CI failure and conda installation of lalsuite failed
Description of problem
- pipeline failure due to LALDetector.h mis-installed in conda.fft?: https://git.ligo.org/wanting.niu/lalsuite-jolien/-/jobs/3108806 (this repo is forked from Jolien's repo, which he forked from lalsuite, and rebased with master)
- pipeline:conda:linux also failed: https://git.ligo.org/wanting.niu/lalsuite-jolien/-/jobs/3108808
- I run into the same error message when I follow the README and conda-install the lalsuite (from master branch)
at the step of make -j && make install
, the error message gives:
for flag in -Werror -Wextra -w314,506,511 -I../include -I$PREFIX/include -DLAL_FALLBACK_DATA_PATH='"$PREFIX/share/lal"' -D_ISOC99_SOURCE -DNDEBUG -D_FORTIFY_SOURCE=2 -MP -MD -MT swiglal.i; do \
case "${flag}" in \
-I*) \
dir=`echo ${flag} | /usr/bin/sed -e 's|^-I||'`; \
stddeffile="${dir}/lal/LALStddef.h"; \
if test -f "${stddeffile}"; then \
break; \
../include/lal/LALDetectors.h:194: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:195: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:196: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:197: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:198: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:199: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:200: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:201: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:202: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:203: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:204: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:205: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:206: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:207: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:208: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:209: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:210: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:211: Error: Type error. Expecting an integral type
../include/lal/LALDetectors.h:212: Error: Type error. Expecting an integral type
make[3]: *** [Makefile:1579: swiglal.i] Error 1
make[2]: *** [Makefile:796: all] Error 2
make[1]: *** [Makefile:633: all-recursive] Error 1
make: *** [Makefile:530: all] Error 2
fi; \
stddeffile=""; \
;; \
Expected behavior
I am not sure if it is a problem from my local conda environment build up (which is built from conda env create -f common/conda/environment.yml
), or it is a potential problem in lalsuite-master. It's possible that this bug has been contained in several commits of lalsuite-master.
Steps to reproduce
The easiest way to reproduce the error is to follow the Building from Source
in README, (also building a new conda environment), and the error should show up in the make -j && make install
step.
Context/environment
System information
</details>
Hostname: ldas-pcdev2.ligo.caltech.edu
Platform: Linux-4.18.0-513.9.1.el8_9.x86_64-x86_64-with-centos-8.9-Green_Obsidian ()
Python version: 3.6.8 (default, Oct 25 2023, 15:15:22)
Conda info
$ conda info
[wanting.niu@ldas-pcdev2 ~]$ conda info
active environment : None
shell level : 0
user config file : /home/wanting.niu/.condarc
populated config files : /cvmfs/software.igwn.org/conda/.condarc
conda version : 23.11.0
conda-build version : 3.27.0
python version : 3.10.12.final.0
solver : libmamba (default)
virtual packages : __archspec=1=zen2
__conda=23.11.0=0
__cuda=12.3=0
__glibc=2.28=0
__linux=4.18.0=0
__unix=0=0
base environment : /cvmfs/software.igwn.org/conda (read only)
conda av data dir : /cvmfs/software.igwn.org/conda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/igwn/linux-64
https://conda.anaconda.org/igwn/noarch
package cache : /cvmfs/software.igwn.org/conda/pkgs
/home/wanting.niu/.conda/pkgs
envs directories : /home/wanting.niu/.conda/envs
/cvmfs/software.igwn.org/conda/envs
platform : linux-64
user-agent : conda/23.11.0 requests/2.31.0 CPython/3.10.12 Linux/4.18.0-513.9.1.el8_9.x86_64 rocky/8.9 glibc/2.28 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.5
UID:GID : 46258:46258
netrc file : None
offline mode : False
</details>
Conda list
$ conda list
# packages in environment at /cvmfs/software.igwn.org/conda:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
anyio 3.7.1 pyhd8ed1ab_0 conda-forge
archspec 0.2.2 pyhd8ed1ab_0 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
boa 0.16.0 pyhd8ed1ab_1 conda-forge
boltons 23.0.0 pyhd8ed1ab_0 conda-forge
brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.24.0 hd590300_0 conda-forge
ca-certificates 2023.11.17 hbcca054_0 conda-forge
certifi 2023.11.17 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py310h2fee648_0 conda-forge
chardet 5.2.0 py310hff52083_1 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
conda 23.11.0 py310hff52083_1 conda-forge
conda-build 3.27.0 py310hff52083_0 conda-forge
conda-index 0.3.0 pyhd8ed1ab_1 conda-forge
conda-libmamba-solver 23.12.0 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.2.0 pyh38be061_0 conda-forge
conda-package-streaming 0.9.0 pyhd8ed1ab_0 conda-forge
conda-verify 3.1.1 py310hff52083_1006 conda-forge
cryptography 41.0.3 py310h75e40e8_0 conda-forge
distro 1.8.0 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.0 pyhd8ed1ab_0 conda-forge
filelock 3.13.1 pyhd8ed1ab_0 conda-forge
fmt 10.1.1 h00ab1b0_1 conda-forge
future 0.18.3 pyhd8ed1ab_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.3.2 pyhd8ed1ab_0 conda-forge
json5 0.9.14 pyhd8ed1ab_0 conda-forge
jsonpatch 1.33 pyhd8ed1ab_0 conda-forge
jsonpointer 2.4 py310hff52083_3 conda-forge
jsonschema 4.20.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.11.2 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libarchive 3.7.2 h2aa1ff5_1 conda-forge
libcurl 8.5.0 hca28451_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_3 conda-forge
libgomp 13.2.0 h807b86a_3 conda-forge
libiconv 1.17 hd590300_2 conda-forge
liblief 0.12.3 h27087fc_0 conda-forge
libmamba 1.5.5 had39da4_0 conda-forge
libmambapy 1.5.5 py310h39ff949_0 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libsolv 0.7.27 hfc55251_0 conda-forge
libsqlite 3.44.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxml2 2.12.3 h232c23b_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 h516909a_1000 conda-forge
mamba 1.5.5 py310h51d5547_0 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.3 py310h2372a71_1 conda-forge
mdurl 0.1.0 pyhd8ed1ab_0 conda-forge
menuinst 2.0.1 py310hff52083_0 conda-forge
more-itertools 10.1.0 pyhd8ed1ab_0 conda-forge
ncurses 6.4 h59595ed_2 conda-forge
openssl 3.2.0 hd590300_1 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
patch 2.7.6 h7f98852_1002 conda-forge
patchelf 0.17.2 h58526e2_0 conda-forge
pip 23.2.1 pyhd8ed1ab_0 conda-forge
pkginfo 1.9.6 pyhd8ed1ab_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.1.0 pyhd8ed1ab_0 conda-forge
pluggy 1.3.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.42 pyha770c72_0 conda-forge
prompt_toolkit 3.0.42 hd8ed1ab_0 conda-forge
psutil 5.9.7 py310h2372a71_0 conda-forge
py-lief 0.12.3 py310hd8f1fbe_0 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.6 py310h2372a71_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.10.12 hd12c33a_0_cpython conda-forge
python-libarchive-c 5.0 py310hff52083_2 conda-forge
python_abi 3.10 4_cp310 conda-forge
pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py310h2372a71_1 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.32.0 pyhd8ed1ab_0 conda-forge
reproc 14.2.4.post0 hd590300_1 conda-forge
reproc-cpp 14.2.4.post0 h59595ed_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rich 13.7.0 pyhd8ed1ab_0 conda-forge
ripgrep 14.0.3 he8a937b_1 conda-forge
rpds-py 0.15.2 py310hcb5633a_0 conda-forge
ruamel.yaml 0.18.5 py310h2372a71_0 conda-forge
ruamel.yaml.clib 0.2.7 py310h2372a71_2 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
truststore 0.8.0 pyhd8ed1ab_0 conda-forge
typing_extensions 4.9.0 pyha770c72_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
urllib3 2.1.0 pyhd8ed1ab_0 conda-forge
watchgod 0.8.2 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.12 pyhd8ed1ab_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yaml-cpp 0.8.0 h59595ed_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zstandard 0.22.0 py310h1275a96_0 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
lalapps_version
$ lalapps_version --verbose
-bash: $: command not found