Xiuwen Zheng
| Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/gdsfmt |
| git_branch: devel |
| git_last_commit: caccdd9 |
| git_last_commit_date: 2025-10-09 21:39:06 -0400 (Thu, 09 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 804/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gdsfmt 1.45.2 (landing page) Xiuwen Zheng
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the gdsfmt package: - 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 Troubleshooting Build Report for more information. - 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: gdsfmt |
| Version: 1.45.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gdsfmt_1.45.2.tar.gz |
| StartedAt: 2025-10-17 09:16:47 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 09:19:13 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 146.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gdsfmt.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gdsfmt_1.45.2.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/gdsfmt.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gdsfmt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gdsfmt’ version ‘1.45.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gdsfmt’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
installed size is 32.0Mb
sub-directories of 1Mb or more:
libs 31.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/gdsfmt.Rcheck/00check.log’
for details.
gdsfmt.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL gdsfmt ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘gdsfmt’ ... ** this is package ‘gdsfmt’ version ‘1.45.2’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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 R_CoreArray.cpp -o R_CoreArray.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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 gdsfmt.cpp -o gdsfmt.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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 digest.cpp -o digest.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/CoreArray.cpp -o CoreArray/CoreArray.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dAllocator.cpp -o CoreArray/dAllocator.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dAny.cpp -o CoreArray/dAny.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dBase.cpp -o CoreArray/dBase.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dBitGDS.cpp -o CoreArray/dBitGDS.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dEndian.cpp -o CoreArray/dEndian.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dFile.cpp -o CoreArray/dFile.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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.cpp -o CoreArray/dParallel.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dPlatform.cpp -o CoreArray/dPlatform.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dRealGDS.cpp -o CoreArray/dRealGDS.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dSerial.cpp -o CoreArray/dSerial.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dStrGDS.cpp -o CoreArray/dStrGDS.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dStream.cpp -o CoreArray/dStream.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dStruct.cpp -o CoreArray/dStruct.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dSparse.cpp -o CoreArray/dSparse.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/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/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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="/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23" CPP="/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -E" CXX="/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-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 '/home/biocbuild/bbs-3.22-bioc/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' Making all in api make[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma/api' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma/api' make[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/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 '/home/biocbuild/bbs-3.22-bioc/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' make[1]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -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 -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/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)
gdsfmt.Rcheck/tests/runTests.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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Platform: aarch64-unknown-linux-gnu
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> options(test.verbose=FALSE)
> BiocGenerics:::testPackage("gdsfmt")
RUNIT TEST PROTOCOL -- Fri Oct 17 09:19:08 2025
***********************************************
Number of test functions: 25
Number of errors: 0
Number of failures: 0
1 Test Suite :
gdsfmt RUnit Tests - 25 test functions, 0 errors, 0 failures
Number of test functions: 25
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
106.752 6.361 115.429
gdsfmt.Rcheck/gdsfmt-Ex.timings
| name | user | system | elapsed | |
| add.gdsn | 0.140 | 0.004 | 0.148 | |
| addfile.gdsn | 0.008 | 0.000 | 0.008 | |
| addfolder.gdsn | 0.036 | 0.004 | 0.040 | |
| append.gdsn | 0.021 | 0.000 | 0.023 | |
| apply.gdsn | 0.034 | 0.005 | 0.041 | |
| assign.gdsn | 0.032 | 0.000 | 0.033 | |
| cache.gdsn | 0.003 | 0.000 | 0.004 | |
| cleanup.gds | 0.019 | 0.000 | 0.020 | |
| closefn.gds | 0.000 | 0.001 | 0.003 | |
| clusterApply.gdsn | 0.055 | 0.004 | 0.598 | |
| cnt.gdsn | 0.001 | 0.000 | 0.003 | |
| compression.gdsn | 0.007 | 0.000 | 0.008 | |
| copyto.gdsn | 0.034 | 0.000 | 0.036 | |
| createfn.gds | 0.008 | 0.000 | 0.010 | |
| delete.attr.gdsn | 0.004 | 0.000 | 0.006 | |
| delete.gdsn | 0.009 | 0.000 | 0.014 | |
| diagnosis.gds | 0.011 | 0.003 | 0.015 | |
| digest.gdsn | 0.041 | 0.008 | 0.053 | |
| exist.gdsn | 0.001 | 0.000 | 0.003 | |
| gdsfmt-package | 0.036 | 0.008 | 0.046 | |
| get.attr.gdsn | 0.004 | 0.000 | 0.005 | |
| getfile.gdsn | 0.007 | 0.000 | 0.008 | |
| getfolder.gdsn | 0.048 | 0.000 | 0.050 | |
| index.gdsn | 0.019 | 0.000 | 0.020 | |
| is.element.gdsn | 0.002 | 0.000 | 0.003 | |
| is.sparse.gdsn | 1.226 | 0.048 | 1.281 | |
| lasterr.gds | 0 | 0 | 0 | |
| ls.gdsn | 0.002 | 0.000 | 0.002 | |
| moveto.gdsn | 0.049 | 0.004 | 0.054 | |
| name.gdsn | 0.001 | 0.000 | 0.002 | |
| objdesp.gdsn | 0.006 | 0.004 | 0.011 | |
| openfn.gds | 0.009 | 0.000 | 0.008 | |
| permdim.gdsn | 0.010 | 0.001 | 0.012 | |
| print.gds.class | 0.019 | 0.006 | 0.026 | |
| put.attr.gdsn | 0.005 | 0.000 | 0.006 | |
| read.gdsn | 0.018 | 0.004 | 0.023 | |
| readex.gdsn | 0.009 | 0.000 | 0.010 | |
| readmode.gdsn | 0.001 | 0.002 | 0.005 | |
| rename.gdsn | 0.004 | 0.003 | 0.009 | |
| setdim.gdsn | 0.009 | 0.007 | 0.016 | |
| showfile.gds | 0.005 | 0.000 | 0.005 | |
| summarize.gdsn | 0.002 | 0.000 | 0.003 | |
| sync.gds | 0.005 | 0.000 | 0.006 | |
| system.gds | 0.005 | 0.000 | 0.004 | |
| unload.gdsn | 0.005 | 0.001 | 0.006 | |
| write.gdsn | 0.000 | 0.002 | 0.002 | |