From 7affdcc006a4d692d616f708f971f99c5d38840b Mon Sep 17 00:00:00 2001 From: aliciaaevans Date: Thu, 26 Dec 2024 22:47:22 +0000 Subject: [PATCH] biocondcutor-cner: add zlib --- .../build_failure.linux-64.yaml | 104 ------------------ recipes/bioconductor-cner/meta.yaml | 1 + 2 files changed, 1 insertion(+), 104 deletions(-) delete mode 100644 recipes/bioconductor-cner/build_failure.linux-64.yaml diff --git a/recipes/bioconductor-cner/build_failure.linux-64.yaml b/recipes/bioconductor-cner/build_failure.linux-64.yaml deleted file mode 100644 index b46f148c90656..0000000000000 --- a/recipes/bioconductor-cner/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 2da629bd37cd69e277b86fb493dd5f941f056cff065a2801166dfc41a274519f # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: false # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip - 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$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/dystring.c -o ucsc/dystring.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/errabort.c -o ucsc/errabort.o - 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$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/intExp.c -o ucsc/intExp.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/kxTok.c -o ucsc/kxTok.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/linefile.c -o ucsc/linefile.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/localmem.c -o ucsc/localmem.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/memalloc.c -o ucsc/memalloc.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/obscure.c -o ucsc/obscure.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/options.c -o ucsc/options.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/pipeline.c -o ucsc/pipeline.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/_portimpl.c -o ucsc/_portimpl.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/sqlList.c -o ucsc/sqlList.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/sqlNum.c -o ucsc/sqlNum.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/verbose.c -o ucsc/verbose.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/os.c -o ucsc/os.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/S4Vectors/include' -I'$PREFIX/lib/R/library/IRanges/include' -I'$PREFIX/lib/R/library/XVector/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -g -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ucsc/wildcmp.c -o ucsc/wildcmp.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -shared -L$PREFIX/lib/R/lib -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$PREFIX/lib -o CNEr.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lz -L$PREFIX/lib/R/lib -lR - /opt/conda/conda-bld/bioconductor-cner_1735248520367/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory - collect2: error: ld returned 1 exit status - make: *** [/opt/conda/conda-bld/bioconductor-cner_1735248520367/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/R/share/make/shlib.mk:10: CNEr.so] Error 1 - ERROR: compilation failed for package CNEr - * removing /opt/conda/conda-bld/bioconductor-cner_1735248520367/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/R/library/CNEr - Traceback (most recent call last): - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-cner_1735248520367/work/conda_build.sh']' returned non-zero exit status 1. - - The above exception was the direct cause of the following exception: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build - raise BuildScriptException(str(exc), caused_by=exc) from exc - conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-cner_1735248520367/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-cner/meta.yaml b/recipes/bioconductor-cner/meta.yaml index f7ebb95c90227..1087a7628f691 100644 --- a/recipes/bioconductor-cner/meta.yaml +++ b/recipes/bioconductor-cner/meta.yaml @@ -62,6 +62,7 @@ requirements: - r-rsqlite >=0.11.4 - libblas - liblapack + - zlib run: - bioconductor-annotate >=1.84.0,<1.85.0