viennarna 2.6.3 #1686
Triggered via pull request
September 16, 2023 01:27
YoshitakaMo
Status
Failure
Total duration
19m 49s
Artifacts
–
Annotations
2 errors and 5 warnings
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`brew install --verbose --build-bottle brewsci/bio/viennarna` failed on Linux!:
Formula/viennarna.rb#L29
gcc-11 -I./src -g -O2 -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_control_pd.c -o src/g2_control_pd.o
gcc-11 -I./src -g -O2 -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_graphic.c -o src/g2_ui_graphic.o
gcc-11 -I./src -g -O2 -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_virtual_device.c -o src/g2_ui_virtual_device.o
gcc-11 -I./src -g -O2 -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_device.c -o src/g2_ui_device.o
gcc-11 -I./src -g -O2 -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_splines.c -o src/g2_splines.o
gcc-11 -I./src -g -O2 -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/PS/g2_PS.c -o src/PS/g2_PS.o
gcc-11 -I./src -g -O2 -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/FIG/g2_FIG.c -o src/FIG/g2_FIG.o
gcc-11 -I./src -g -O2 -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/X11/g2_X11.c -o src/X11/g2_X11.o
gcc-ar cr libg2.a ./src/g2_device.o ./src/g2_ui_control.o ./src/g2_util.o ./src/g2_fif.o ./src/g2_virtual_device.o ./src/g2_physical_device.o ./src/g2_graphic_pd.o ./src/g2_control_pd.o ./src/g2_ui_graphic.o ./src/g2_ui_virtual_device.o ./src/g2_ui_device.o ./src/
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build-bottles (ubuntu-latest)
Process completed with exit code 1.
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build-bottles (ubuntu-latest)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/cache@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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build-bottles (ubuntu-latest)
No files were found with the provided path: *.bottle.*. No artifacts will be uploaded.
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build-bottles (macos-latest)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/cache@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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build-bottles (macos-latest)
No files were found with the provided path: *.bottle.*. No artifacts will be uploaded.
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`brew install --verbose --build-bottle brewsci/bio/viennarna` failed on macOS Monterey (12)!:
Formula/viennarna.rb#L29
/usr/bin/install -c -m 644 ./Data/qrna/coding.fa ./Data/qrna/tRNA.fa '/usr/local/Cellar/viennarna/2.6.3/share/ViennaRNA/tutorial/qrna'
.././config/install-sh -c -d '/usr/local/Cellar/viennarna/2.6.3/share/ViennaRNA/tutorial/rnaz'
.././config/install-sh -c -d '/usr/local/Cellar/viennarna/2.6.3/share/ViennaRNA/tutorial/rnaz/herpes'
/usr/bin/install -c -m 644 ./Data/rnaz/IRE.aln ./Data/rnaz/snoRNA.aln ./Data/rnaz/tRNA.aln ./Data/rnaz/unknown.aln ./Data/rnaz/miRNA.maf ./Data/rnaz/tRNA.maf '/usr/local/Cellar/viennarna/2.6.3/share/ViennaRNA/tutorial/rnaz'
/usr/bin/install -c -m 644 ./Data/rnaz/herpes/annotation.bed ./Data/rnaz/herpes/NC_004367 ./Data/rnaz/herpes/NC_006146 ./Data/rnaz/herpes/NC_007605 '/usr/local/Cellar/viennarna/2.6.3/share/ViennaRNA/tutorial/rnaz/herpes'
.././config/install-sh -c -d '/usr/local/Cellar/viennarna/2.6.3/share/ViennaRNA/tutorial/rnaz/herpes/x'
.././config/install-sh -c -d '/usr/local/Cellar/viennarna/2.6.3/share/ViennaRNA/tutorial/rnaz/human'
/usr/bin/install -c -m 644 ./Data/rnaz/herpes/x/annotation.bed ./Data/rnaz/herpes/x/NC_006146.NC_004367.orig.maf ./Data/rnaz/herpes/x/NC_006146.NC_004367.sing.maf ./Data/rnaz/herpes/x/NC_007605.NC_004367.orig.maf ./Data/rnaz/herpes/x/NC_007605.NC_004367.sing.maf ./Data/rnaz/herpes/x/NC_007605.NC_006146.orig.maf ./Data/rnaz/herpes/x/NC_007605.NC_006146.sing.maf ./Data/rnaz/herpes/x/final.maf ./Data/rnaz/herpes/x/random.maf ./Data/rnaz/herpes/x/raw-tba.maf ./Data/rnaz/herpes/x/windows.maf ./Data/rnaz/herpes/x/windows_random.maf ./Data/rnaz/herpes/x/results.dat ./Data/rnaz/herpes/x/results_annotated.dat ./Data/rnaz/herpes/x/results_random.dat ./Data/rnaz/herpes/x/rnaz.out ./Data/rnaz/herpes/x/rnaz_random.out '/usr/local/Cellar/viennarna/2.6.3/share/ViennaRNA/tutorial/rnaz/herpes/x'
/usr/bin/install -c -m 644 ./Data/rnaz/human/annotation.bed '/usr/local/Cellar/viennarna/2.6.3/share/ViennaRNA/tutorial/rnaz/human'
.././config/install-sh -c -d '/usr/local/Cellar/viennarna/2.6.3/share/ViennaRNA/tutorial/rnaz/human/x'
/usr/bin/install -c -m 644 ./Data/rnaz/human/x/annotation.bed ./Data/rnaz/human/x/prediction.bed ./Data/rnaz/human/x/region.maf ./Data/rnaz/human/x/windows.maf ./Data/rnaz/human/x/results.dat ./Data/rnaz/human/x/results_annotated.dat ./Data/rnaz/human/x/rnaz.out '/usr/local/Cellar/viennarna/2.6.3/share/ViennaRNA/tutorial/rnaz/human/x'
test -f ./RNA-tutorial-2.6.3.pdf || ln -s ./RNA-tutorial-2.6.3.pdf ./RNA-tutorial-2.6.3.pdf
/usr/bin/install -c -m 644 ./RNA-tutorial-2.6.3.pdf /usr/local/Cellar/viennarna/2.6.3/share/doc/ViennaRNA
{ test ! -h ./RNA-tutorial-2.6.3.pdf || rm -f ./RNA-tutorial-2.6.3.pdf; }
Making install in interfaces
Making install in Perl
SWIG RNA_wrap.cpp
SWIG RNA.pm
./../neighbor.i:5: Warning 453: Can't apply (std::vector< vrna_move_t > *OUTPUT). No typemaps are defined.
./../neighbor.i:5: Warning 453: Can't apply (std::vector< vrna_move_t > *OUTPUT). No typemaps are defined.
CXX RNA_la-RNA_wrap.lo
CXXLD RNA.la
GEN auto/RNA/RNA.bundle
make[3]: Nothing to be done for `install-exec-am'.
../.././config/install-sh -c -d '/usr/local/Cellar/viennarna/2.6.3/Library/Perl/5.30'
../.././config/install-sh -c -d '/usr/local/Cellar/viennarna/2.6.3/Library/Perl/5.30/RNA'
/usr/bin/install -c -m 644 RNA/Benchmark.pm RNA/Design.pm RNA/Files.pm RNA/Reliability.pm RNA/Utils.pm RNA/Params.pm '/usr/local/Cellar/viennarna/2.6.3/Library/Perl/5.30/RNA'
../.././config/install-sh -c -d '/usr/local/Cellar/viennarna/2.6.3/Library/Perl/5.30/darwin-thread-multi-2level/auto/RNA'
/usr/bin/install -c -m 644 RNA.pm '/usr/local/Cellar/viennarna/2.6.3/Library/Perl/5.30/.'
/bin/sh ../../libtool --mode=install /usr/bin/install -c RNA.la '/usr/local/Cellar/viennarna/2.6.3/Library/Perl/5.30/darwin-thread-multi-2level/auto/RNA'
libtool: install: /usr/bin/install -c .libs/RNA.bundle /usr/local/Cellar/viennarna/2.6.3/Library/Perl/5.30/darwin-thread-multi-2level/auto/RNA/RNA.bundle
libtool: install: /usr/bin/install -c .libs/RNA.lai /usr/local/Cellar/viennarna/2.6.3/Library/Perl/5.30/darwin-thread
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