Open eliocamp opened 1 month ago
I think in this case the same as in a "regular" r session happens, essentially the most recent version stays
@b-rodrigues @eliocamp when nix-build
or rix::nix_build()
the above generated default.nix
, I get
Unable to checkout 1dd5d391d5da6a80fde03301671aea5582643914 from https://github.com/eliocamp/metR.
error: builder for '/nix/store/wp02mgjjcyvi73kkv8flsf3i0npbg9xw-metR-1dd5d39.drv' failed with exit code 1;
last 19 log lines:
> exporting https://github.com/eliocamp/metR (rev 1dd5d391d5da6a80fde03301671aea5582643914) into /nix/store/5q4724c4jy7pfgdl2cqbl82dfxw05q82-metR-1dd5d39
> Initialized empty Git repository in /nix/store/5q4724c4jy7pfgdl2cqbl82dfxw05q82-metR-1dd5d39/.git/
> remote: Enumerating objects: 308, done.
> remote: Counting objects: 100% (308/308), done.
> remote: Compressing objects: 100% (255/255), done.
> error: RPC failed; curl 18 Transferred a partial fileiB/s
> error: 3338 bytes of body are still expected
> fetch-pack: unexpected disconnect while reading sideband packet
> fatal: early EOF
> fatal: fetch-pack: invalid index-pack output
> remote: Enumerating objects: 13745, done.
> remote: Counting objects: 100% (3592/3592), done.
> remote: Compressing objects: 100% (1613/1613), done.
> error: RPC failed; curl 92 HTTP/2 stream 5 was not closed cleanly: CANCEL (err 8)
> error: 7502 bytes of body are still expected
> fetch-pack: unexpected disconnect while reading sideband packet
> fatal: early EOF
> fatal: fetch-pack: invalid index-pack output
> Unable to checkout 1dd5d391d5da6a80fde03301671aea5582643914 from https://github.com/eliocamp/metR.
For full logs, run 'nix log /nix/store/wp02mgjjcyvi73kkv8flsf3i0npbg9xw-metR-1dd5d39.drv'.
error: 1 dependencies of derivation '/nix/store/kkdyb5g529dac6ysng7mfn9q4jbndidy-r-metR.drv' failed to build
error: 1 dependencies of derivation '/nix/store/gygd0vpxbprsl52mi3m73085915dyyqg-nix-shell.drv' failed to build
>
>
> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Zurich
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.3 tools_4.3.3 curl_5.2.1 rix_0.8.0
[5] codetools_0.2-18 jsonlite_1.8.8 sys_3.4.2
right now in WSL Ubuntu. Can you reproduce this?
No. I get a long series of compilation steps and then a compilation error right at the end
[100%] Built target python_binding
make: *** [Makefile:146: all] Error 2
error: builder for '/nix/store/vss6vy5px8fw1wh8rq5zrbpj9xx563vk-gdal-3.8.4.drv' failed with exit code 2;
last 25 log lines:
>
> compile:
> [mkdir] Created dir: /build/source/build/swig/java/build/classes
> [javac] Compiling 88 source files to /build/source/build/swig/java/build/classes
> [javac] warning: [options] bootstrap class path not set in conjunction with -source 7
> [javac] error: Source option 7 is no longer supported. Use 8 or later.
> [javac] error: Target option 7 is no longer supported. Use 8 or later.
>
> BUILD FAILED
> /build/source/swig/java/build.xml:25: Compile failed; see the compiler error output for details.
>
> Total time: 0 seconds
> make[2]: *** [swig/java/CMakeFiles/java_binding.dir/build.make:107: swig/java/gdal.jar] Error 1
> make[1]: *** [CMakeFiles/Makefile2:10036: swig/java/CMakeFiles/java_binding.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs....
> g++ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -I/nix/store/iygsjhqpc4s47y0xar4pi5pi6pmfigad-libxcrypt-4.4.36/include -shared build/temp.linux-x86_64-cpython-311/extensions/ogr_wrap.o -L/build/source/build -L/nix/store/3v2ch16fkl50i85n05h5ckss8pxx6836-python3-3.11.8/lib -lgdal -o build/lib.linux-x86_64-cpython-311/osgeo/_ogr.cpython-311-x86_64-linux-gnu.so
> g++ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -I/nix/store/iygsjhqpc4s47y0xar4pi5pi6pmfigad-libxcrypt-4.4.36/include -shared build/temp.linux-x86_64-cpython-311/extensions/gdal_wrap.o -L/build/source/build -L/nix/store/3v2ch16fkl50i85n05h5ckss8pxx6836-python3-3.11.8/lib -lgdal -o build/lib.linux-x86_64-cpython-311/osgeo/_gdal.cpython-311-x86_64-linux-gnu.so
> copying build/lib.linux-x86_64-cpython-311/osgeo/_gdal.cpython-311-x86_64-linux-gnu.so -> osgeo
> copying build/lib.linux-x86_64-cpython-311/osgeo/_gdalconst.cpython-311-x86_64-linux-gnu.so -> osgeo
> copying build/lib.linux-x86_64-cpython-311/osgeo/_osr.cpython-311-x86_64-linux-gnu.so -> osgeo
> copying build/lib.linux-x86_64-cpython-311/osgeo/_ogr.cpython-311-x86_64-linux-gnu.so -> osgeo
> copying build/lib.linux-x86_64-cpython-311/osgeo/_gnm.cpython-311-x86_64-linux-gnu.so -> osgeo
> copying build/lib.linux-x86_64-cpython-311/osgeo/_gdal_array.cpython-311-x86_64-linux-gnu.so -> osgeo
> [100%] Built target python_binding
> make: *** [Makefile:146: all] Error 2
For full logs, run 'nix log /nix/store/vss6vy5px8fw1wh8rq5zrbpj9xx563vk-gdal-3.8.4.drv'.
error: 1 dependencies of derivation '/nix/store/2rdsad5bw8sx94h5g0cz2wvpa1c8m9yz-r-sf-1.0-15.drv' failed to build
error: 1 dependencies of derivation '/nix/store/bahk5q5w2vxrcw2s5s87zkncx301q722-r-metR-0.14.1.drv' failed to build
error: 1 dependencies of derivation '/nix/store/gygd0vpxbprsl52mi3m73085915dyyqg-nix-shell.drv' failed to build
No. I get a long series of compilation steps and then a compilation error right at the end
[100%] Built target python_binding make: *** [Makefile:146: all] Error 2 error: builder for '/nix/store/vss6vy5px8fw1wh8rq5zrbpj9xx563vk-gdal-3.8.4.drv' failed with exit code 2; last 25 log lines: > > compile: > [mkdir] Created dir: /build/source/build/swig/java/build/classes > [javac] Compiling 88 source files to /build/source/build/swig/java/build/classes > [javac] warning: [options] bootstrap class path not set in conjunction with -source 7 > [javac] error: Source option 7 is no longer supported. Use 8 or later. > [javac] error: Target option 7 is no longer supported. Use 8 or later. > > BUILD FAILED > /build/source/swig/java/build.xml:25: Compile failed; see the compiler error output for details. > > Total time: 0 seconds > make[2]: *** [swig/java/CMakeFiles/java_binding.dir/build.make:107: swig/java/gdal.jar] Error 1 > make[1]: *** [CMakeFiles/Makefile2:10036: swig/java/CMakeFiles/java_binding.dir/all] Error 2 > make[1]: *** Waiting for unfinished jobs.... > g++ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -I/nix/store/iygsjhqpc4s47y0xar4pi5pi6pmfigad-libxcrypt-4.4.36/include -shared build/temp.linux-x86_64-cpython-311/extensions/ogr_wrap.o -L/build/source/build -L/nix/store/3v2ch16fkl50i85n05h5ckss8pxx6836-python3-3.11.8/lib -lgdal -o build/lib.linux-x86_64-cpython-311/osgeo/_ogr.cpython-311-x86_64-linux-gnu.so > g++ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -I/nix/store/iygsjhqpc4s47y0xar4pi5pi6pmfigad-libxcrypt-4.4.36/include -shared build/temp.linux-x86_64-cpython-311/extensions/gdal_wrap.o -L/build/source/build -L/nix/store/3v2ch16fkl50i85n05h5ckss8pxx6836-python3-3.11.8/lib -lgdal -o build/lib.linux-x86_64-cpython-311/osgeo/_gdal.cpython-311-x86_64-linux-gnu.so > copying build/lib.linux-x86_64-cpython-311/osgeo/_gdal.cpython-311-x86_64-linux-gnu.so -> osgeo > copying build/lib.linux-x86_64-cpython-311/osgeo/_gdalconst.cpython-311-x86_64-linux-gnu.so -> osgeo > copying build/lib.linux-x86_64-cpython-311/osgeo/_osr.cpython-311-x86_64-linux-gnu.so -> osgeo > copying build/lib.linux-x86_64-cpython-311/osgeo/_ogr.cpython-311-x86_64-linux-gnu.so -> osgeo > copying build/lib.linux-x86_64-cpython-311/osgeo/_gnm.cpython-311-x86_64-linux-gnu.so -> osgeo > copying build/lib.linux-x86_64-cpython-311/osgeo/_gdal_array.cpython-311-x86_64-linux-gnu.so -> osgeo > [100%] Built target python_binding > make: *** [Makefile:146: all] Error 2 For full logs, run 'nix log /nix/store/vss6vy5px8fw1wh8rq5zrbpj9xx563vk-gdal-3.8.4.drv'. error: 1 dependencies of derivation '/nix/store/2rdsad5bw8sx94h5g0cz2wvpa1c8m9yz-r-sf-1.0-15.drv' failed to build error: 1 dependencies of derivation '/nix/store/bahk5q5w2vxrcw2s5s87zkncx301q722-r-metR-0.14.1.drv' failed to build error: 1 dependencies of derivation '/nix/store/gygd0vpxbprsl52mi3m73085915dyyqg-nix-shell.drv' failed to build
Hmm, interesting case. Elio are we using the same expression?
Yes, the same code on my original comment.
Yes, the same code on my original comment.
yeah.
Buildfile: /build/source/swig/java/build.xml
init:
[echo] version = 3.8.4
compile:
[mkdir] Created dir: /build/source/build/swig/java/build/classes
[javac] Compiling 88 source files to /build/source/build/swig/java/build/classes
[javac] warning: [options] bootstrap class path not set in conjunction with -source 7
[javac] error: Source option 7 is no longer supported. Use 8 or later.
[javac] error: Target option 7 is no longer supported. Use 8 or later.
BUILD FAILED
/build/source/swig/java/build.xml:25: Compile failed; see the compiler error output for details.
Total time: 0 seconds
make[2]: *** [swig/java/CMakeFiles/java_binding.dir/build.make:107: swig/java/gdal.jar] Error 1
make[1]: *** [CMakeFiles/Makefile2:10036: swig/java/CMakeFiles/java_binding.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[100%] Linking CXX executable gdal_unit_test
[100%] Built target gdal_unit_test
g++ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -I/nix/store/iygsjhqpc4s47y0xar4pi5pi6pmfigad-libxcrypt-4.4.36/include -shared build/temp.linux-x86_64-cpython-311/extensions/gdal_wrap.o -L/build/source/build -L/nix/store/3v2ch16fkl50i85n05h5ckss8pxx6836-python3-3.11.8/lib -lgdal -o build/lib.linux-x86_64-cpython-311/osgeo/_gdal.cpython-311-x86_64-linux-gnu.so
copying build/lib.linux-x86_64-cpython-311/osgeo/_gdal.cpython-311-x86_64-linux-gnu.so -> osgeo
copying build/lib.linux-x86_64-cpython-311/osgeo/_gdalconst.cpython-311-x86_64-linux-gnu.so -> osgeo
copying build/lib.linux-x86_64-cpython-311/osgeo/_osr.cpython-311-x86_64-linux-gnu.so -> osgeo
copying build/lib.linux-x86_64-cpython-311/osgeo/_ogr.cpython-311-x86_64-linux-gnu.so -> osgeo
copying build/lib.linux-x86_64-cpython-311/osgeo/_gnm.cpython-311-x86_64-linux-gnu.so -> osgeo
copying build/lib.linux-x86_64-cpython-311/osgeo/_gdal_array.cpython-311-x86_64-linux-gnu.so -> osgeo
[100%] Built target python_binding
make: *** [Makefile:146: all] Error 2
error: builder for '/nix/store/vss6vy5px8fw1wh8rq5zrbpj9xx563vk-gdal-3.8.4.drv' failed with exit code 2
error: 1 dependencies of derivation '/nix/store/2rdsad5bw8sx94h5g0cz2wvpa1c8m9yz-r-sf-1.0-15.drv' failed to build
error: 1 dependencies of derivation '/nix/store/bahk5q5w2vxrcw2s5s87zkncx301q722-r-metR-0.14.1.drv' failed to build
error: 1 dependencies of derivation '/nix/store/kkdyb5g529dac6ysng7mfn9q4jbndidy-r-metR.drv' failed to build
error: 1 dependencies of derivation '/nix/store/gygd0vpxbprsl52mi3m73085915dyyqg-nix-shell.drv' failed to build
@eliocamp could you briefly post your .libPaths()
output in the Nix-RStudio session in the integrated terminal? I'm afraid your custom .Rprofile
that removes system's native user library is not being propagated by Nix-RStudio startup. I am in a WSL2 session for a project with rstudioWrapper and some project-specific packages, and the first position is the user library which should not happen.
.libPaths()
[1] "/home/philipp/R/x86_64-pc-linux-gnu-library/4.4"
[2] "/nix/store/qh0diphsk40cpmfgmpnanwgbk79v26zd-r-rix/library"
[3] "/nix/store/73xzygmdns8nz8zyqkf6hmzwrgxgxjk2-r-codetools-0.2-20/library"
[4] "/nix/store/iagh7mv84ymk7gpkd561h94rq427rdmm-r-curl-5.2.1/library"
[5] "/nix/store/4r42c4smdjzw7qfd5pf323p4xl9702hh-r-jsonlite-1.8.8/library"
[6] "/nix/store/wvh4h0hdm5xrka9rd01l6dsg4hlqi0d6-r-sys-3.4.2/library"
[7] "/nix/store/spkqylmqxn0671sq3iv0kls5xx70j8k2-r-fnmate/library"
# ...
Respectively, does your expression build after source(".Rprofile")
This rix command uses the metR package both as in
git_pkgs
andr_pkgs
and runs fine.It seems to me that a contradictory environment description (use the nix version of metR but also this particular git version); shouldn't this throw an error? Also relevant to
local_r_pkgs
, probably.