Xiuwen Zheng
| Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/SeqArray |
| git_branch: RELEASE_3_18 |
| git_last_commit: 2f9f929 |
| git_last_commit_date: 2024-02-16 23:45:06 -0500 (Fri, 16 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:51 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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 1921/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqArray 1.42.2 (landing page) Xiuwen Zheng
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.42.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SeqArray_1.42.2.tar.gz |
| StartedAt: 2024-03-03 23:26:00 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 23:29:59 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 239.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SeqArray.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SeqArray_1.42.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/SeqArray.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqArray’ version ‘1.42.2’
* 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 ‘SeqArray’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 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 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 is not available
File ‘SeqArray/libs/SeqArray.so’:
Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
‘R_WriteConnection’, ‘R_new_custom_connection’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
‘/Users/biocbuild/bbs-3.18-bioc/meat/SeqArray.Rcheck/00check.log’
for details.
SeqArray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SeqArray ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘SeqArray’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ConvToGDS.cpp -o ConvToGDS.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FileMerge.cpp -o FileMerge.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GetData.cpp -o GetData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Index.cpp -o Index.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LinkSNPRelate.cpp -o LinkSNPRelate.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Methods.cpp -o Methods.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_SeqArray.c -o R_SeqArray.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBySample.cpp -o ReadBySample.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ReadByUnit.cpp -o ReadByUnit.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ReadByVariant.cpp -o ReadByVariant.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SeqArray.cpp -o SeqArray.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pkg_test.cpp -o pkg_test.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c samtools_ext.c -o samtools_ext.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vectorization.c -o vectorization.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o SeqArray.so 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-SeqArray/00new/SeqArray/libs ** 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 ** 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 (SeqArray)
SeqArray.Rcheck/tests/test.Rout
R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
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")
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following object is masked from 'package:SeqArray':
rowRanges
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from 'package:SeqArray':
rowRanges
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'SummarizedExperiment'
The following object is masked from 'package:SeqArray':
colData
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'VariantAnnotation'
The following objects are masked from 'package:SeqArray':
alt, filt, fixed, geno, header, info, qual, ref
The following object is masked from 'package:base':
tabulate
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
# of selected variants: 898
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 2s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 2s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 4s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
# of selected variants: 655
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 4s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Attaching package: 'Matrix'
The following object is masked from 'package:VariantAnnotation':
expand
The following object is masked from 'package:S4Vectors':
expand
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
RUNIT TEST PROTOCOL -- Sun Mar 3 23:29:48 2024
***********************************************
Number of test functions: 28
Number of errors: 0
Number of failures: 0
1 Test Suite :
SeqArray RUnit Tests - 28 test functions, 0 errors, 0 failures
Number of test functions: 28
Number of errors: 0
Number of failures: 0
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
67.277 19.334 88.015
SeqArray.Rcheck/SeqArray-Ex.timings
| name | user | system | elapsed | |
| SeqArray-package | 0.410 | 0.097 | 0.527 | |
| SeqVarGDSClass-class | 0.139 | 0.010 | 0.151 | |
| seqAddValue | 0.146 | 0.034 | 0.188 | |
| seqAlleleFreq | 0.062 | 0.008 | 0.071 | |
| seqApply | 0.131 | 0.027 | 0.161 | |
| seqAsVCF | 0.003 | 0.001 | 0.005 | |
| seqBED2GDS | 0.284 | 0.078 | 0.385 | |
| seqBlockApply | 0.062 | 0.008 | 0.073 | |
| seqCheck | 0.026 | 0.004 | 0.031 | |
| seqDelete | 0.102 | 0.012 | 0.117 | |
| seqDigest | 0.023 | 0.003 | 0.027 | |
| seqEmptyFile | 0.022 | 0.014 | 0.037 | |
| seqExampleFileName | 0.003 | 0.002 | 0.004 | |
| seqExport | 0.817 | 1.167 | 2.060 | |
| seqGDS2SNP | 0.065 | 0.110 | 0.190 | |
| seqGDS2VCF | 0.821 | 0.050 | 0.880 | |
| seqGet2bGeno | 0.011 | 0.002 | 0.014 | |
| seqGetData | 1.566 | 0.063 | 1.647 | |
| seqGetFilter | 0.057 | 0.006 | 0.065 | |
| seqMerge | 0.813 | 0.459 | 1.370 | |
| seqMissing | 0.068 | 0.011 | 0.081 | |
| seqNewVarData | 0.003 | 0.001 | 0.005 | |
| seqNumAllele | 0.003 | 0.001 | 0.004 | |
| seqOpen | 0.072 | 0.009 | 0.082 | |
| seqOptimize | 0.199 | 0.072 | 0.288 | |
| seqParallel | 0.156 | 0.363 | 0.348 | |
| seqParallelSetup | 0.084 | 0.068 | 0.135 | |
| seqRecompress | 0.322 | 0.403 | 0.738 | |
| seqResetVariantID | 0.021 | 0.045 | 0.068 | |
| seqSNP2GDS | 1.468 | 0.209 | 1.708 | |
| seqSetFilter | 0.085 | 0.023 | 0.108 | |
| seqSetFilterCond | 0.067 | 0.012 | 0.080 | |
| seqStorageOption | 0.669 | 0.263 | 0.991 | |
| seqSummary | 0.130 | 0.037 | 0.167 | |
| seqSystem | 0.000 | 0.000 | 0.001 | |
| seqTranspose | 0.256 | 0.076 | 0.349 | |
| seqUnitApply | 0.320 | 0.198 | 0.404 | |
| seqUnitFilterCond | 0.077 | 0.015 | 0.093 | |
| seqUnitSlidingWindows | 0.045 | 0.008 | 0.054 | |
| seqUnitSubset | 0.062 | 0.010 | 0.073 | |
| seqVCF2GDS | 0.677 | 0.527 | 1.123 | |
| seqVCF_Header | 0.105 | 0.012 | 0.119 | |
| seqVCF_SampID | 0.003 | 0.001 | 0.004 | |