aelkhouly85
commented
3 years ago I could resolve this issue by using different cmake version , but now it is stopped here.
Install the project... -- Install configuration: "Release" -- Installing: /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/cget/cget/pkg/xiaoyelisuperlu/install/lib64/pkgconfig/superlu.pc -- Installing: /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/cget/cget/pkg/xiaoyelisuperlu/install/lib64/libsuperlu.a -- Installing: /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/cget/cget/pkg/xiaoyelisuperlu/install/include/supermatrix.h -- Installing: /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/cget/cget/pkg/xiaoyelisuperlu/install/include/slu_Cnames.h -- Installing: /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/cget/cget/pkg/xiaoyelisuperlu/install/include/slu_dcomplex.h -- Installing: /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/cget/cget/pkg/xiaoyeli__superlu/install/include/slu_scomplex.h -- Installing: /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/cget/cget/pkg/xiaoyelisuperlu/install/include/slu_util.h -- Installing: /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/cget/cget/pkg/xiaoyelisuperlu/install/include/superlu_enum_consts.h -- Installing: /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/cget/cget/pkg/xiaoyelisuperlu/install/include/slu_sdefs.h -- Installing: /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/cget/cget/pkg/xiaoyelisuperlu/install/include/slu_ddefs.h -- Installing: /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/cget/cget/pkg/xiaoyeli__superlu/install/include/slu_cdefs.h -- Installing: /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/cget/cget/pkg/xiaoyelisuperlu/install/include/slu_zdefs.h Successfully installed xiaoyeli/superlu invalid lock file in /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/bgen Setting top to : /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/bgen Setting out to : /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/bgen/build Checking for 'gcc' (C compiler) : /xx/xx/xx/SAIGE/0.44.5/envs/RSAIGE/bin/x86_64-conda_cos6-linux-gnu-cc Checking for 'g++' (C++ compiler) : /xx/xx/xx/xx/xx/envs/RSAIGE/bin/x86_64-conda_cos6-linux-gnu-c++ zlib : not found The configuration failed (complete log in /tmp/RtmpS4c3u3/R.INSTALL3f3418b2f990/SAIGE/thirdParty/bgen/build/config.log) ERROR: configuration failed for package ‘SAIGE’
- removing ‘/gpfs/software/genomics/SAIGE/0.44.5/envs/RSAIGE/lib/R/library/SAIGE’ Error: Failed to install 'SAIGE' from GitHub: (converted from warning) installation of package ‘/tmp/Rtmp5OR29G/file33e43e5371ee/SAIGE_0.44.5.tar.gz’ had non-zero exit status
jingydz
Hello
I'm trting to install the latest Saige using Conda but it is not getting successful because of the below issue, can you please help?
[ 33%] Building CXX object CMakeFiles/sav.dir/src/sav/import.cpp.o [ 50%] Building CXX object CMakeFiles/sav.dir/src/sav/head.cpp.o [ 50%] Building CXX object CMakeFiles/sav.dir/src/sav/merge.cpp.o [ 58%] Building CXX object CMakeFiles/sav.dir/src/sav/rehead.cpp.o [ 66%] Building CXX object CMakeFiles/sav.dir/src/sav/index.cpp.o [ 75%] Building CXX object CMakeFiles/sav.dir/src/sav/sort.cpp.o [ 91%] Building CXX object CMakeFiles/sav.dir/src/sav/utility.cpp.o [ 91%] Building CXX object CMakeFiles/sav.dir/src/sav/stat.cpp.o In file included from /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/include/savvy/reader.hpp:13:0, from /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/src/sav/concat.cpp:9: /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/include/savvy/csi.hpp:10:10: fatal error: shrinkwrap/gz.hpp: No such file or directory
include <shrinkwrap/gz.hpp>
compilation terminated. make[2]: [CMakeFiles/sav.dir/build.make:76: CMakeFiles/sav.dir/src/sav/concat.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... In file included from /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/include/savvy/reader.hpp:13:0, from /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/src/sav/index.cpp:9: /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/include/savvy/csi.hpp:10:10: fatal error: shrinkwrap/gz.hpp: No such file or directory
include <shrinkwrap/gz.hpp>
compilation terminated. make[2]: *** [CMakeFiles/sav.dir/build.make:128: CMakeFiles/sav.dir/src/sav/index.cpp.o] Error 1 In file included from /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/include/savvy/reader.hpp:13:0, from /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/src/sav/rehead.cpp:9: /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/include/savvy/csi.hpp:10:10: fatal error: shrinkwrap/gz.hpp: No such file or directory
include <shrinkwrap/gz.hpp>
compilation terminated. In file included from /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/include/savvy/reader.hpp:13:0, from /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/src/sav/head.cpp:8: /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/include/savvy/csi.hpp:10:10: fatal error: shrinkwrap/gz.hpp: No such file or directory
include <shrinkwrap/gz.hpp>
compilation terminated. make[2]: [CMakeFiles/sav.dir/build.make:154: CMakeFiles/sav.dir/src/sav/rehead.cpp.o] Error 1 make[2]: [CMakeFiles/sav.dir/build.make:102: CMakeFiles/sav.dir/src/sav/head.cpp.o] Error 1 In file included from /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/include/savvy/reader.hpp:13:0, from /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/src/sav/stat.cpp:11: /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/include/savvy/csi.hpp:10:10: fatal error: shrinkwrap/gz.hpp: No such file or directory
include <shrinkwrap/gz.hpp>
compilation terminated. make[2]: *** [CMakeFiles/sav.dir/build.make:180: CMakeFiles/sav.dir/src/sav/stat.cpp.o] Error 1 In file included from /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/src/sav/main.cpp:14:0: /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/include/sav/sort.hpp:13:10: fatal error: shrinkwrap/zstd.hpp: No such file or directory
include <shrinkwrap/zstd.hpp>
compilation terminated. make[2]: *** [CMakeFiles/sav.dir/build.make:63: CMakeFiles/sav.dir/src/sav/main.cpp.o] Error 1 In file included from /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/src/sav/sort.cpp:7:0: /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/include/sav/sort.hpp:13:10: fatal error: shrinkwrap/zstd.hpp: No such file or directory
include <shrinkwrap/zstd.hpp>
compilation terminated. make[2]: *** [CMakeFiles/sav.dir/build.make:167: CMakeFiles/sav.dir/src/sav/sort.cpp.o] Error 1 In file included from /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/src/sav/export.cpp:9:0: /tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/savvy-2.0.1/include/sav/sort.hpp:13:10: fatal error: shrinkwrap/zstd.hpp: No such file or directory
include <shrinkwrap/zstd.hpp>
compilation terminated. make[2]: [CMakeFiles/sav.dir/build.make:89: CMakeFiles/sav.dir/src/sav/export.cpp.o] Error 1 make[1]: [CMakeFiles/Makefile2:73: CMakeFiles/sav.dir/all] Error 2 gmake: *** [all] Error 2 Command failed: ['/path/path/path/SAIGE/0.44.5/envs/RSAIGE/bin/cmake', '--build', u'/tmp/RtmpBsny8R/R.INSTALL46254803656d/SAIGE/thirdParty/cget/cget/build/tmp-26ff8f0417844f4fb68dcb122aa38ddf/build', '--config', 'Release', '--', '-j', '32'] Failed to build package statgen/savvy ERROR: configuration failed for package ‘SAIGE’