Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 813/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicAlignments 1.43.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | ||||||||||
To the developers/maintainers of the GenomicAlignments package: - 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 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: GenomicAlignments |
Version: 1.43.0 |
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_1.43.0.tar.gz |
StartedAt: 2024-12-23 19:26:20 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 19:28:10 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 110.2 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_1.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GenomicAlignments.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK * this is package ‘GenomicAlignments’ version ‘1.43.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO 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 * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since Cannot process chunk/lines: version 1.18.0 Cannot process chunk/lines: No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since Cannot process chunk/lines: version 1.16.0 Cannot process chunk/lines: The first version of GenomicAlignments was included in Bioconductor 2.14. Cannot process chunk/lines: The package was created from existing code in IRanges, ShortRead, Cannot process chunk/lines: Rsamtools and GenomicRanges. * 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 dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘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 ... NOTE checkRd: (-1) coordinate-mapping-methods.Rd:69-83: Lost braces in \itemize; meant \describe ? checkRd: (-1) coordinate-mapping-methods.Rd:84-101: Lost braces in \itemize; meant \describe ? checkRd: (-1) coordinate-mapping-methods.Rd:102-114: Lost braces in \itemize; meant \describe ? checkRd: (-1) coordinate-mapping-methods.Rd:115-120: Lost braces in \itemize; meant \describe ? checkRd: (-1) findSpliceOverlaps-methods.Rd:99-102: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) findSpliceOverlaps-methods.Rd:103-105: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) findSpliceOverlaps-methods.Rd:106-107: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) intra-range-methods.Rd:52-60: Lost braces 52 | \item(){ | ^ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: GAlignmentPairs-class.Rd: seqlevels, GRanges, GRangesList GAlignments-class.Rd: seqlevels, GRanges, GRangesList GAlignmentsList-class.Rd: GRanges, GRangesList coordinate-mapping-methods.Rd: GenomicRanges-class findCompatibleOverlaps-methods.Rd: GRangesList findOverlaps-methods.Rd: GRangesList, GRanges-class, GRangesList-class intra-range-methods.Rd: GRanges, GRangesList readGAlignments.Rd: scanBam, ScanBamParam-class sequenceLayer.Rd: XStringSet stackStringsFromGAlignments.Rd: scanBam, ScanBamParam summarizeOverlaps-methods.Rd: BamFile, ScanBamParam, register 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 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 6.061 0.625 6.706 junctions-methods 5.958 0.508 6.492 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.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: 6 NOTEs See ‘/Users/biocbuild/bbs-3.21-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/4.5-arm64/Resources/library’ * installing *source* package ‘GenomicAlignments’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cigar_utils.c -o cigar_utils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.5-arm64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min 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: 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 Dec 23 19:28:05 2024 *********************************************** 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 9.165 0.526 9.652
GenomicAlignments.Rcheck/GenomicAlignments-Ex.timings
name | user | system | elapsed | |
GAlignmentPairs-class | 0.276 | 0.009 | 0.285 | |
GAlignments-class | 0.344 | 0.006 | 0.351 | |
GAlignmentsList-class | 0.631 | 0.020 | 0.653 | |
GappedReads-class | 0.025 | 0.000 | 0.025 | |
OverlapEncodings-class | 0.264 | 0.018 | 0.282 | |
cigar-utils | 0.049 | 0.003 | 0.053 | |
coordinate-mapping-methods | 2.908 | 0.088 | 3.006 | |
coverage-methods | 1.018 | 0.031 | 1.048 | |
encodeOverlaps-methods | 0.009 | 0.001 | 0.009 | |
findCompatibleOverlaps-methods | 0.355 | 0.015 | 0.371 | |
findMateAlignment | 0.039 | 0.000 | 0.040 | |
findOverlaps-methods | 0.131 | 0.006 | 0.137 | |
findSpliceOverlaps-methods | 1.512 | 0.082 | 1.600 | |
intra-range-methods | 0.090 | 0.004 | 0.094 | |
junctions-methods | 5.958 | 0.508 | 6.492 | |
pileLettersAt | 0.154 | 0.005 | 0.159 | |
readGAlignments | 6.061 | 0.625 | 6.706 | |
sequenceLayer | 2.291 | 0.485 | 2.782 | |
setops-methods | 0.032 | 0.001 | 0.032 | |
stackStringsFromGAlignments | 1.541 | 0.093 | 1.635 | |
summarizeOverlaps-methods | 2.402 | 1.172 | 3.447 | |