Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:09 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 GenomicAlignments package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicAlignments.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 782/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicAlignments 1.34.1 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: GenomicAlignments |
Version: 1.34.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicAlignments_1.34.1.tar.gz |
StartedAt: 2023-04-10 20:23:08 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 20:27:29 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 260.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicAlignments.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicAlignments_1.34.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/GenomicAlignments.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK * this is package ‘GenomicAlignments’ version ‘1.34.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'SummarizedExperiment', 'Biostrings', 'Rsamtools' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘GenomicAlignments’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘Biostrings’ ‘Rsamtools’ A package should be listed in only one of these fields. * 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 ... NOTE ':::' calls which should be '::': ‘S4Vectors:::makeClassinfoRowForCompactPrinting’ ‘S4Vectors:::makePrettyMatrixForCompactPrinting’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘Biostrings:::.normarg_padding.letter’ ‘Rsamtools:::.BamViews_delegate’ ‘Rsamtools:::.findMateWithinGroups’ ‘Rsamtools:::.load_bamcols_from_scanBam_res’ See the note in ?`:::` about the use of this operator. * 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 compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed readGAlignments 11.296 3.550 15.125 junctions-methods 12.499 1.339 13.949 summarizeOverlaps-methods 6.521 2.669 8.633 coordinate-mapping-methods 7.472 0.279 7.783 sequenceLayer 5.842 1.013 6.948 findSpliceOverlaps-methods 4.916 0.276 5.245 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/GenomicAlignments.Rcheck/00check.log’ for details.
GenomicAlignments.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomicAlignments ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘GenomicAlignments’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I/usr/local/include -fPIC -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cigar_utils.c -o cigar_utils.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I/usr/local/include -fPIC -Wall -g -O2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I/usr/local/include -fPIC -Wall -g -O2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o clang -mmacosx-version-min=10.13 -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 GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-GenomicAlignments/00new/GenomicAlignments/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 (GenomicAlignments)
GenomicAlignments.Rcheck/tests/run_unitTests.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 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. > require("GenomicAlignments") || stop("unable to load GenomicRanges package") Loading required package: GenomicAlignments 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: 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: GenomeInfoDb Loading required package: GenomicRanges Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats 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 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 Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: Rsamtools [1] TRUE > GenomicAlignments:::.test() RUNIT TEST PROTOCOL -- Mon Apr 10 20:27:15 2023 *********************************************** Number of test functions: 42 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicAlignments RUnit Tests - 42 test functions, 0 errors, 0 failures Number of test functions: 42 Number of errors: 0 Number of failures: 0 Warning message: In .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode, : 4 alignments with ambiguous pairing were dumped. Use 'getDumpedAlignments()' to retrieve them from the dump environment. > > proc.time() user system elapsed 21.934 1.380 22.908
GenomicAlignments.Rcheck/GenomicAlignments-Ex.timings
name | user | system | elapsed | |
GAlignmentPairs-class | 0.777 | 0.073 | 0.851 | |
GAlignments-class | 0.313 | 0.024 | 0.337 | |
GAlignmentsList-class | 2.418 | 0.090 | 2.517 | |
GappedReads-class | 0.086 | 0.003 | 0.090 | |
OverlapEncodings-class | 0.855 | 0.031 | 0.890 | |
cigar-utils | 0.196 | 0.022 | 0.220 | |
coordinate-mapping-methods | 7.472 | 0.279 | 7.783 | |
coverage-methods | 1.684 | 0.087 | 1.777 | |
encodeOverlaps-methods | 0.023 | 0.001 | 0.024 | |
findCompatibleOverlaps-methods | 1.005 | 0.045 | 1.054 | |
findMateAlignment | 0.107 | 0.005 | 0.112 | |
findOverlaps-methods | 0.371 | 0.013 | 0.384 | |
findSpliceOverlaps-methods | 4.916 | 0.276 | 5.245 | |
intra-range-methods | 0.278 | 0.010 | 0.288 | |
junctions-methods | 12.499 | 1.339 | 13.949 | |
pileLettersAt | 0.525 | 0.030 | 0.556 | |
readGAlignments | 11.296 | 3.550 | 15.125 | |
sequenceLayer | 5.842 | 1.013 | 6.948 | |
setops-methods | 0.087 | 0.003 | 0.090 | |
stackStringsFromGAlignments | 3.254 | 0.227 | 3.503 | |
summarizeOverlaps-methods | 6.521 | 2.669 | 8.633 | |