| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-26 06:18:08 -0000 (Fri, 26 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4254 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 755/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gdsfmt 1.37.0 (landing page) Xiuwen Zheng
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: gdsfmt |
| Version: 1.37.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings gdsfmt_1.37.0.tar.gz |
| StartedAt: 2023-05-26 04:41:57 -0000 (Fri, 26 May 2023) |
| EndedAt: 2023-05-26 04:42:09 -0000 (Fri, 26 May 2023) |
| EllapsedTime: 12.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: gdsfmt.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings gdsfmt_1.37.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/gdsfmt.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘gdsfmt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gdsfmt’ version ‘1.37.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
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: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 45.4Mb
sub-directories of 1Mb or more:
libs 44.7Mb
* 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 R 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 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘gdsfmt.Rmd’... failed to complete the test
ERROR
Errors in running code in vignettes:
when running code in ‘gdsfmt.Rmd’
...
> proc.time()
user system elapsed
0.168 0.038 0.200
... incomplete output. Crash?
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX Warning in close.connection(con) :
Problem closing connection: No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) :
Error writing to connection: No space left on device
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/gdsfmt.Rcheck/00check.log’
for details.
gdsfmt.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL gdsfmt ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘gdsfmt’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c R_CoreArray.cpp -o R_CoreArray.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c gdsfmt.cpp -o gdsfmt.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c digest.cpp -o digest.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dAny.cpp -o CoreArray/dAny.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dBase.cpp -o CoreArray/dBase.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dFile.cpp -o CoreArray/dFile.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dRealGDS.cpp -o CoreArray/dRealGDS.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dStrGDS.cpp -o CoreArray/dStrGDS.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dStream.cpp -o CoreArray/dStream.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dSparse.cpp -o CoreArray/dSparse.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c -g0 ZLIB/adler32.c -o ZLIB/adler32.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c -g0 ZLIB/compress.c -o ZLIB/compress.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c -g0 ZLIB/crc32.c -o ZLIB/crc32.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c -g0 ZLIB/deflate.c -o ZLIB/deflate.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c -g0 ZLIB/infback.c -o ZLIB/infback.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c -g0 ZLIB/inffast.c -o ZLIB/inffast.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c -g0 ZLIB/inflate.c -o ZLIB/inflate.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c -g0 ZLIB/inftrees.c -o ZLIB/inftrees.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c -g0 ZLIB/trees.c -o ZLIB/trees.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c -g0 ZLIB/uncompr.c -o ZLIB/uncompr.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c -g0 ZLIB/zutil.c -o ZLIB/zutil.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c LZ4/lz4.c -o LZ4/lz4.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c LZ4/lz4hc.c -o LZ4/lz4hc.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -c LZ4/lz4frame.c -o LZ4/lz4frame.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -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 '/home/biocbuild/bbs-3.18-bioc/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' Making all in api make[2]: Entering directory '/home/biocbuild/bbs-3.18-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-3.18-bioc/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma/api' make[2]: Entering directory '/home/biocbuild/bbs-3.18-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-3.18-bioc/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' make[1]: Leaving directory '/home/biocbuild/bbs-3.18-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 g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/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-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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)