Install of igraph 1.6.0 fails under R 4.2.1

[stephenashton-dhsc]

What happens?

When try to compile/install igraph 1.6.0 under R 4.2.1, I receive a compile error

* installing *source* package 'igraph' ...
** package 'igraph' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc  -I"C:/PROGRA~1/R/R-42~1.1/include" -DNDEBUG -IC:/Program Files/rtools42/x86_64-w64-mingw32.static.posix/include/libxml2 -IC:/Program Files/rtools42/x86_64-w64-mingw32.static.posix/include -DLIBXML_STATIC -DUSING_R -DHAVE_FMEMOPEN=0 -DHAVE_OPEN_MEMSTREAM=0 -DHAVE_RINTF -DHAVE_STRCASECMP -DWin32 -DHAVE_LIBXML=1 -DHAVE_UNISTD_H -Wall -DHAVE_FMIN=1 -DHAVE_LOG2=1 -DHAVE_GFORTRAN -DINTERNAL_ARPACK -IC:/Program Files/rtools42/x86_64-w64-mingw32.static.posix/include -DHAVE_GLPK=1 -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -I. -Icore -Iinclude -Ivendor -DNDEBUG -DNTIMER -DNPRINT -IC:/Program Files/rtools42/x86_64-w64-mingw32.static.posix/include -I'C:/Users/SAshton/AppData/Local/R/win-library/4.2.1/cpp11/include'   -I"C:/Program Files/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core/centrality/betweenness.c -o core/centrality/betweenness.o
gcc.exe: error: Files/rtools42/x86_64-w64-mingw32.static.posix/include/libxml2: No such file or directory
gcc.exe: error: Files/rtools42/x86_64-w64-mingw32.static.posix/include: No such file or directory
gcc.exe: error: Files/rtools42/x86_64-w64-mingw32.static.posix/include: No such file or directory
gcc.exe: error: Files/rtools42/x86_64-w64-mingw32.static.posix/include: No such file or directory
make: *** [C:/PROGRA~1/R/R-42~1.1/etc/x64/Makeconf:253: core/centrality/betweenness.o] Error 1
ERROR: compilation failed for package 'igraph'
* removing 'C:/Users/SAshton/AppData/Local/R/win-library/4.2.1/igraph'
* restoring previous 'C:/Users/SAshton/AppData/Local/R/win-library/4.2.1/igraph'

If you need any additional information, please let me know.

To Reproduce

install.packages("igraph")
#> Installing package into 'C:/Users/SAshton/AppData/Local/R/win-library/4.2.1'
#> (as 'lib' is unspecified)
#> 
#>   There is a binary version available but the source version is later:
#>        binary source needs_compilation
#> igraph  1.5.1  1.6.0              TRUE
#> installing the source package 'igraph'
#> Warning in install.packages("igraph"): installation of package 'igraph' had
#> non-zero exit status

^{Created on 2023-12-11 with reprex v2.0.2}

[szhorvat]

@krlmlr You probably know this already, but just in case I wanted to mention that this seems related to the space in Program Files

[stephenashton-dhsc]

Could it also be to do with the dependency on libxml2?

I'm not 100% sure if we've got this (as this is on a corporate laptop, where we've got a lot of restrictions on what can be installed/accessed).

Apologies if it is this (as I know it's mentioned elsewhere) - I can always wait for the binary :)

[szhorvat]

That may be an additional issue, and for your convenience I recommend waiting for the binary. But clearly the path after the -I flags should be quoted. Without the quoting this won't work.

[krlmlr]

@Antonov548: Can you please take a look?

In the meantime, can you install from r-universe: https://igraph.r-universe.dev/igraph# ? Binaries are available there too.

[stephenashton-dhsc]

Just to confirm, it does appear that the issue is being caused by the space in the path - if I run Sys.setenv(RTOOLS42_HOME="C:\\PROGRA~1\\rtools42") to use the alias for the Program Files directory, it all works without issue.

[Antonov548]

Also can confirm that installation happens without errors for me.

[krlmlr]

@Antonov548: As @stephenashton-dhsc wrote, this depends on where the RTools are installed. On a path with spaces, it fails now. We need quotes after or around -I (and perhaps other path-related switches) in Makevars.win .

[Antonov548]

I just don't see any " in the 1.5 version. @stephenashton-dhsc is it only with latest 1.6?
I think if it worked before it will help to find a way to fix it, because simply adding " doesn't add it for commpilation.

To properly reproduce it I have to install R in some folder with space.

[stephenashton-dhsc]

Apologies, I've just checked and it does appear to be a historical issue (not just related to 1.6.0), as I can also reproduce the error with my default setup for both 1.5.1 and 1.5.0 - I'm sure I've installed igraph from source on this machine previously, but clearly not!

[krlmlr]

Thanks, this helps.

@Antonov548: I think the installation location of RTools is critical, the one of R itself less so, but could also play a role.

[krlmlr]

Is this really an igraph issue? Can you install, e.g., rlang from source?

https://github.com/r-lib/rlang/

[stephenashton-dhsc]

It looks like rlang is working - although it looks like the -I arguments being processed are quoted, so the space in the file path won't matter.

I suspect it's a broader issue to be honest - if a path with a space if passed unquoted, I presume it would fail within any package source build.

> install.packages("rlang", type = "source")
Installing package into ‘C:/Users/SAshton/AppData/Local/R/win-library/4.2.1’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://cloud.r-project.org/src/contrib/rlang_1.1.2.tar.gz'
Content type 'application/x-gzip' length 763521 bytes (745 KB)
downloaded 745 KB

* installing *source* package 'rlang' ...
** package 'rlang' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc  -I"C:/PROGRA~1/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/Program Files/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~1/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/Program Files/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c internal.c -o internal.o
gcc  -I"C:/PROGRA~1/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/Program Files/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~1/R/R-42~1.1/include" -DNDEBUG -I./rlang/    -I"C:/Program Files/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c version.c -o version.o
gcc -shared -s -static-libgcc -o rlang.dll tmp.def capture.o internal.o rlang.o version.o -LC:/Program Files/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/Program Files/rtools42/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~1/R/R-42~1.1/bin/x64 -lR
installing to C:/Users/SAshton/AppData/Local/R/win-library/4.2.1/00LOCK-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\SAshton\AppData\Local\Temp\1\RtmpAz05Vc\downloaded_packages’

[krlmlr]

@Antonov548: I think Makevars.ucrt is to blame here.

[Antonov548]

@Antonov548: I think Makevars.ucrt is to blame here.

Yes, you are right. It's in ucrt. I forgot that it's used. I have tried with quotes locally and it works, it actually add quotes to compilation #1000