Xiuwen Zheng
| Snapshot Date: 2024-11-01 13:40 -0400 (Fri, 01 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/gdsfmt |
| git_branch: RELEASE_3_20 |
| git_last_commit: 8dd26f3 |
| git_last_commit_date: 2024-10-29 09:57:52 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-02 12:07 -0400 (Sat, 02 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4500 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4505 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 783/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gdsfmt 1.42.0 (landing page) Xiuwen Zheng
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.42.0 |
| 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_1.42.0.tar.gz |
| StartedAt: 2024-11-02 07:38:28 -0000 (Sat, 02 Nov 2024) |
| EndedAt: 2024-11-02 07:41:07 -0000 (Sat, 02 Nov 2024) |
| EllapsedTime: 159.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: gdsfmt.Rcheck |
| Warnings: 1 |
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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_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gdsfmt.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gdsfmt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gdsfmt’ version ‘1.42.0’
* 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 ... WARNING
Found the following significant warnings:
CoreArray/dFile.cpp:129:17: warning: ignoring return value of 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::at(size_type) [with _Tp = CoreArray::CdObjAttr::TdPair*; _Alloc = std::allocator<CoreArray::CdObjAttr::TdPair*>; reference = CoreArray::CdObjAttr::TdPair*&; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/gdsfmt.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... NOTE
installed size is 31.9Mb
sub-directories of 1Mb or more:
libs 31.2Mb
* 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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/gdsfmt.Rcheck/00check.log’
for details.
gdsfmt.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL gdsfmt
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘gdsfmt’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c R_CoreArray.cpp -o R_CoreArray.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c gdsfmt.cpp -o gdsfmt.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c digest.cpp -o digest.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dAny.cpp -o CoreArray/dAny.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dBase.cpp -o CoreArray/dBase.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dFile.cpp -o CoreArray/dFile.o
CoreArray/dFile.cpp: In member function 'void CoreArray::CdObjAttr::Delete(int)':
CoreArray/dFile.cpp:129:17: warning: ignoring return value of 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::at(size_type) [with _Tp = CoreArray::CdObjAttr::TdPair*; _Alloc = std::allocator<CoreArray::CdObjAttr::TdPair*>; reference = CoreArray::CdObjAttr::TdPair*&; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result]
129 | fList.at(Index); // check range
| ~~~~~~~~^~~~~~~
In file included from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/vector:66,
from CoreArray/dPlatform.h:48,
from CoreArray/dEndian.h:40,
from CoreArray/dBase.h:41,
from CoreArray/dFile.h:40,
from CoreArray/dFile.cpp:28:
/home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:1180:7: note: declared here
1180 | at(size_type __n)
| ^~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dRealGDS.cpp -o CoreArray/dRealGDS.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dStrGDS.cpp -o CoreArray/dStrGDS.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dStream.cpp -o CoreArray/dStream.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dSparse.cpp -o CoreArray/dSparse.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c -g0 ZLIB/adler32.c -o ZLIB/adler32.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c -g0 ZLIB/compress.c -o ZLIB/compress.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c -g0 ZLIB/crc32.c -o ZLIB/crc32.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c -g0 ZLIB/deflate.c -o ZLIB/deflate.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c -g0 ZLIB/infback.c -o ZLIB/infback.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c -g0 ZLIB/inffast.c -o ZLIB/inffast.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c -g0 ZLIB/inflate.c -o ZLIB/inflate.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c -g0 ZLIB/inftrees.c -o ZLIB/inftrees.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c -g0 ZLIB/trees.c -o ZLIB/trees.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c -g0 ZLIB/uncompr.c -o ZLIB/uncompr.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c -g0 ZLIB/zutil.c -o ZLIB/zutil.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c LZ4/lz4.c -o LZ4/lz4.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c LZ4/lz4hc.c -o LZ4/lz4hc.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -c LZ4/lz4frame.c -o LZ4/lz4frame.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fPIC -g -O2 -Wall -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-3.20-bioc/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma'
Making all in api
make[2]: Entering directory '/home/biocbuild/bbs-3.20-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-3.20-bioc/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma/api'
make[2]: Entering directory '/home/biocbuild/bbs-3.20-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-3.20-bioc/meat/gdsfmt/src/XZ/xz-5.2.9/src/liblzma'
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-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-4.4.1/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-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life"
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Platform: aarch64-unknown-linux-gnu
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> options(test.verbose=FALSE)
> BiocGenerics:::testPackage("gdsfmt")
RUNIT TEST PROTOCOL -- Sat Nov 2 07:41:03 2024
***********************************************
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
121.373 7.766 130.996
gdsfmt.Rcheck/gdsfmt-Ex.timings
| name | user | system | elapsed | |
| add.gdsn | 0.121 | 0.011 | 0.149 | |
| addfile.gdsn | 0.007 | 0.000 | 0.008 | |
| addfolder.gdsn | 0.030 | 0.001 | 0.030 | |
| append.gdsn | 0.020 | 0.003 | 0.024 | |
| apply.gdsn | 0.033 | 0.001 | 0.036 | |
| assign.gdsn | 0.024 | 0.004 | 0.028 | |
| cache.gdsn | 0.003 | 0.000 | 0.004 | |
| cleanup.gds | 0.016 | 0.000 | 0.016 | |
| closefn.gds | 0.001 | 0.000 | 0.002 | |
| clusterApply.gdsn | 0.045 | 0.004 | 0.559 | |
| cnt.gdsn | 0.001 | 0.000 | 0.002 | |
| compression.gdsn | 0.002 | 0.004 | 0.008 | |
| copyto.gdsn | 0.035 | 0.000 | 0.036 | |
| createfn.gds | 0.009 | 0.000 | 0.010 | |
| delete.attr.gdsn | 0.001 | 0.003 | 0.006 | |
| delete.gdsn | 0.009 | 0.000 | 0.009 | |
| diagnosis.gds | 0.016 | 0.000 | 0.015 | |
| digest.gdsn | 0.052 | 0.004 | 0.060 | |
| exist.gdsn | 0.001 | 0.000 | 0.003 | |
| gdsfmt-package | 0.037 | 0.012 | 0.051 | |
| get.attr.gdsn | 0.005 | 0.000 | 0.006 | |
| getfile.gdsn | 0.004 | 0.004 | 0.008 | |
| getfolder.gdsn | 0.049 | 0.000 | 0.050 | |
| index.gdsn | 0.023 | 0.040 | 0.065 | |
| is.element.gdsn | 0.004 | 0.000 | 0.004 | |
| is.sparse.gdsn | 1.467 | 0.075 | 1.548 | |
| lasterr.gds | 0 | 0 | 0 | |
| ls.gdsn | 0.001 | 0.000 | 0.002 | |
| moveto.gdsn | 0.042 | 0.004 | 0.047 | |
| name.gdsn | 0.000 | 0.001 | 0.002 | |
| objdesp.gdsn | 0.008 | 0.001 | 0.010 | |
| openfn.gds | 0.007 | 0.000 | 0.008 | |
| permdim.gdsn | 0.011 | 0.000 | 0.012 | |
| print.gds.class | 0.023 | 0.000 | 0.024 | |
| put.attr.gdsn | 0.005 | 0.000 | 0.005 | |
| read.gdsn | 0.011 | 0.007 | 0.020 | |
| readex.gdsn | 0.005 | 0.004 | 0.010 | |
| readmode.gdsn | 0.004 | 0.000 | 0.005 | |
| rename.gdsn | 0.006 | 0.000 | 0.008 | |
| setdim.gdsn | 0.010 | 0.004 | 0.016 | |
| showfile.gds | 0.001 | 0.004 | 0.004 | |
| summarize.gdsn | 0.002 | 0.000 | 0.003 | |
| sync.gds | 0.004 | 0.000 | 0.006 | |
| system.gds | 0.000 | 0.004 | 0.005 | |
| unload.gdsn | 0.004 | 0.001 | 0.005 | |
| write.gdsn | 0.000 | 0.002 | 0.002 | |