Installation issue: r-uqsa (JUSUF)

Summary

Summary	Spack package build failure
Package info	r-uqsa
System	JUSUF
Related

Steps to reproduce the issue

$ spack install r-uqsa

Error message

Error message

==> Installing serf-1.3.9-6imgzyzk6w7dxl737ppp2xglahy75amz
==> No binary for serf-1.3.9-6imgzyzk6w7dxl737ppp2xglahy75amz found: installing from source
==> Warning: using "openssl@1.1.1k" which is a deprecated version
==> Warning: Missing a source id for wf-multi-area-model@0.1
==> Warning: Missing a source id for wf-uq-akar4@0.1
==> Warning: Missing a source id for pynn-brainscales@4.0-rc1-fixup1
==> Warning: Missing a source id for hxtorch@4.0-rc1-fixup1
==> Using cached archive: /p/scratch/icei-hbp-2020-0003/ebrains-software/spack-installation/spack/var/spack/cache/_source-cache/archive/54/549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc.tar.bz2
==> Applied patch /p/scratch/icei-hbp-2020-0003/ebrains-software/spack-installation/spack/var/spack/repos/builtin/packages/serf/py3syntax.patch
==> Applied patch /p/scratch/icei-hbp-2020-0003/ebrains-software/spack-installation/spack/var/spack/repos/builtin/packages/serf/py3-hashbang.patch
==> serf: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
    'scons' '-j16' 'PREFIX=/p/scratch/icei-hbp-2020-0003/ebrains-software/spack-installation/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/serf-1.3.9-6imgzyzk6w7dxl737ppp2xglahy75amz' 'APR=/p/usersoftware/swmanage/deepu1/EBRAINS/jusuf/stage2022/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/apr-1.7.0-dy2ijotwiusow4ru5wgdxmswicprpomy' 'APU=/p/usersoftware/swmanage/deepu1/EBRAINS/jusuf/stage2022/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/apr-util-1.6.1-qceot4lvu7evrq6eozdb3pnpken7ueqc' 'OPENSSL=/p/software/jusuf/stages/2022/software/OpenSSL/1.1/' 'ZLIB=/p/scratch/icei-hbp-2020-0003/ebrains-software/spack-installation/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/zlib-1.2.12-l7mris2plmjfkymeenltddo6bzwprqys' 'DEBUG=no' 'CC=/p/software/jusuf/stages/2022/software/GCCcore/11.2.0/bin/gcc' 'LINKFLAGS=-L/p/usersoftware/swmanage/deepu1/EBRAINS/jusuf/stage2022/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/apr-1.7.0-dy2ijotwiusow4ru5wgdxmswicprpomy/lib -L/p/usersoftware/swmanage/deepu1/EBRAINS/jusuf/stage2022/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/apr-util-1.6.1-qceot4lvu7evrq6eozdb3pnpken7ueqc/lib -L/p/software/jusuf/stages/2022/software/OpenSSL/1.1/lib -L/p/scratch/icei-hbp-2020-0003/ebrains-software/spack-installation/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/util-linux-uuid-2.37.4-4gt5bdy4fqtnk4xix5jyuu7eyqc4cnkn/lib -L/p/scratch/icei-hbp-2020-0003/ebrains-software/spack-installation/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/zlib-1.2.12-l7mris2plmjfkymeenltddo6bzwprqys/lib -Wl,-rpath,/p/usersoftware/swmanage/deepu1/EBRAINS/jusuf/stage2022/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/apr-1.7.0-dy2ijotwiusow4ru5wgdxmswicprpomy/lib -Wl,-rpath,/p/usersoftware/swmanage/deepu1/EBRAINS/jusuf/stage2022/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/apr-util-1.6.1-qceot4lvu7evrq6eozdb3pnpken7ueqc/lib -Wl,-rpath,/p/software/jusuf/stages/2022/software/OpenSSL/1.1/lib -Wl,-rpath,/p/scratch/icei-hbp-2020-0003/ebrains-software/spack-installation/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/util-linux-uuid-2.37.4-4gt5bdy4fqtnk4xix5jyuu7eyqc4cnkn/lib -Wl,-rpath,/p/scratch/icei-hbp-2020-0003/ebrains-software/spack-installation/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/zlib-1.2.12-l7mris2plmjfkymeenltddo6bzwprqys/lib' 'CPPFLAGS=-I/p/usersoftware/swmanage/deepu1/EBRAINS/jusuf/stage2022/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/apr-1.7.0-dy2ijotwiusow4ru5wgdxmswicprpomy/include -I/p/usersoftware/swmanage/deepu1/EBRAINS/jusuf/stage2022/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/apr-util-1.6.1-qceot4lvu7evrq6eozdb3pnpken7ueqc/include -I/p/software/jusuf/stages/2022/software/OpenSSL/1.1/include -I/p/scratch/icei-hbp-2020-0003/ebrains-software/spack-installation/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/util-linux-uuid-2.37.4-4gt5bdy4fqtnk4xix5jyuu7eyqc4cnkn/include -I/p/scratch/icei-hbp-2020-0003/ebrains-software/spack-installation/spack/opt/spack/linux-rocky8-zen2/gcc-11.2/zlib-1.2.12-l7mris2plmjfkymeenltddo6bzwprqys/include'
4 warnings found in build log:
112    scons: *** [buckets/buckets.o] Error 1
113    as: unrecognized option '--gdwarf-5'
114    scons: *** [buckets/limit_buckets.o] Error 1
115    as: unrecognized option '--gdwarf-5'
116    scons: *** [buckets/bwtp_buckets.o] Error 1
117    buckets/headers_buckets.c: In function 'serf_headers_read_iovec':


118    buckets/headers_buckets.c:363:8: warning: 'avail' may be used uninitialized in this function [-Wmaybe-uninitialized]
119      363 |     if (requested >= avail) {
120          |        ^
121    buckets/headers_buckets.c:355:16: note: 'avail' was declared here
122      355 |     apr_size_t avail;
123          |                ^~~~~
124    buckets/headers_buckets.c:429:39: warning: 'data' may be used uninitialized in this function [-Wmaybe-uninitialized]
125      429 |             vecs[vecs_used].iov_base = (char)data;
126          |             ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
127    as: unrecognized option '--gdwarf-5'
128    scons: *** [buckets/deflate_buckets.o] Error 1
129    buckets/headers_buckets.c: In function 'serf_headers_read':
130    buckets/headers_buckets.c:365:14: warning: 'avail' may be used uninitialized in this function [-Wmaybe-uninitialized]
131      365 |         *len = avail;
132          |         ~~~~~^~~~~~~
133    as: unrecognized option '--gdwarf-5'
134    scons: *** [buckets/headers_buckets.o] Error 1
135    as: unrecognized option '--gdwarf-5'
136    scons: *** [outgoing.o] Error 1


See build log for details:
/tmp/mathioulaki1/spack-stage/spack-stage-serf-1.3.9-6imgzyzk6w7dxl737ppp2xglahy75amz/spack-build-out.txt
==> Warning: Skipping build of subversion-1.14.1-7mzbvgfk5bu6qv6ptmkawrz3hpyuga37 since serf-1.3.9-6imgzyzk6w7dxl737ppp2xglahy75amz failed
==> Warning: Skipping build of r-remotes-2.4.2-fxb5bpk7e2msx3vq3rn2oeuvnt43bua2 since subversion-1.14.1-7mzbvgfk5bu6qv6ptmkawrz3hpyuga37 failed
==> Warning: Skipping build of r-dynutils-1.0.11-7fz2o6d5fjhpopehcti6ipnyohisep3g since r-remotes-2.4.2-fxb5bpk7e2msx3vq3rn2oeuvnt43bua2 failed
==> Warning: Skipping build of r-gillespiessa2-0.3.0-jlzaxurzdnnxnfqcep7l5znkzfeema7c since r-dynutils-1.0.11-7fz2o6d5fjhpopehcti6ipnyohisep3g failed
==> Warning: Skipping build of r-uqsa-2.2-kut7soamcdukfmsd6x4rk7oy4zaacxxo since r-gillespiessa2-0.3.0-jlzaxurzdnnxnfqcep7l5znkzfeema7c failed

Information on your system

$ spack debug report
* **Spack:** 0.18.1 (13e6f87ef6527954b152eaea303841978e83b992)
* **Python:** 3.6.8
* **Platform:** linux-rocky8-zen2
* **Concretizer:** clingo

Additional information

• spack-build-out.txt
• spack-build-env.txt

added build-error label

(this can be avoided by disabling the X variant for r: r~X)

Just encountered the same issue while installing software on JURECA.

According to StackOverflow, it's related to a wrong version of binutils being used. To solve this issue, the module StdEnv/2023 has to be added to the modules section of the site-specific compilers.yaml like this:

[...]
  2 - compiler:
  3     spec: gcc@11.3.0
  4     paths:
  5       cc: /p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/bin/gcc
  6       cxx: /p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/bin/g++
  7       f77: /p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/bin/gfortran
  8       fc: /p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/bin/gfortran
  9     flags: {}
 10     operating_system: rocky8
 11     target: x86_64
 12     modules:
 13       - StdEnv/2023
 14     environment: {}
 15     extra_rpaths: []
 16 - compiler:
[...]

While my installation is currently running, it seems like the issue has been solved (for me). I'll wait for the installation to finish and report again (+ add a MR for jureca config) later.

fixed with !385 (merged) and !388 (merged) for jureca and jusuf, thx @andreasmueller

closed