Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
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 1927/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SeqArray 1.46.0 (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 | 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: 1.46.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SeqArray_1.46.0.tar.gz |
StartedAt: 2024-11-20 09:34:40 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 09:39:55 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 315.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SeqArray.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SeqArray_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/SeqArray.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘SeqArray/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SeqArray’ version ‘1.46.0’ * 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 * used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking installed package size ... NOTE installed size is 7.3Mb sub-directories of 1Mb or more: extdata 1.6Mb libs 4.9Mb * 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 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 ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/SeqArray.Rcheck/00check.log’ for details.
SeqArray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SeqArray ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘SeqArray’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c ConvToGDS.cpp -o ConvToGDS.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c FileMerge.cpp -o FileMerge.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c GetData.cpp -o GetData.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c Index.cpp -o Index.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c LinkSNPRelate.cpp -o LinkSNPRelate.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c Methods.cpp -o Methods.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_SeqArray.c -o R_SeqArray.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c ReadBySample.cpp -o ReadBySample.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c ReadByUnit.cpp -o ReadByUnit.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c ReadByVariant.cpp -o ReadByVariant.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c SeqArray.cpp -o SeqArray.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c pkg_test.cpp -o pkg_test.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c samtools_ext.c -o samtools_ext.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSING_R -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -c vectorization.cpp -o vectorization.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/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 -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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, saveRDS, setdiff, 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, 12s [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 13s [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 8s [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 4s # of selected variants: 655 [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 7s [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 6s [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 5s [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 2s 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 -- Wed Nov 20 09:38:10 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 42.812 66.535 108.926
SeqArray.Rcheck/SeqArray-Ex.timings
name | user | system | elapsed | |
SeqArray-package | 0.257 | 0.039 | 0.597 | |
SeqVarGDSClass-class | 0.084 | 0.000 | 0.168 | |
seqAddValue | 0.082 | 0.018 | 0.200 | |
seqAlleleFreq | 0.048 | 0.000 | 0.058 | |
seqApply | 0.092 | 0.005 | 0.096 | |
seqAsVCF | 0.001 | 0.000 | 0.001 | |
seqBED2GDS | 0.149 | 0.032 | 0.190 | |
seqBlockApply | 0.037 | 0.002 | 0.038 | |
seqCheck | 0.014 | 0.003 | 0.017 | |
seqDelete | 0.058 | 0.002 | 0.079 | |
seqDigest | 0.016 | 0.001 | 0.018 | |
seqEmptyFile | 0.008 | 0.002 | 0.010 | |
seqExampleFileName | 0.002 | 0.000 | 0.001 | |
seqExport | 0.362 | 0.129 | 0.491 | |
seqGDS2SNP | 0.031 | 0.017 | 0.048 | |
seqGDS2VCF | 0.360 | 0.016 | 0.381 | |
seqGet2bGeno | 0.007 | 0.001 | 0.012 | |
seqGetData | 1.006 | 0.020 | 1.029 | |
seqGetFilter | 0.040 | 0.004 | 0.076 | |
seqMerge | 0.592 | 0.105 | 0.770 | |
seqMissing | 0.048 | 0.001 | 0.099 | |
seqNewVarData | 0.002 | 0.000 | 0.006 | |
seqNumAllele | 0.003 | 0.000 | 0.006 | |
seqOpen | 0.031 | 0.001 | 0.061 | |
seqOptimize | 0.136 | 0.020 | 0.315 | |
seqParallel | 0.095 | 0.400 | 0.574 | |
seqParallelSetup | 0.048 | 0.087 | 0.203 | |
seqRecompress | 0.215 | 0.374 | 0.703 | |
seqResetVariantID | 0.011 | 0.020 | 0.032 | |
seqSNP2GDS | 0.809 | 0.072 | 1.095 | |
seqSetFilter | 0.049 | 0.009 | 0.058 | |
seqSetFilterCond | 0.034 | 0.012 | 0.046 | |
seqStorageOption | 0.386 | 0.061 | 0.475 | |
seqSummary | 0.079 | 0.013 | 0.091 | |
seqSystem | 0 | 0 | 0 | |
seqTranspose | 0.149 | 0.011 | 0.160 | |
seqUnitApply | 0.173 | 0.154 | 0.401 | |
seqUnitFilterCond | 0.046 | 0.007 | 0.107 | |
seqUnitSlidingWindows | 0.022 | 0.007 | 0.057 | |
seqUnitSubset | 0.037 | 0.005 | 0.084 | |
seqVCF2GDS | 0.366 | 0.273 | 0.819 | |
seqVCF_Header | 0.056 | 0.006 | 0.064 | |
seqVCF_SampID | 0.000 | 0.001 | 0.001 | |