o rlang.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c version.c -o version.o
g++ -shared -s -static-libgcc -o rlang.dll tmp.def capture.o internal.o rlang-rcc.o rlang.o version.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~2/R/R-42~1.1/bin/x64 -lR
installing to C:/Users/cpsievert/AppData/Local/R/win-library/4.2/00LOCK-rlang/00new/rlang/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rlang)

The downloaded source packages are in
	‘C:\Users\cpsievert\AppData\Local\Temp\Rtmp0ErltS\downloaded_packages’

> sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.2.1 tools_4.2.1    remotes_2.4.2

The text was updated successfully, but these errors were encountered:

gaborcsardi · 2022-07-11T15:35:23Z

** testing if installed package can be loaded from temporary location
ERROR: loading failed

Can you try to find the actual error message? E.g. install the package with R CMD INSTALL --no-test-load and then try to load the installed package with library()?

cpsievert · 2022-07-11T15:39:02Z

Huh, after installing that way library(cli) works (and same with setwd(tempdir()); library(cli))

cpsievert · 2022-07-11T15:53:58Z

There still appears to be some issues with lazy loading, though:

> remotes::install_github("rstudio/htmltools", INSTALL_opts = "--no-test-load --no-byte-compile")
Downloading GitHub repo rstudio/htmltools@HEAD
Running `R CMD build`...
* checking for file 'C:\Users\cpsievert\AppData\Local\Temp\RtmpigI9PP\remotes118c32634b0d\rstudio-htmltools-5d297d4/DESCRIPTION' ... OK
* preparing 'htmltools':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building 'htmltools_0.5.2.9000.tar.gz'
Installing package into ‘C:/Users/cpsievert/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
* installing *source* package 'htmltools' ...
** using staged installation
** libs
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c template.c -o template.o
gcc -shared -s -static-libgcc -o htmltools.dll tmp.def init.o template.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~2/R/R-42~1.1/bin/x64 -lR
installing to C:/Users/cpsievert/AppData/Local/R/win-library/4.2/00LOCK-htmltools/00new/htmltools/libs/x64
** R
** preparing package for lazy loading
ERROR: lazy loading failed for package 'htmltools'
* removing 'C:/Users/cpsievert/AppData/Local/R/win-library/4.2/htmltools'
* restoring previous 'C:/Users/cpsievert/AppData/Local/R/win-library/4.2/htmltools'
Warning message:
In i.p(...) :
  installation of package ‘C:/Users/CPSIEV~1/AppData/Local/Temp/RtmpigI9PP/file118c157f75fb/htmltools_0.5.2.9000.tar.gz’ had non-zero exit status

> remove.packages("cli")

Removing package from ‘C:/Users/cpsievert/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)

> remotes::install_github("rstudio/htmltools", INSTALL_opts = "--no-test-load")
Downloading GitHub repo rstudio/htmltools@HEAD
Running `R CMD build`...
* checking for file 'C:\Users\cpsievert\AppData\Local\Temp\Rtmp0ErltS\remotes14d41610b9f\rstudio-htmltools-5d297d4/DESCRIPTION' ... OK
* preparing 'htmltools':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building 'htmltools_0.5.2.9000.tar.gz'
Installing package into ‘C:/Users/cpsievert/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
* installing *source* package 'htmltools' ...
** using staged installation
** libs
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
gcc  -I"C:/PROGRA~2/R/R-42~1.1/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c template.c -o template.o
gcc -shared -s -static-libgcc -o htmltools.dll tmp.def init.o template.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~2/R/R-42~1.1/bin/x64 -lR
installing to C:/Users/cpsievert/AppData/Local/R/win-library/4.2/00LOCK-htmltools/00new/htmltools/libs/x64
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
* DONE (htmltools)

gaborcsardi · 2022-07-11T17:25:53Z

Try setting the CLI_NO_THREAD="true" env var.

gaborcsardi · 2022-07-11T18:14:12Z

What version of Windows is this exactly, btw?

cpsievert · 2022-07-11T18:52:16Z

That appears to have fixed it, thanks! I'm running Windows 11 (via parallels on an M1 mac):

gaborcsardi · 2022-07-11T19:03:55Z

We haven't seen anything like this on intel hardware and nothing has changed in cli for a while, so it is very likely that this is an issue in the x86_64 emulation of arm64 Windows. (Which is very buggy, btw. so brace yourself if you intend to use it for daily work.) Or it could be an issue in the pthread implementation in MinGW.

gaborcsardi added this to the 3.4.0 milestone Aug 23, 2022

gaborcsardi closed this as completed Aug 23, 2022

kevinushey mentioned this issue Aug 23, 2022

don't cancel tick thread in Windows on Arm #508

Merged

kevinushey mentioned this issue Feb 27, 2024

Unable to find the install of R on Windows 11 under Parallels quarto-dev/quarto-cli#6960

Closed

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Unable to install cli from source on Windows 4.2 (and binary install causes other source installations to fail) #494

Unable to install cli from source on Windows 4.2 (and binary install causes other source installations to fail) #494

cpsievert commented Jul 11, 2022 •

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gaborcsardi commented Jul 11, 2022

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Unable to install cli from source on Windows 4.2 (and binary install causes other source installations to fail) #494

Unable to install cli from source on Windows 4.2 (and binary install causes other source installations to fail) #494

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