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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=ixvyVxTs; spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Migadu-Spam-Score: -1.36 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=ixvyVxTs; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Migadu-Queue-Id: 247862C684 X-Spam-Score: -1.36 X-Migadu-Scanner: scn0.migadu.com X-TUID: 8ymWUy1ClkFa Hi, Packaging Julia stuff, I note something as a bug, I guess. Julia seems to keep references to the build directory in the output. --8<---------------cut here---------------start------------->8--- $ find $(guix build julia --no-grafts) -type f \ -exec grep '/tmp/guix-build-julia-1.5.3.drv-0' {} \; Binary file /gnu/store/i1dgzqfjvkkjlfhpcwc33lz17vslq50y-julia-1.5.3/lib/lib= julia.so.1.5 matches Binary file /gnu/store/i1dgzqfjvkkjlfhpcwc33lz17vslq50y-julia-1.5.3/lib/jul= ia/sys.so matches Binary file /gnu/store/i1dgzqfjvkkjlfhpcwc33lz17vslq50y-julia-1.5.3/lib/jul= ia/libccalltest.so.debug matches Binary file /gnu/store/i1dgzqfjvkkjlfhpcwc33lz17vslq50y-julia-1.5.3/lib/jul= ia/libllvmcalltest.so matches Binary file /gnu/store/i1dgzqfjvkkjlfhpcwc33lz17vslq50y-julia-1.5.3/bin/.ju= lia-real matches Binary file /gnu/store/i1dgzqfjvkkjlfhpcwc33lz17vslq50y-julia-1.5.3/share/j= ulia/base.cache matches Binary file /gnu/store/i1dgzqfjvkkjlfhpcwc33lz17vslq50y-julia-1.5.3/share/j= ulia/test/depot/compiled/v1.5/Bar/HXSAn_w3IH9.ji matches Binary file /gnu/store/i1dgzqfjvkkjlfhpcwc33lz17vslq50y-julia-1.5.3/share/j= ulia/test/depot/compiled/v1.5/Foo/MYb1d_w3IH9.ji matches Binary file /gnu/store/i1dgzqfjvkkjlfhpcwc33lz17vslq50y-julia-1.5.3/share/j= ulia/test/depot/compiled/v1.5/Foo/TeeT6_w3IH9.ji matches Binary file /gnu/store/i1dgzqfjvkkjlfhpcwc33lz17vslq50y-julia-1.5.3/share/j= ulia/test/depot/compiled/v1.5/Qux/YFfiR_w3IH9.ji matches Binary file /gnu/store/i1dgzqfjvkkjlfhpcwc33lz17vslq50y-julia-1.5.3/share/j= ulia/test/depot/compiled/v1.5/Baz/rONVA_w3IH9.ji matches --8<---------------cut here---------------end--------------->8--- The consequence is =E2=80=99dlopen=E2=80=99 is broken and some Julia packag= es cannot be pre-compiled. Here, an example using the Julia package manager: --8<---------------cut here---------------start------------->8--- $ rm -fr ~/.julia # for the sake of the illustration ;-) $ cat /tmp/foo.jl using Pkg Pkg.add("GZip") println("# =3D> Now let pre-compile") using GZip exit() $ guix environment --ad-hoc julia -- julia --load /tmp/foo.jl Installing known registries into `~/.julia` ######################################################################### 1= 00.0% Added registry `General` to `~/.julia/registries/General` Resolving package versions... Installed GZip =E2=94=80 v0.5.1 Updating `~/.julia/environments/v1.5/Project.toml` [92fee26a] + GZip v0.5.1 Updating `~/.julia/environments/v1.5/Manifest.toml` [92fee26a] + GZip v0.5.1 [8f399da3] + Libdl # =3D> Now let pre-compile ERROR: LoadError: LoadError: could not load library "libz" libz.so: cannot open shared object file: No such file or directory Stacktrace: [...] in expression starting at /home/simon/.julia/packages/GZip/JNmGn/src/zlib_h= .jl:13 in expression starting at /home/simon/.julia/packages/GZip/JNmGn/src/GZip.j= l:73 ERROR: LoadError: Failed to precompile GZip [92fee26a-97fe-5a0c-ad85-20a5f3= 185b63] to /home/simon/.julia/compiled/v1.5/GZip/s2LKY_jQTtL.ji. =E2=80=A6 --8<---------------cut here---------------end--------------->8--- Let tweak the GZip =E2=80=99ccall=E2=80=99 and pre-compile again to show th= at the build-directory is contained in the output, and the Julia internal trace raises it. --8<---------------cut here---------------start------------->8--- $ diff ~/.julia/packages/GZip/JNmGn/src/GZip.jl{,.orig}=20 75c75 < const GZLIB_VERSION =3D unsafe_string(ccall(:zlibVersion, Ptr{UInt8}, ())) --- > const GZLIB_VERSION =3D unsafe_string(ccall((:zlibVersion, GZip._zlib), P= tr{UInt8}, ())) $ diff ~/.julia/packages/GZip/JNmGn/src/zlib_h.jl{,.orig}=20 13c13 < zlib_version =3D unsafe_string(ccall(:zlibVersion, Ptr{UInt8}, ())) --- > zlib_version =3D unsafe_string(ccall((:zlibVersion, _zlib), Ptr{UInt8}, = ())) 84c84 < const zlib_compile_flags =3D ccall(:zlibCompileFlags, UInt, ()) --- > const zlib_compile_flags =3D ccall((:zlibCompileFlags, _zlib), UInt, ()) $ guix environment --ad-hoc julia -- julia -e 'using GZip' ERROR: LoadError: could not load library "libz" libz.so: cannot open shared object file: No such file or directory Stacktrace: [1] dlopen(::String, ::UInt32; throw_error::Bool) at /tmp/guix-build-julia= -1.5.3.drv-0/julia-1.5.3/usr/share/julia/stdlib/v1.5/Libdl/src/Libdl.jl:109 [2] dlopen at /tmp/guix-build-julia-1.5.3.drv-0/julia-1.5.3/usr/share/juli= a/stdlib/v1.5/Libdl/src/Libdl.jl:109 [inlined] (repeats 2 times) [...] in expression starting at /home/simon/.julia/packages/GZip/JNmGn/src/GZip.j= l:206 =E2=80=A6 --8<---------------cut here---------------end--------------->8--- I have tried to tweak LD_LIBRARY_PATH in the julia definition and rebuild it. Still the same error. Note building the julia package takes ~2h on my machine, so the trial-error takes ages. ;-) Another illustration: --8<---------------cut here---------------start------------->8--- $ cat /tmp/bar/pkg.scm (define-module (pkg) #:use-module (guix packages) #:use-module (guix git-download) #:use-module (guix build-system julia) #:use-module ((guix licenses) #:prefix license:)) (define-public julia-gzip (package (name "julia-gzip") (version "0.5.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/JuliaIO/GZip.jl") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "06bx3l1nsvdswgl344347cjh6ffd2r1hw3lz4h0aicayc566717f")))) (build-system julia-build-system) (home-page "https://github.com/JuliaIO/GZip.jl") (synopsis "TODO") (description "TODO") (license license:expat))) $ guix build -L /tmp/bar/ julia-gzip The following derivation will be built: /gnu/store/2wiyhvqrhq8bbiw34gyxclv6zzf98vy3-julia-gzip-0.5.1.drv building /gnu/store/2wiyhvqrhq8bbiw34gyxclv6zzf98vy3-julia-gzip-0.5.1.drv... starting phase `set-SOURCE-DATE-EPOCH' phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds starting phase `set-paths' environment variable `PATH' set to `/gnu/store/i1dgzqfjvkkjlfhpcwc33lz17vsl= q50y-julia-1.5.3/bin:/gnu/store/v6f44zccwh9z5zk3pjlywjybbi8n2hjh-tar-1.32/b= in:/gnu/store/ncydgq2znms5n1d2k5yqshhf58nsixwv-gzip-1.10/bin:/gnu/store/i8h= 2pcxqdq07ijm3ibkka8f4smn1w48v-bzip2-1.0.8/bin:/gnu/store/9860f1abqj8wjjnwl8= a9v54pdcc3bhgf-xz-5.2.4/bin:/gnu/store/60g7r3l01fd7c58yjbm6krgcwj1jkpwg-fil= e-5.38/bin:/gnu/store/n4n560pfvvw50a9369axw5vj5rrqfj1n-diffutils-3.7/bin:/g= nu/store/cd5qf3kcnlq35p9k392pjdpdzpsnds70-patch-2.7.6/bin:/gnu/store/hic7sn= hayfl7m6cpfqqr73nmm19bpqkg-findutils-4.7.0/bin:/gnu/store/swqdvwri9dbv6zssg= 6v0by7l05hd6wxp-gawk-5.0.1/bin:/gnu/store/ishk7fswcs4gkwcp8mh788z4mvvl9bxh-= sed-4.8/bin:/gnu/store/bhs4rj58v8j1narb2454raan2ps38xd8-grep-3.4/bin:/gnu/s= tore/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/bin:/gnu/store/hm40bxn= v8jxmbc1lpb7zfimii4xm9m81-make-4.3/bin:/gnu/store/pwcp239kjf7lnj5i4lkdzcfcx= wcfyk72-bash-minimal-5.0.16/bin:/gnu/store/mpa04aq8lblbcviyxywxcsb1zbi0mf39= -ld-wrapper-0/bin:/gnu/store/m1z7cdbqsqyp9xnjw5cvlb4a7gkcg3m4-binutils-2.34= /bin:/gnu/store/rn75fm7adgx3pw5j8pg3bczfqq1y17lk-gcc-7.5.0/bin:/gnu/store/f= a6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/bin:/gnu/store/fa6wj5bxkj5ll1d72= 92a70knmyl7a0cr-glibc-2.31/sbin' environment variable `JULIA_LOAD_PATH' unset environment variable `JULIA_DEPOT_PATH' set to `/gnu/store/i1dgzqfjvkkjlfhp= cwc33lz17vslq50y-julia-1.5.3/share/julia/' environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/i1dgzqfjvkkjlfhpcw= c33lz17vslq50y-julia-1.5.3/include:/gnu/store/i8h2pcxqdq07ijm3ibkka8f4smn1w= 48v-bzip2-1.0.8/include:/gnu/store/9860f1abqj8wjjnwl8a9v54pdcc3bhgf-xz-5.2.= 4/include:/gnu/store/60g7r3l01fd7c58yjbm6krgcwj1jkpwg-file-5.38/include:/gn= u/store/swqdvwri9dbv6zssg6v0by7l05hd6wxp-gawk-5.0.1/include:/gnu/store/hm40= bxnv8jxmbc1lpb7zfimii4xm9m81-make-4.3/include:/gnu/store/m1z7cdbqsqyp9xnjw5= cvlb4a7gkcg3m4-binutils-2.34/include:/gnu/store/rn75fm7adgx3pw5j8pg3bczfqq1= y17lk-gcc-7.5.0/include:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2= .31/include:/gnu/store/gfapkk5c6hvl1d94m4sqnhn7f9l5gqyh-linux-libre-headers= -5.4.20/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/i1dgzqfjvkkjlf= hpcwc33lz17vslq50y-julia-1.5.3/include:/gnu/store/i8h2pcxqdq07ijm3ibkka8f4s= mn1w48v-bzip2-1.0.8/include:/gnu/store/9860f1abqj8wjjnwl8a9v54pdcc3bhgf-xz-= 5.2.4/include:/gnu/store/60g7r3l01fd7c58yjbm6krgcwj1jkpwg-file-5.38/include= :/gnu/store/swqdvwri9dbv6zssg6v0by7l05hd6wxp-gawk-5.0.1/include:/gnu/store/= hm40bxnv8jxmbc1lpb7zfimii4xm9m81-make-4.3/include:/gnu/store/m1z7cdbqsqyp9x= njw5cvlb4a7gkcg3m4-binutils-2.34/include:/gnu/store/rn75fm7adgx3pw5j8pg3bcz= fqq1y17lk-gcc-7.5.0/include/c++:/gnu/store/rn75fm7adgx3pw5j8pg3bczfqq1y17lk= -gcc-7.5.0/include:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/i= nclude:/gnu/store/gfapkk5c6hvl1d94m4sqnhn7f9l5gqyh-linux-libre-headers-5.4.= 20/include' environment variable `LIBRARY_PATH' set to `/gnu/store/i1dgzqfjvkkjlfhpcwc3= 3lz17vslq50y-julia-1.5.3/lib:/gnu/store/i8h2pcxqdq07ijm3ibkka8f4smn1w48v-bz= ip2-1.0.8/lib:/gnu/store/9860f1abqj8wjjnwl8a9v54pdcc3bhgf-xz-5.2.4/lib:/gnu= /store/60g7r3l01fd7c58yjbm6krgcwj1jkpwg-file-5.38/lib:/gnu/store/swqdvwri9d= bv6zssg6v0by7l05hd6wxp-gawk-5.0.1/lib:/gnu/store/m1z7cdbqsqyp9xnjw5cvlb4a7g= kcg3m4-binutils-2.34/lib:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-= 2.31/lib:/gnu/store/s3dcqzwqaakv1yx37by9chksdbkgih17-glibc-2.31-static/lib:= /gnu/store/hwcky7446s952w0mwchhmm211ll07zrq-glibc-utf8-locales-2.31/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/hwcky7446s952w0mwchh= mm211ll07zrq-glibc-utf8-locales-2.31/lib/locale' phase `set-paths' succeeded after 0.0 seconds starting phase `install-locale' using 'en_US.utf8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' [...] phase `unpack' succeeded after 0.0 seconds starting phase `patch-source-shebangs' phase `patch-source-shebangs' succeeded after 0.0 seconds starting phase `patch-generated-file-shebangs' phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `install' [...] phase `install' succeeded after 0.0 seconds starting phase `check' ERROR: LoadError: LoadError: could not load library "libz" libz.so: cannot open shared object file: No such file or directory Stacktrace: [...] in expression starting at /gnu/store/dak0gnj5kqdma55xy279345qzsal9zdq-julia= -gzip-0.5.1/share/julia/packages/GZip/src/zlib_h.jl:13 in expression starting at /gnu/store/dak0gnj5kqdma55xy279345qzsal9zdq-julia= -gzip-0.5.1/share/julia/packages/GZip/src/GZip.jl:73 ERROR: LoadError: Failed to precompile GZip [92fee26a-97fe-5a0c-ad85-20a5f3= 185b63] to /tmp/.julia/compiled/v1.5/GZip/s2LKY_y94HW.ji. Stacktrace: [...] in expression starting at /gnu/store/dak0gnj5kqdma55xy279345qzsal9zdq-julia= -gzip-0.5.1/share/julia/packages/GZip/test/runtests.jl:1 command "julia" "--depwarn=3Dyes" "/gnu/store/dak0gnj5kqdma55xy279345qzsal9= zdq-julia-gzip-0.5.1/share/julia/packages/GZip/test/runtests.jl" failed wit= h status 1 builder for `/gnu/store/2wiyhvqrhq8bbiw34gyxclv6zzf98vy3-julia-gzip-0.5.1.d= rv' failed with exit code 1 build of /gnu/store/2wiyhvqrhq8bbiw34gyxclv6zzf98vy3-julia-gzip-0.5.1.drv f= ailed View build log at '/var/log/guix/drvs/2w/iyhvqrhq8bbiw34gyxclv6zzf98vy3-jul= ia-gzip-0.5.1.drv.bz2'. guix build: error: build of `/gnu/store/2wiyhvqrhq8bbiw34gyxclv6zzf98vy3-ju= lia-gzip-0.5.1.drv' failed --8<---------------cut here---------------end--------------->8--- Cheers, simon