Xiuwen Zheng
| Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/SeqArray |
| git_branch: devel |
| git_last_commit: aac465b |
| git_last_commit_date: 2025-07-31 11:36:25 -0400 (Thu, 31 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 1943/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqArray 1.49.4 (landing page) Xiuwen Zheng
| nebbiolo2 | Linux (Ubuntu 24.04.3 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 | | ||||||||
| 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 SeqArray package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SeqArray.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. |
| Package: SeqArray |
| Version: 1.49.4 |
| Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SeqArray.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings SeqArray_1.49.4.tar.gz |
| StartedAt: 2025-08-15 07:47:46 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 07:50:49 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 182.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SeqArray.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SeqArray.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings SeqArray_1.49.4.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/SeqArray.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SeqArray/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqArray' version '1.49.4'
* 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 whether package 'SeqArray' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* checking installed package size ... OK
* 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 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'seqGDS2VCF.Rd':
'[Rsamtools:zip]{bgzip}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
SeqVarGDSClass-class.Rd: gds.class, DNAStringSet, DNAStringSetList,
DataFrameList
seqAddValue.Rd: add.gdsn
seqApply.Rd: gdsn.class
seqBED2GDS.Rd: cleanup.gds
seqBlockApply.Rd: gdsn.class
seqClose.Rd: gds.class
seqExport.Rd: cleanup.gds
seqGDS2SNP.Rd: add.gdsn, cleanup.gds
seqMerge.Rd: cleanup.gds
seqNewVarData.Rd: IntegerList
seqOpen.Rd: openfn.gds, gds.class
seqRecompress.Rd: cleanup.gds
seqResetVariantID.Rd: cleanup.gds
seqSNP2GDS.Rd: add.gdsn, cleanup.gds
seqSetFilter.Rd: GRanges, GRangesList, IRanges
seqStorageOption.Rd: add.gdsn, compression.gdsn
seqTranspose.Rd: add.gdsn
seqUnitApply.Rd: gdsn.class
seqVCF2GDS.Rd: cleanup.gds
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.22-bioc/R/library/SeqArray/libs/x64/SeqArray.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'SeqArray/libs/x64/SeqArray.dll':
Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
'R_WriteConnection', 'R_new_custom_connection'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
seqVCF2GDS 1.16 0.23 5.69
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'test.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: 2 NOTEs
See
'F:/biocbuild/bbs-3.22-bioc/meat/SeqArray.Rcheck/00check.log'
for details.
SeqArray.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL SeqArray
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'SeqArray' ...
** this is package 'SeqArray' version '1.49.4'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvToGDS.cpp -o ConvToGDS.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FileMerge.cpp -o FileMerge.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GetData.cpp -o GetData.o
GetData.cpp:159:17: warning: 'LANG_NEW_RLE' initialized and declared 'extern'
159 | extern "C" SEXP LANG_NEW_RLE = NULL;
| ^~~~~~~~~~~~
GetData.cpp:871:17: warning: 'OBJ_CompressedList' initialized and declared 'extern'
871 | extern "C" SEXP OBJ_CompressedList = NULL;
| ^~~~~~~~~~~~~~~~~~
GetData.cpp:873:17: warning: 'LANG_AS_LIST' initialized and declared 'extern'
873 | extern "C" SEXP LANG_AS_LIST = NULL;
| ^~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Index.cpp -o Index.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Methods.cpp -o Methods.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c R_SeqArray.c -o R_SeqArray.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadBySample.cpp -o ReadBySample.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadByUnit.cpp -o ReadByUnit.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadByVariant.cpp -o ReadByVariant.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SeqArray.cpp -o SeqArray.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pkg_test.cpp -o pkg_test.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c samtools_ext.c -o samtools_ext.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'F:/biocbuild/bbs-3.22-bioc/R/library/gdsfmt/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vectorization.cpp -o vectorization.o
g++ -std=gnu++17 -shared -s -static-libgcc -o SeqArray.dll tmp.def ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByUnit.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-SeqArray/00new/SeqArray/libs/x64
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SeqArray)
SeqArray.Rcheck/tests/test.Rout
R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> if (.Platform$OS.type != "windows")
+ BiocGenerics:::testPackage("SeqArray")
>
> proc.time()
user system elapsed
0.14 0.07 0.18
SeqArray.Rcheck/SeqArray-Ex.timings
| name | user | system | elapsed | |
| SeqArray-package | 0.53 | 0.07 | 0.69 | |
| SeqVarGDSClass-class | 0.18 | 0.00 | 0.19 | |
| seqAddValue | 0.20 | 0.08 | 0.30 | |
| seqAlleleFreq | 0.05 | 0.00 | 0.05 | |
| seqApply | 0.15 | 0.00 | 0.17 | |
| seqAsVCF | 0.02 | 0.00 | 0.02 | |
| seqBED2GDS | 0.27 | 0.11 | 0.48 | |
| seqBlockApply | 0.09 | 0.00 | 0.09 | |
| seqCheck | 0.03 | 0.00 | 0.04 | |
| seqDelete | 0.09 | 0.02 | 0.17 | |
| seqDigest | 0.04 | 0.00 | 0.03 | |
| seqEmptyFile | 0.03 | 0.00 | 0.09 | |
| seqExampleFileName | 0.00 | 0.01 | 0.02 | |
| seqExport | 0.42 | 0.55 | 1.23 | |
| seqGDS2SNP | 0.03 | 0.09 | 0.19 | |
| seqGDS2VCF | 0.38 | 0.00 | 0.41 | |
| seqGet2bGeno | 0.01 | 0.00 | 0.01 | |
| seqGetData | 1.53 | 0.07 | 1.60 | |
| seqGetFilter | 0.06 | 0.01 | 0.09 | |
| seqMerge | 1.18 | 0.31 | 1.83 | |
| seqMissing | 0.06 | 0.05 | 0.11 | |
| seqNewVarData | 0.00 | 0.01 | 0.02 | |
| seqNumAllele | 0 | 0 | 0 | |
| seqOpen | 0.09 | 0.02 | 0.11 | |
| seqOptimize | 0.22 | 0.05 | 0.39 | |
| seqParallel | 0.10 | 0.00 | 4.31 | |
| seqParallelSetup | 0.07 | 0.01 | 4.02 | |
| seqRecompress | 0.24 | 0.19 | 2.17 | |
| seqResetVariantID | 0.01 | 0.05 | 0.53 | |
| seqSNP2GDS | 1.39 | 0.14 | 1.72 | |
| seqSetFilter | 0.07 | 0.01 | 0.08 | |
| seqSetFilterCond | 0.04 | 0.00 | 0.04 | |
| seqStorageOption | 0.82 | 0.13 | 1.17 | |
| seqSummary | 0.17 | 0.03 | 0.21 | |
| seqSystem | 0 | 0 | 0 | |
| seqTranspose | 0.31 | 0.03 | 0.53 | |
| seqUnitApply | 0.13 | 0.01 | 4.51 | |
| seqUnitFilterCond | 0.09 | 0.00 | 0.10 | |
| seqUnitSlidingWindows | 0.05 | 0.00 | 0.05 | |
| seqUnitSubset | 0.06 | 0.02 | 0.07 | |
| seqVCF2GDS | 1.16 | 0.23 | 5.69 | |
| seqVCF_Header | 0.20 | 0.02 | 0.22 | |
| seqVCF_SampID | 0.02 | 0.00 | 0.01 | |