Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:46 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 SeqArray package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/SeqArray.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1762/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SeqArray 1.34.0 (landing page) Xiuwen Zheng
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: SeqArray |
Version: 1.34.0 |
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_1.34.0.tar.gz |
StartedAt: 2022-04-12 18:25:20 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 18:30:09 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 288.5 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_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/SeqArray.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SeqArray/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SeqArray’ version ‘1.34.0’ * 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 ‘SeqArray’ can be installed ... OK * 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 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 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-3.14-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/4.1/Resources/library’ * installing *source* package ‘SeqArray’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ConvToGDS.cpp -o ConvToGDS.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FileMerge.cpp -o FileMerge.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c GetData.cpp -o GetData.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Index.cpp -o Index.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c LinkSNPRelate.cpp -o LinkSNPRelate.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Methods.cpp -o Methods.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R_SeqArray.c -o R_SeqArray.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ReadBySample.cpp -o ReadBySample.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ReadByUnit.cpp -o ReadByUnit.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ReadByVariant.cpp -o ReadByVariant.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c SeqArray.cpp -o SeqArray.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pkg_test.cpp -o pkg_test.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c samtools_ext.c -o samtools_ext.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gdsfmt/include' -I/usr/local/include -fPIC -Wall -g -O2 -c vectorization.c -o vectorization.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.1/Resources/library/00LOCK-SeqArray/00new/SeqArray/libs ** R ** data ** 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 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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, 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 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: --- [=>................................................] 1%, ETC: 7.4m [==================================================] 100%, completed, 6s [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 1s # of selected variants: 655 [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 1s [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 1s [..................................................] 0%, ETC: --- [=>................................................] 2%, ETC: 7.2m [==================================================] 100%, completed, 6s [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s # 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 -- Tue Apr 12 18:29:56 2022 *********************************************** Number of test functions: 27 Number of errors: 0 Number of failures: 0 1 Test Suite : SeqArray RUnit Tests - 27 test functions, 0 errors, 0 failures Number of test functions: 27 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 85.348 18.833 108.414
SeqArray.Rcheck/SeqArray-Ex.timings
name | user | system | elapsed | |
SeqArray-package | 0.655 | 0.091 | 0.752 | |
SeqVarGDSClass-class | 0.256 | 0.010 | 0.328 | |
seqAddValue | 0.208 | 0.083 | 0.292 | |
seqAlleleFreq | 0.086 | 0.009 | 0.095 | |
seqApply | 0.202 | 0.039 | 0.242 | |
seqAsVCF | 0.001 | 0.000 | 0.002 | |
seqBED2GDS | 0.395 | 0.131 | 0.530 | |
seqBlockApply | 0.116 | 0.017 | 0.134 | |
seqCheck | 0.060 | 0.010 | 0.069 | |
seqDelete | 0.141 | 0.012 | 0.153 | |
seqDigest | 0.024 | 0.002 | 0.026 | |
seqExampleFileName | 0.003 | 0.001 | 0.004 | |
seqExport | 1.152 | 0.757 | 1.911 | |
seqGDS2SNP | 0.089 | 0.064 | 0.154 | |
seqGDS2VCF | 0.895 | 0.058 | 0.954 | |
seqGetData | 0.097 | 0.014 | 0.110 | |
seqGetFilter | 0.112 | 0.008 | 0.120 | |
seqMerge | 1.239 | 0.267 | 1.510 | |
seqMissing | 0.126 | 0.007 | 0.133 | |
seqNewVarData | 0.003 | 0.001 | 0.003 | |
seqNumAllele | 0.002 | 0.001 | 0.004 | |
seqOpen | 0.086 | 0.003 | 0.089 | |
seqOptimize | 0.241 | 0.052 | 0.295 | |
seqParallel | 0.258 | 0.260 | 0.383 | |
seqParallelSetup | 0.146 | 0.069 | 0.197 | |
seqRecompress | 0.424 | 0.255 | 0.680 | |
seqResetVariantID | 0.025 | 0.030 | 0.054 | |
seqSNP2GDS | 1.751 | 0.187 | 1.943 | |
seqSetFilter | 0.133 | 0.023 | 0.157 | |
seqSetFilterCond | 0.076 | 0.011 | 0.086 | |
seqStorageOption | 0.854 | 0.159 | 1.016 | |
seqSummary | 0.210 | 0.029 | 0.237 | |
seqSystem | 0.000 | 0.001 | 0.001 | |
seqTranspose | 0.309 | 0.043 | 0.353 | |
seqUnitApply | 0.618 | 0.205 | 0.655 | |
seqUnitFilterCond | 0.124 | 0.022 | 0.146 | |
seqUnitSlidingWindows | 0.052 | 0.008 | 0.060 | |
seqVCF2GDS | 0.886 | 0.396 | 1.144 | |
seqVCF_Header | 0.127 | 0.008 | 0.134 | |
seqVCF_SampID | 0.002 | 0.002 | 0.003 | |