| Back to Rapid builds (Linux only) of a subset of BioC 3.21 Report updated every 6 hours |
This page was generated on 2024-12-23 09:40 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-12-18 r87448) -- "Unsuffered Consequences" | 852 |
| 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 | ||||
| Package 91/216 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| gdsfmt 1.43.0 (landing page) Xiuwen Zheng
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
|
To the developers/maintainers of the gdsfmt package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: gdsfmt |
| Version: 1.43.0 |
| Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL gdsfmt |
| StartedAt: 2024-12-23 06:06:14 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 06:09:35 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 200.6 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL gdsfmt ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’ * installing *source* package ‘gdsfmt’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c R_CoreArray.cpp -o R_CoreArray.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c gdsfmt.cpp -o gdsfmt.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c digest.cpp -o digest.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dAny.cpp -o CoreArray/dAny.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dBase.cpp -o CoreArray/dBase.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dFile.cpp -o CoreArray/dFile.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dRealGDS.cpp -o CoreArray/dRealGDS.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dStrGDS.cpp -o CoreArray/dStrGDS.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dStream.cpp -o CoreArray/dStream.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dSparse.cpp -o CoreArray/dSparse.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c -g0 ZLIB/adler32.c -o ZLIB/adler32.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c -g0 ZLIB/compress.c -o ZLIB/compress.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c -g0 ZLIB/crc32.c -o ZLIB/crc32.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c -g0 ZLIB/deflate.c -o ZLIB/deflate.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c -g0 ZLIB/infback.c -o ZLIB/infback.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c -g0 ZLIB/inffast.c -o ZLIB/inffast.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c -g0 ZLIB/inflate.c -o ZLIB/inflate.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c -g0 ZLIB/inftrees.c -o ZLIB/inftrees.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c -g0 ZLIB/trees.c -o ZLIB/trees.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c -g0 ZLIB/uncompr.c -o ZLIB/uncompr.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c -g0 ZLIB/zutil.c -o ZLIB/zutil.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c LZ4/lz4.c -o LZ4/lz4.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c LZ4/lz4hc.c -o LZ4/lz4hc.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c LZ4/lz4frame.c -o LZ4/lz4frame.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c LZ4/xxhash.c -o LZ4/xxhash.o cd XZ && tar -xzf xz-5.2.9.tar.gz cd XZ/xz-5.2.9 && \ ./configure CC="gcc" CPP="gcc -E" CXX="g++ -std=gnu++17" CXXCPP="" --build="" \ --with-pic --enable-silent-rules --quiet --disable-xz --disable-shared > /dev/null cd XZ/xz-5.2.9/src/liblzma && make make[1]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' Making all in api make[2]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma/api' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma/api' make[2]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' 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 make[2]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' make[1]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' cp XZ/xz-5.2.9/src/liblzma/.libs/liblzma.a . rm -rf XZ/xz-5.2.9/dos rm -rf XZ/xz-5.2.9/po g++ -std=gnu++17 -shared -L/usr/local/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 installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/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)