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SKESA recipe update, 'make' cannot find BOOST libraries #38476

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gregdenay opened this issue Dec 19, 2022 · 4 comments
Closed

SKESA recipe update, 'make' cannot find BOOST libraries #38476

gregdenay opened this issue Dec 19, 2022 · 4 comments

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@gregdenay
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I am trying to update skesa to the latest version to have the newly included 'saute' executables available through bioconda.
I updated the existing recipe (#38473) but the build keeps failing because make doesn't find the boost libraries:

.16:34:01 BIOCONDA INFO (ERR) /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671463868129/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lboost_program_options: No such file or directory
16:34:01 BIOCONDA INFO (ERR) /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671463868129/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lboost_iostreams: No such file or directory
16:34:01 BIOCONDA INFO (ERR) /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671463868129/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lboost_regex: No such file or directory
16:34:01 BIOCONDA INFO (ERR) /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671463868129/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lboost_timer: No such file or directory
16:34:01 BIOCONDA INFO (ERR) /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671463868129/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lboost_chrono: No such file or directory
16:34:01 BIOCONDA INFO (ERR) /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671463868129/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lboost_system: No such file or directory
16:34:01 BIOCONDA INFO (ERR) collect2: error: ld returned 1 exit status

./include/boost/ is present in the build environement and the ./lib/ folder different files in form libboost_name.so

Now I have no idea about c++ and how conda internally works but I am guessing that there is something wrong in my build.sh file. I checked the Bioconda and conda documentations but could not find anything except trying to set the LDFLAGs, which did not work.

Here is the build.sh file:

#!/bin/bash

export LIBRARY_PATH=${PREFIX}/lib
export LD_LIBRARY_PATH=${PREFIX}/lib
export CPP_INCLUDE_PATH=${PREFIX}/include
export CPLUS_INCLUDE_PATH=${PREFIX}/include
export CXX_INCLUDE_PATH=${PREFIX}/include

if [ "$(uname)" == "Darwin" ]; then
  sed -i.bak 's/-Wl,-Bstatic//' $makefile
  sed -i.bak 's/-Wl,-Bdynamic -lrt//' $makefile
fi

LDFLAGS=-L${PREFIX}/lib

make -f Makefile.nongs \
    BOOST_PATH=${PREFIX} \
    CC="$CXX $CXXFLAGS" \
    LDFLAGS=$LDFLAGS

mkdir -p ${PREFIX}/bin
mv skesa ${PREFIX}/bin/
mv saute ${PREFIX}/bin/
mv saute_prot ${PREFIX}/bin/

Does anyone has an idea on how to fix this?
@gregdenay
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I see that @tseemann has been active in both the skesa repository and building the last recipe version in bioconda :)

@gregdenay gregdenay mentioned this issue Dec 20, 2022
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@gregdenay
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gregdenay commented Dec 21, 2022 •
edited
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Update.
The Skesa recipe was on bioconda blacklist because the source URL was not valid anymore. I tried to modify the existing recipe with a simple change of source (giving github release URL instead of the broken NCBI FTP address and changing the checksum.

This fails to install with the exact same error as the newest version. Here is the full BUILD part of the log:

11:18:09 BIOCONDA INFO BUILD START recipes/skesa
Updating build index: /home/debian/anaconda3/envs/bioconda/conda-bld

11:18:11 BIOCONDA INFO (COMMAND) /home/debian/anaconda3/envs/bioconda/bin/conda mambabuild --override-channels --no-anaconda-upload -c conda-forge -c bioconda -c defaults -e /home/debian/anaconda3/envs/bioconda/conda_build_config.yaml -e /home/debian/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml recipes/skesa/meta.yaml
11:18:12 BIOCONDA INFO (ERR) /home/debian/anaconda3/envs/bioconda/lib/python3.7/site-packages/conda_build/cli/main_build.py:390: UserWarning: RECIPE_PATH received is a file. File: recipes/skesa/meta.yaml
11:18:12 BIOCONDA INFO (ERR) It should be a path to a folder.
11:18:12 BIOCONDA INFO (ERR) Forcing conda-build to use the recipe file.
11:18:12 BIOCONDA INFO (ERR)   UserWarning
11:18:12 BIOCONDA INFO (ERR) No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.16
11:18:12 BIOCONDA INFO (ERR) WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.16
11:18:12 BIOCONDA INFO (OUT) Updating build index: /home/debian/anaconda3/envs/bioconda/conda-bld
11:18:12 BIOCONDA INFO (OUT)
11:18:12 BIOCONDA INFO (OUT) Adding in variants from internal_defaults
11:18:12 BIOCONDA INFO (ERR) INFO:conda_build.variants:Adding in variants from internal_defaults
11:18:12 BIOCONDA INFO (OUT) Adding in variants from /home/debian/anaconda3/envs/bioconda/conda_build_config.yaml
11:18:12 BIOCONDA INFO (ERR) INFO:conda_build.variants:Adding in variants from /home/debian/anaconda3/envs/bioconda/conda_build_config.yaml
11:18:12 BIOCONDA INFO (OUT) Adding in variants from /home/debian/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
11:18:12 BIOCONDA INFO (ERR) INFO:conda_build.variants:Adding in variants from /home/debian/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
11:18:14 BIOCONDA INFO (OUT) Attempting to finalize metadata for skesa
11:18:14 BIOCONDA INFO (ERR) INFO:conda_build.metadata:Attempting to finalize metadata for skesa
11:18:15 BIOCONDA INFO (OUT) conda-forge/linux-64                                        Using cache
11:18:15 BIOCONDA INFO (OUT) conda-forge/noarch                                          Using cache
11:18:15 BIOCONDA INFO (OUT) bioconda/linux-64                                           Using cache
11:18:15 BIOCONDA INFO (OUT) bioconda/noarch                                             Using cache
11:18:15 BIOCONDA INFO (OUT) r/linux-64                                                  Using cache
11:18:15 BIOCONDA INFO (OUT) r/noarch                                                    Using cache
11:18:17 BIOCONDA INFO (OUT) Reloading output folder: /home/debian/anaconda3/envs/bioconda/conda-bld
11:19:06 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
11:19:06 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/linux-64/repodata.json HTTP/1.1" 304 0
11:19:09 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/noarch/repodata.json HTTP/1.1" 304 0
11:19:10 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/linux-64/repodata.json HTTP/1.1" 304 0
11:19:10 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/noarch/repodata.json HTTP/1.1" 304 0
.11:19:37 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/channeldata.json HTTP/1.1" 200 None
11:19:37 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443
11:19:37 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /bioconda/channeldata.json HTTP/1.1" 200 None
11:19:38 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/channeldata.json HTTP/1.1" 200 None
11:19:40 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /r/channeldata.json HTTP/1.1" 200 None
11:19:40 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /conda-forge/channeldata.json HTTP/1.1" 200 None
11:19:41 BIOCONDA INFO (OUT) Reloading output folder: /home/debian/anaconda3/envs/bioconda/conda-bld
11:19:43 BIOCONDA INFO (OUT) Reloading output folder: /home/debian/anaconda3/envs/bioconda/conda-bld
11:19:45 BIOCONDA INFO (OUT) BUILD START: ['skesa-2.4.0-hd03093a_2.tar.bz2']
11:19:45 BIOCONDA INFO (OUT) Reloading output folder: /home/debian/anaconda3/envs/bioconda/conda-bld
11:19:47 BIOCONDA INFO (OUT)
11:19:47 BIOCONDA INFO (OUT) ## Package Plan ##
11:19:47 BIOCONDA INFO (OUT)
11:19:47 BIOCONDA INFO (OUT)   environment location: /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671617892372/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p
11:19:47 BIOCONDA INFO (OUT)
11:19:47 BIOCONDA INFO (OUT)
11:19:47 BIOCONDA INFO (OUT) The following NEW packages will be INSTALLED:
11:19:47 BIOCONDA INFO (OUT)
11:19:47 BIOCONDA INFO (OUT)     _libgcc_mutex:    0.1-conda_forge            conda-forge
11:19:47 BIOCONDA INFO (OUT)     _openmp_mutex:    4.5-2_gnu                  conda-forge
11:19:47 BIOCONDA INFO (OUT)     boost:            1.80.0-py311h59ea3da_4     conda-forge
11:19:47 BIOCONDA INFO (OUT)     boost-cpp:        1.80.0-h75c5d50_0          conda-forge
11:19:47 BIOCONDA INFO (OUT)     bzip2:            1.0.8-h7f98852_4           conda-forge
11:19:47 BIOCONDA INFO (OUT)     ca-certificates:  2022.12.7-ha878542_0       conda-forge
11:19:47 BIOCONDA INFO (OUT)     icu:              70.1-h27087fc_0            conda-forge
11:19:47 BIOCONDA INFO (OUT)     ld_impl_linux-64: 2.39-hcc3a1bd_1            conda-forge
11:19:47 BIOCONDA INFO (OUT)     libblas:          3.9.0-16_linux64_openblas  conda-forge
11:19:47 BIOCONDA INFO (OUT)     libcblas:         3.9.0-16_linux64_openblas  conda-forge
11:19:47 BIOCONDA INFO (OUT)     libffi:           3.4.2-h7f98852_5           conda-forge
11:19:47 BIOCONDA INFO (OUT)     libgcc-ng:        12.2.0-h65d4601_19         conda-forge
11:19:47 BIOCONDA INFO (OUT)     libgfortran-ng:   12.2.0-h69a702a_19         conda-forge
11:19:47 BIOCONDA INFO (OUT)     libgfortran5:     12.2.0-h337968e_19         conda-forge
11:19:47 BIOCONDA INFO (OUT)     libgomp:          12.2.0-h65d4601_19         conda-forge
11:19:47 BIOCONDA INFO (OUT)     liblapack:        3.9.0-16_linux64_openblas  conda-forge
11:19:47 BIOCONDA INFO (OUT)     libnsl:           2.0.0-h7f98852_0           conda-forge
11:19:47 BIOCONDA INFO (OUT)     libopenblas:      0.3.21-pthreads_h78a6416_3 conda-forge
11:19:47 BIOCONDA INFO (OUT)     libsqlite:        3.40.0-h753d276_0          conda-forge
11:19:47 BIOCONDA INFO (OUT)     libstdcxx-ng:     12.2.0-h46fd767_19         conda-forge
11:19:47 BIOCONDA INFO (OUT)     libuuid:          2.32.1-h7f98852_1000       conda-forge
11:19:47 BIOCONDA INFO (OUT)     libzlib:          1.2.13-h166bdaf_4          conda-forge
11:19:47 BIOCONDA INFO (OUT)     ncurses:          6.3-h27087fc_1             conda-forge
11:19:47 BIOCONDA INFO (OUT)     numpy:            1.24.0-py311hbde0eaa_0     conda-forge
11:19:47 BIOCONDA INFO (OUT)     openssl:          3.0.7-h0b41bf4_1           conda-forge
11:19:47 BIOCONDA INFO (OUT)     pip:              22.3.1-pyhd8ed1ab_0        conda-forge
11:19:47 BIOCONDA INFO (OUT)     python:           3.11.0-ha86cf86_0_cpython  conda-forge
11:19:47 BIOCONDA INFO (OUT)     python_abi:       3.11-3_cp311               conda-forge
11:19:47 BIOCONDA INFO (OUT)     readline:         8.2-h5eee18b_0
11:19:47 BIOCONDA INFO (OUT)     setuptools:       65.6.3-pyhd8ed1ab_0        conda-forge
11:19:47 BIOCONDA INFO (OUT)     tk:               8.6.12-h27826a3_0          conda-forge
11:19:47 BIOCONDA INFO (OUT)     tzdata:           2022g-h191b570_0           conda-forge
11:19:47 BIOCONDA INFO (OUT)     wheel:            0.38.4-pyhd8ed1ab_0        conda-forge
11:19:47 BIOCONDA INFO (OUT)     xz:               5.2.8-h5eee18b_0
11:19:47 BIOCONDA INFO (OUT)     zlib:             1.2.13-h166bdaf_4          conda-forge
11:19:47 BIOCONDA INFO (OUT)     zstd:             1.5.2-h6239696_4           conda-forge
11:19:47 BIOCONDA INFO (OUT)
11:19:47 BIOCONDA INFO (OUT) Preparing transaction: ...working... done
11:19:50 BIOCONDA INFO (OUT) Verifying transaction: ...working... done
11:19:52 BIOCONDA INFO (OUT) Executing transaction: ...working... done
11:19:52 BIOCONDA INFO (OUT) Reloading output folder: /home/debian/anaconda3/envs/bioconda/conda-bld
11:19:52 BIOCONDA INFO (OUT) Reloading output folder: /home/debian/anaconda3/envs/bioconda/conda-bld
11:19:55 BIOCONDA INFO (OUT)
11:19:55 BIOCONDA INFO (OUT) ## Package Plan ##
11:19:55 BIOCONDA INFO (OUT)
11:19:55 BIOCONDA INFO (OUT)   environment location: /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671617892372/_build_env
11:19:55 BIOCONDA INFO (OUT)
11:19:55 BIOCONDA INFO (OUT)
11:19:55 BIOCONDA INFO (OUT) The following NEW packages will be INSTALLED:
11:19:55 BIOCONDA INFO (OUT)
11:19:55 BIOCONDA INFO (OUT)     _libgcc_mutex:            0.1-conda_forge    conda-forge
11:19:55 BIOCONDA INFO (OUT)     _openmp_mutex:            4.5-2_gnu          conda-forge
11:19:55 BIOCONDA INFO (OUT)     binutils_impl_linux-64:   2.39-he00db2b_1    conda-forge
11:19:55 BIOCONDA INFO (OUT)     binutils_linux-64:        2.39-h5fc0e48_11   conda-forge
11:19:55 BIOCONDA INFO (OUT)     gcc_impl_linux-64:        10.4.0-h5231bdf_19 conda-forge
11:19:55 BIOCONDA INFO (OUT)     gcc_linux-64:             10.4.0-h9215b83_11 conda-forge
11:19:55 BIOCONDA INFO (OUT)     gxx_impl_linux-64:        10.4.0-h5231bdf_19 conda-forge
11:19:55 BIOCONDA INFO (OUT)     gxx_linux-64:             10.4.0-h6e491c6_11 conda-forge
11:19:55 BIOCONDA INFO (OUT)     kernel-headers_linux-64:  2.6.32-he073ed8_15 conda-forge
11:19:55 BIOCONDA INFO (OUT)     ld_impl_linux-64:         2.39-hcc3a1bd_1    conda-forge
11:19:55 BIOCONDA INFO (OUT)     libgcc-devel_linux-64:    10.4.0-hd38fd1e_19 conda-forge
11:19:55 BIOCONDA INFO (OUT)     libgcc-ng:                12.2.0-h65d4601_19 conda-forge
11:19:55 BIOCONDA INFO (OUT)     libgomp:                  12.2.0-h65d4601_19 conda-forge
11:19:55 BIOCONDA INFO (OUT)     libsanitizer:             10.4.0-h5246dfb_19 conda-forge
11:19:55 BIOCONDA INFO (OUT)     libstdcxx-devel_linux-64: 10.4.0-hd38fd1e_19 conda-forge
11:19:55 BIOCONDA INFO (OUT)     libstdcxx-ng:             12.2.0-h46fd767_19 conda-forge
11:19:55 BIOCONDA INFO (OUT)     make:                     4.3-hd18ef5c_1     conda-forge
11:19:55 BIOCONDA INFO (OUT)     sysroot_linux-64:         2.12-he073ed8_15   conda-forge
11:19:55 BIOCONDA INFO (OUT)
11:19:55 BIOCONDA INFO (OUT) Preparing transaction: ...working... done
11:19:55 BIOCONDA INFO (OUT) Verifying transaction: ...working... done
11:19:55 BIOCONDA INFO (OUT) Executing transaction: ...working... done
11:19:55 BIOCONDA INFO (OUT) Source cache directory is: /home/debian/anaconda3/envs/bioconda/conda-bld/src_cache
11:19:55 BIOCONDA INFO (ERR) INFO:conda_build.source:Source cache directory is: /home/debian/anaconda3/envs/bioconda/conda-bld/src_cache
11:19:55 BIOCONDA INFO (OUT) Downloading source to cache: 2.4.0_c07b56dfa3.tar.gz
11:19:55 BIOCONDA INFO (ERR) INFO:conda_build.source:Downloading source to cache: 2.4.0_c07b56dfa3.tar.gz
11:19:55 BIOCONDA INFO (OUT) Downloading https://github.com/ncbi/SKESA/archive/refs/tags/2.4.0.tar.gz
11:19:55 BIOCONDA INFO (ERR) INFO:conda_build.source:Downloading https://github.com/ncbi/SKESA/archive/refs/tags/2.4.0.tar.gz
11:19:55 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): github.com:443
11:19:56 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:https://github.com:443 "GET /ncbi/SKESA/archive/refs/tags/2.4.0.tar.gz HTTP/1.1" 302 0
11:19:56 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): codeload.github.com:443
11:19:56 BIOCONDA INFO (ERR) DEBUG:urllib3.connectionpool:https://codeload.github.com:443 "GET /ncbi/SKESA/tar.gz/refs/tags/2.4.0 HTTP/1.1" 200 None
11:19:56 BIOCONDA INFO (OUT) Success
11:19:56 BIOCONDA INFO (ERR) INFO:conda_build.source:Success
..11:21:15 BIOCONDA INFO (ERR) /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671617892372/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lboost_program_options: No such file or directory
11:21:15 BIOCONDA INFO (ERR) /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671617892372/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lboost_iostreams: No such file or directory
11:21:15 BIOCONDA INFO (ERR) /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671617892372/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lboost_regex: No such file or directory
11:21:15 BIOCONDA INFO (ERR) /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671617892372/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lboost_timer: No such file or directory
11:21:15 BIOCONDA INFO (ERR) /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671617892372/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lboost_chrono: No such file or directory
11:21:15 BIOCONDA INFO (ERR) /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671617892372/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lboost_system: No such file or directory
11:21:15 BIOCONDA INFO (ERR) collect2: error: ld returned 1 exit status
11:21:15 BIOCONDA INFO (ERR) make: *** [Makefile.nongs:62: skesa] Error 1
11:21:16 BIOCONDA INFO (OUT) Extracting download
11:21:16 BIOCONDA INFO (OUT) source tree in: /home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671617892372/work
11:21:16 BIOCONDA INFO (OUT) export PREFIX=/home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671617892372/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p
11:21:16 BIOCONDA INFO (OUT) export BUILD_PREFIX=/home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671617892372/_build_env
11:21:16 BIOCONDA INFO (OUT) export SRC_DIR=/home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671617892372/work
11:21:16 BIOCONDA INFO (OUT) INFO: activate-binutils_linux-64.sh made the following environmental changes:
11:21:16 BIOCONDA INFO (OUT) +ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line
11:21:16 BIOCONDA INFO (OUT) +AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar
11:21:16 BIOCONDA INFO (OUT) +AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as
11:21:16 BIOCONDA INFO (OUT) +CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++filt
11:21:16 BIOCONDA INFO (OUT) +ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit
11:21:16 BIOCONDA INFO (OUT) +GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof
11:21:16 BIOCONDA INFO (OUT) +LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld
11:21:16 BIOCONDA INFO (OUT) +LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold
11:21:16 BIOCONDA INFO (OUT) +NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm
11:21:16 BIOCONDA INFO (OUT) +OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy
11:21:16 BIOCONDA INFO (OUT) +OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump
11:21:16 BIOCONDA INFO (OUT) +RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib
11:21:16 BIOCONDA INFO (OUT) +READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf
11:21:16 BIOCONDA INFO (OUT) +SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size
11:21:16 BIOCONDA INFO (OUT) +STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings
11:21:16 BIOCONDA INFO (OUT) +STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip
11:21:16 BIOCONDA INFO (OUT) INFO: activate-gcc_linux-64.sh made the following environmental changes:
11:21:16 BIOCONDA INFO (OUT) +BUILD=x86_64-conda-linux-gnu
11:21:16 BIOCONDA INFO (OUT) +CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc
11:21:16 BIOCONDA INFO (OUT) +CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc
11:21:16 BIOCONDA INFO (OUT) +CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/skesa-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
11:21:16 BIOCONDA INFO (ERR) Traceback (most recent call last):
11:21:16 BIOCONDA INFO (ERR)   File "/home/debian/anaconda3/envs/bioconda/bin/conda-mambabuild", line 10, in <module>
11:21:16 BIOCONDA INFO (ERR)     sys.exit(main())
11:21:16 BIOCONDA INFO (OUT) +CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin
11:21:16 BIOCONDA INFO (OUT) +CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr
11:21:16 BIOCONDA INFO (OUT) +CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot
11:21:16 BIOCONDA INFO (OUT) +CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu
11:21:16 BIOCONDA INFO (OUT) +CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu
11:21:16 BIOCONDA INFO (OUT) +CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp
11:21:16 BIOCONDA INFO (OUT) +CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include
11:21:16 BIOCONDA INFO (ERR)   File "/home/debian/anaconda3/envs/bioconda/lib/python3.7/site-packages/boa/cli/mambabuild.py", line 239, in main
11:21:16 BIOCONDA INFO (ERR)     call_conda_build(action, config)
11:21:16 BIOCONDA INFO (OUT) +DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/skesa-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
11:21:16 BIOCONDA INFO (OUT) +DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include
11:21:16 BIOCONDA INFO (OUT) +GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc
11:21:16 BIOCONDA INFO (OUT) +GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar
11:21:16 BIOCONDA INFO (ERR)   File "/home/debian/anaconda3/envs/bioconda/lib/python3.7/site-packages/boa/cli/mambabuild.py", line 218, in call_conda_build
11:21:16 BIOCONDA INFO (OUT) +GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm
11:21:16 BIOCONDA INFO (OUT) +GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib
11:21:16 BIOCONDA INFO (OUT) +HOST=x86_64-conda-linux-gnu
11:21:16 BIOCONDA INFO (ERR)     **kwargs,
11:21:16 BIOCONDA INFO (OUT) +LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib
11:21:16 BIOCONDA INFO (OUT) +_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
11:21:16 BIOCONDA INFO (OUT) +build_alias=x86_64-conda-linux-gnu
11:21:16 BIOCONDA INFO (OUT) +host_alias=x86_64-conda-linux-gnu
11:21:16 BIOCONDA INFO (OUT) -BUILD=x86_64-conda_cos6-linux-gnu
11:21:16 BIOCONDA INFO (OUT) -CONDA_BUILD_SYSROOT=
11:21:16 BIOCONDA INFO (OUT) INFO: activate-gxx_linux-64.sh made the following environmental changes:
11:21:16 BIOCONDA INFO (ERR)   File "/home/debian/anaconda3/envs/bioconda/lib/python3.7/site-packages/conda_build/api.py", line 195, in build
11:21:16 BIOCONDA INFO (OUT) +CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++
11:21:16 BIOCONDA INFO (ERR)     variants=variants
11:21:16 BIOCONDA INFO (ERR)   File "/home/debian/anaconda3/envs/bioconda/lib/python3.7/site-packages/conda_build/build.py", line 3093, in build_tree
11:21:16 BIOCONDA INFO (ERR)     notest=notest,
11:21:16 BIOCONDA INFO (OUT) +CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/skesa-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
11:21:16 BIOCONDA INFO (OUT) +CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++
11:21:16 BIOCONDA INFO (ERR)   File "/home/debian/anaconda3/envs/bioconda/lib/python3.7/site-packages/conda_build/build.py", line 2212, in build
11:21:16 BIOCONDA INFO (ERR)     cwd=src_dir, stats=build_stats)
11:21:16 BIOCONDA INFO (OUT) +DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/skesa-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
11:21:16 BIOCONDA INFO (OUT) +GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g++
11:21:16 BIOCONDA INFO (ERR)   File "/home/debian/anaconda3/envs/bioconda/lib/python3.7/site-packages/conda_build/utils.py", line 410, in check_call_env
11:21:16 BIOCONDA INFO (ERR)     return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
11:21:16 BIOCONDA INFO (OUT) $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++ -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/skesa-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c -o skesa.o skesa.cpp -D NO_NGS -Wall -Wno-format-y2k  -pthread -fPIC -O3 -finline-functions -fstrict-aliasing -fomit-frame-pointer -msse4.2 -I $PREFIX/include
11:21:16 BIOCONDA INFO (ERR)   File "/home/debian/anaconda3/envs/bioconda/lib/python3.7/site-packages/conda_build/utils.py", line 390, in _func_defaulting_env_to_os_environ
11:21:16 BIOCONDA INFO (OUT) $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++ -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/skesa-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c -o glb_align.o glb_align.cpp -D NO_NGS -Wall -Wno-format-y2k  -pthread -fPIC -O3 -finline-functions -fstrict-aliasing -fomit-frame-pointer -msse4.2 -I $PREFIX/include
11:21:16 BIOCONDA INFO (ERR)     raise subprocess.CalledProcessError(proc.returncode, _args)
11:21:16 BIOCONDA INFO (OUT) $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++ -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/skesa-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o skesa skesa.o glb_align.o -Wl,-Bstatic -L $PREFIX/lib -lboost_program_options -lboost_iostreams -lboost_regex -lboost_timer -lboost_chrono -lboost_system -Wl,-Bdynamic -lrt -ldl -lm  -lpthread -lz
11:21:16 BIOCONDA INFO (ERR) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/home/debian/anaconda3/envs/bioconda/conda-bld/skesa_1671617892372/work/conda_build.sh']' returned non-zero exit status 2.
11:21:24 BIOCONDA ERROR COMMAND FAILED (exited with 1): /home/debian/anaconda3/envs/bioconda/bin/conda mambabuild --override-channels --no-anaconda-upload -c conda-forge -c bioconda -c defaults -e /home/debian/anaconda3/envs/bioconda/conda_build_config.yaml -e /home/debian/anaconda3/envs/bioconda/lib/python3.7/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml recipes/skesa/meta.yaml

11:21:24 BIOCONDA ERROR BUILD FAILED recipes/skesa
11:21:24 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
11:21:24 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe recipes/skesa

It seem that make does not find the -lboost_program_options and other boost libraries.
Here is how the `conda-bld/skesa_xxx' folder looks like:

work/  # content of the skesa release archive
pip_cache/ # empty
_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/ # Typical conda env structure with boost under /include and libboost_program_options.so under lib/
_build_env/ # also a conda typical conda env structure but onlycontains what is required for build as far as I can tell (make and coimpilers)
prefix_files.txt # long list of paths, including some like 'include/boost/program_options.hpp'

I also tried to put boost as a build dependency but it did not change anything.

Trying to manually install skesa in an environment with zlib and boost also fails:

$ mamba create -n skesa_test -c bioconda -c conda-forge make zlib boost
$ wget https://github.com/ncbi/SKESA/archive/refs/tags/2.4.0.tar.gz
$ tar -xzf 2.4.0.tar.gz
$ cd SKESA-2.4.0/
$ conda activate skesa_test
$ ls -d ~/anaconda3/envs/skesa_test/include/boost
/home/debian/anaconda3/envs/skesa_test/include/boost
$ ls ~/anaconda3/envs/skesa_test/lib/libboost_program_options.so
/home/debian/anaconda3/envs/skesa_test/lib/libboost_program_options.so
$ BOOST_PATH=~/anaconda3/envs/skesa_test
$ make -f Makefile.nongs BOOST_PATH=$BOOST_PATH
c++ -std=c++11 -o skesa skesa.o glb_align.o -Wl,-Bstatic -L /home/debian/anaconda3/envs/skesa_test/lib -lboost_program_options -lboost_iostreams -lboost_regex -lboost_timer -lboost_chrono -lboost_system -Wl,-Bdynamic -lrt -ldl -lm  -lpthread -lz
/usr/bin/ld: cannot find -lboost_program_options
/usr/bin/ld: cannot find -lboost_iostreams
/usr/bin/ld: cannot find -lboost_regex
/usr/bin/ld: cannot find -lboost_timer
/usr/bin/ld: cannot find -lboost_chrono
/usr/bin/ld: cannot find -lboost_system
collect2: error: ld returned 1 exit status
make: *** [Makefile.nongs:62: skesa] Error 1

Worth mentionning, manual boost and skesa installation (without going through conda) works.

I must be missing something but I cannot see what

@gregdenay gregdenay changed the title Trouble finding c++ libraries in build.sh SKESA recipe update, 'make' cannot find BOOST libraries Dec 21, 2022
@gregdenay
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gregdenay commented Dec 22, 2022 •
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After researching this further I found that the BOOST static libraries are missing from $PREFIX/lib, only the dynamic libraries are generated, which seems to be the reason SKESA cannot be built.
conda-forge/boost-feedstock#159

@gregdenay
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bioconda recipe solved. closing this. Refer to PR #38473

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