daqana
Cannot install on Windows because of symlink
PR #62 added a symbolic link from include to inst/include.
Unfortunately I cannot get dqrng to install on WIndows anymore, since it seems symbolic links on Windows require admin permissions.
I added this repository to my Remotes in DESCRIPTION:
Remotes:
daqana/dqrng
See the CI run here: https://github.com/mrc-ide/malariasimulation/actions/runs/7726106082/job/21061725003
Downloading GitHub repo daqana/dqrng@HEAD
sitmo (NA -> 2.0.2 ) [CRAN]
BH (NA -> 1.84.0-0) [CRAN]
Installing 2 packages: sitmo, BH
Installing packages into 'D:/a/_temp/Library'
(as 'lib' is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/sitmo_2.0.2.zip'
Content type 'application/zip' length 585033 bytes (571 KB)
==================================================
downloaded 571 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/BH_1.84.0-0.zip'
Content type 'application/zip' length 21468566 bytes (20.5 MB)
==================================================
downloaded 20.5 MB
package 'sitmo' successfully unpacked and MD5 sums checked
package 'BH' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\runneradmin\AppData\Local\Temp\RtmpW41gcK\downloaded_packages
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file 'C:\Users\runneradmin\AppData\Local\Temp\RtmpW41gcK\remotesd842c9b3950\daqana-dqrng-dcaaa0e/DESCRIPTION' ... OK
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\daqana-dqrng-dcaaa0e\include to C:\Users\RUNNER~1\AppData\Local\Temp\RtmpOKpL14\Rbuild1bc43a887ed3\daqana-dqrng-dcaaa0e\include: Permission denied
ERROR
copying to build directory failed
Error: Error: Failed to install 'dqrng' from GitHub:
! System command 'Rcmd.exe' failed
Execution halted
Error: Process completed with exit code 1.
Honestly I don't really understand WIndows' support for symlinks, or how the repo could even have been cloned in the first place.
This is odd. I don't understand this since the package is tested regularly on Windows via GHA. But I don't have a Windows environment at the moment, so it is difficult to debug. As potential workaround: Can you remove daqana/dqrng from Remotes and add
Additional_repositories: https://rstub.r-universe.dev
instead?
Sorry for the delayed response. Using the Additional_repositories syntax works without any issues, thanks! I'm guessing the released tarball on r-universe does not contain that symbolic link anymore.
I finally managed to get my hands on a windows machine to try and reproduce the original issue I'd seen on CI, installing from the Git repository again. Oddly enough I get a similar message but only as a warning, not a hard error:
> remotes::install_github("daqana/dqrng")
Downloading GitHub repo daqana/dqrng@HEAD
daqana-dqrng-dcaaa0e/include: Can't create '\\\\?\\C:\\Users\\pl2113\\AppData\\Local\\Temp\\6\\RtmpwReeHJ\\remotes14e03c0d547\\daqana-dqrng-dcaaa0e\\include'
tar.exe: Error exit delayed from previous errors.
-- R CMD build ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
checking for file 'C:\Users\pl2113\AppData\Local\Temp\6\RtmpwReeHJ\remotes14e03c0d547\daqana-dqrng-dcaaa0e/DESCRIPTION' ... checking for file 'C:\Users\pl2113\AppData\Local\Temp\6\RtmpwReeHJ\remotes14e03c0d547\daqana-dqrng-dcaaa0e/DESCRIPTION' ... v checking for file 'C:\Users\pl2113\AppData\Local\Temp\6\RtmpwReeHJ\remotes14e03c0d547\daqana-dqrng-dcaaa0e/DESCRIPTION'
- preparing 'dqrng':
checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... v checking DESCRIPTION meta-information
- cleaning src
- running 'cleanup.win'
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'dqrng_0.3.2.2.tar.gz'
Warning: Warning: file 'dqrng/cleanup' did not have execute permissions: corrected
* installing *source* package 'dqrng' ...
** using staged installation
** libs
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I../inst/include -DSTRICT_R_HEADERS -I'C:/Program Files/R/R-4.2.2/library/Rcpp/include' -I'C:/Program Files/R/R-4.2.2/library/BH/include' -I'C:/Program Files/R/R-4.2.2/library/sitmo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I../inst/include -DSTRICT_R_HEADERS -I'C:/Program Files/R/R-4.2.2/library/Rcpp/include' -I'C:/Program Files/R/R-4.2.2/library/BH/include' -I'C:/Program Files/R/R-4.2.2/library/sitmo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dqrng.cpp -o dqrng.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I../inst/include -DSTRICT_R_HEADERS -I'C:/Program Files/R/R-4.2.2/library/Rcpp/include' -I'C:/Program Files/R/R-4.2.2/library/BH/include' -I'C:/Program Files/R/R-4.2.2/library/sitmo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c generateSeedVectors.cpp -o generateSeedVectors.o
g++ -std=gnu++11 -shared -s -static-libgcc -o dqrng.dll tmp.def RcppExports.o dqrng.o generateSeedVectors.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~1/R/R-42~1.2/bin/x64 -lR
installing to C:/Program Files/R/R-4.2.2/library/00LOCK-dqrng/00new/dqrng/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (dqrng)
Warning message:
In utils::untar(tarfile, ...) :
‘tar.exe -xf "C:\Users\pl2113\AppData\Local\Temp\6\RtmpwReeHJ\file14e076095cbc.tar.gz" -C "C:/Users/pl2113/AppData/Local/Temp/6/RtmpwReeHJ/remotes14e03c0d547"’ returned error code 1
I can use the package just fine afterwards. I'm not sure why I am not getting the same behaviour as on CI, could be down to a difference in Windows version (I think GitHub Actions uses Windows Server 2022, whereas my machine runs 2019), or in user permissions.
I don't know whether you want to take any further action or not on this issue. Personally don't intend on doing any development on dqrng from a WIndows and the Additional_repositories workaround is fine for me. Feel free to close the issue if you think the status quo is acceptable.