Xiuwen Zheng
| Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022) |
| git_url: https://git.bioconductor.org/packages/gdsfmt |
| git_branch: master |
| git_last_commit: a71f957 |
| git_last_commit_date: 2022-04-26 11:23:25 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.16 |
|
This page was generated on 2022-07-07 11:11:10 -0400 (Thu, 07 Jul 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" | 4343 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" | 4148 |
| lconway | macOS 12.2.1 Monterey | x86_64 | 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" | 4160 |
| kjohnson | macOS 12.4 Monterey | arm64 | 4.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" | 3115 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the gdsfmt package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gdsfmt.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 726/2124 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gdsfmt 1.33.0 (landing page) Xiuwen Zheng
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.2.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson | macOS 12.4 Monterey / arm64 | OK | OK | NA | ERROR | |||||||||
| Package: gdsfmt |
| Version: 1.33.0 |
| Command: rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gdsfmt_1.33.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gdsfmt.buildbin-libdir |
| StartedAt: 2022-07-07 08:00:54 -0400 (Thu, 07 Jul 2022) |
| EndedAt: 2022-07-07 08:08:31 -0400 (Thu, 07 Jul 2022) |
| EllapsedTime: 457.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gdsfmt_1.33.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gdsfmt.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gdsfmt.buildbin-libdir gdsfmt_1.33.0.tar.gz' >>>>>>> * installing *source* package ‘gdsfmt’ ... ** using staged installation ** libs clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_CoreArray.cpp -o R_CoreArray.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gdsfmt.cpp -o gdsfmt.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c digest.cpp -o digest.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dAny.cpp -o CoreArray/dAny.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dBase.cpp -o CoreArray/dBase.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dFile.cpp -o CoreArray/dFile.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dRealGDS.cpp -o CoreArray/dRealGDS.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dStrGDS.cpp -o CoreArray/dStrGDS.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dStream.cpp -o CoreArray/dStream.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dSparse.cpp -o CoreArray/dSparse.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/adler32.c -o ZLIB/adler32.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/compress.c -o ZLIB/compress.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/crc32.c -o ZLIB/crc32.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/deflate.c -o ZLIB/deflate.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/infback.c -o ZLIB/infback.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/inffast.c -o ZLIB/inffast.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/inflate.c -o ZLIB/inflate.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/inftrees.c -o ZLIB/inftrees.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/trees.c -o ZLIB/trees.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/uncompr.c -o ZLIB/uncompr.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/zutil.c -o ZLIB/zutil.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LZ4/lz4.c -o LZ4/lz4.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LZ4/lz4hc.c -o LZ4/lz4hc.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LZ4/lz4frame.c -o LZ4/lz4frame.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LZ4/xxhash.c -o LZ4/xxhash.o cd XZ && tar -xzf xz-5.2.5.tar.gz cd XZ/xz-5.2.5 && \ ./configure CC="clang -arch arm64" CPP="clang -arch arm64 -E" CXX="clang++ -arch arm64 -std=gnu++14" CXXCPP="" --build="" \ --with-pic --enable-silent-rules --quiet --disable-xz > /dev/null configure: WARNING: immintrin.h: present but cannot be compiled configure: WARNING: immintrin.h: check for missing prerequisite headers? configure: WARNING: immintrin.h: see the Autoconf documentation configure: WARNING: immintrin.h: section "Present But Cannot Be Compiled" configure: WARNING: immintrin.h: proceeding with the compiler's result configure: WARNING: ## --------------------------------------- ## configure: WARNING: ## Report this to lasse.collin@tukaani.org ## configure: WARNING: ## --------------------------------------- ## cd XZ/xz-5.2.5/src/liblzma && make Making all in api make[2]: Nothing to be done for `all'. CC liblzma_la-tuklib_physmem.lo CC liblzma_la-tuklib_cpucores.lo CC liblzma_la-common.lo CC liblzma_la-block_util.lo CC liblzma_la-easy_preset.lo CC liblzma_la-filter_common.lo CC liblzma_la-hardware_physmem.lo CC liblzma_la-index.lo CC liblzma_la-stream_flags_common.lo CC liblzma_la-vli_size.lo CC liblzma_la-hardware_cputhreads.lo CC liblzma_la-alone_encoder.lo CC liblzma_la-block_buffer_encoder.lo CC liblzma_la-block_encoder.lo CC liblzma_la-block_header_encoder.lo CC liblzma_la-easy_buffer_encoder.lo CC liblzma_la-easy_encoder.lo CC liblzma_la-easy_encoder_memusage.lo CC liblzma_la-filter_buffer_encoder.lo CC liblzma_la-filter_encoder.lo CC liblzma_la-filter_flags_encoder.lo CC liblzma_la-index_encoder.lo CC liblzma_la-stream_buffer_encoder.lo CC liblzma_la-stream_encoder.lo CC liblzma_la-stream_flags_encoder.lo CC liblzma_la-vli_encoder.lo CC liblzma_la-outqueue.lo CC liblzma_la-stream_encoder_mt.lo CC liblzma_la-alone_decoder.lo CC liblzma_la-auto_decoder.lo CC liblzma_la-block_buffer_decoder.lo CC liblzma_la-block_decoder.lo CC liblzma_la-block_header_decoder.lo CC liblzma_la-easy_decoder_memusage.lo CC liblzma_la-filter_buffer_decoder.lo CC liblzma_la-filter_decoder.lo CC liblzma_la-filter_flags_decoder.lo CC liblzma_la-index_decoder.lo CC liblzma_la-index_hash.lo CC liblzma_la-stream_buffer_decoder.lo CC liblzma_la-stream_decoder.lo CC liblzma_la-stream_flags_decoder.lo CC liblzma_la-vli_decoder.lo CC liblzma_la-check.lo CC liblzma_la-crc32_table.lo CC liblzma_la-crc32_fast.lo CC liblzma_la-crc64_table.lo CC liblzma_la-crc64_fast.lo CC liblzma_la-sha256.lo CC liblzma_la-lz_encoder.lo CC liblzma_la-lz_encoder_mf.lo CC liblzma_la-lz_decoder.lo CC liblzma_la-lzma_encoder_presets.lo CC liblzma_la-lzma_encoder.lo CC liblzma_la-lzma_encoder_optimum_fast.lo CC liblzma_la-lzma_encoder_optimum_normal.lo CC liblzma_la-fastpos_table.lo CC liblzma_la-lzma_decoder.lo CC liblzma_la-lzma2_encoder.lo CC liblzma_la-lzma2_decoder.lo CC liblzma_la-price_table.lo CC liblzma_la-delta_common.lo CC liblzma_la-delta_encoder.lo CC liblzma_la-delta_decoder.lo CC liblzma_la-simple_coder.lo CC liblzma_la-simple_encoder.lo CC liblzma_la-simple_decoder.lo CC liblzma_la-x86.lo CC liblzma_la-powerpc.lo CC liblzma_la-ia64.lo CC liblzma_la-arm.lo CC liblzma_la-armthumb.lo CC liblzma_la-sparc.lo CCLD liblzma.la PC liblzma.pc cp XZ/xz-5.2.5/src/liblzma/.libs/liblzma.a . rm -rf XZ/xz-5.2.5/dos rm -rf XZ/xz-5.2.5/po clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o gdsfmt.so R_CoreArray.o gdsfmt.o digest.o CoreArray/CoreArray.o CoreArray/dAllocator.o CoreArray/dAny.o CoreArray/dBase.o CoreArray/dBitGDS.o CoreArray/dEndian.o CoreArray/dFile.o CoreArray/dParallel.o CoreArray/dParallel_Ext.o CoreArray/dPlatform.o CoreArray/dRealGDS.o CoreArray/dSerial.o CoreArray/dStrGDS.o CoreArray/dStream.o CoreArray/dStruct.o CoreArray/dSparse.o CoreArray/dVLIntGDS.o ZLIB/adler32.o ZLIB/compress.o ZLIB/crc32.o ZLIB/deflate.o ZLIB/infback.o ZLIB/inffast.o ZLIB/inflate.o ZLIB/inftrees.o ZLIB/trees.o ZLIB/uncompr.o ZLIB/zutil.o LZ4/lz4.o LZ4/lz4hc.o LZ4/lz4frame.o LZ4/xxhash.o ./liblzma.a -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.16-bioc/meat/gdsfmt.buildbin-libdir/00LOCK-gdsfmt/00new/gdsfmt/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gdsfmt) >>>>>>> >>>>>>> FIXING LINKS FOR gdsfmt.buildbin-libdir/gdsfmt/libs/gdsfmt.so >>>>>>> ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib not found!