Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:52:16 -0400 (Wed, 17 Oct 2018).
Package 592/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GenomicAlignments 1.16.0 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
Package: GenomicAlignments |
Version: 1.16.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomicAlignments_1.16.0.tar.gz |
StartedAt: 2018-10-16 21:38:05 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 21:43:02 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 297.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GenomicAlignments.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomicAlignments_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/GenomicAlignments.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK * this is package ‘GenomicAlignments’ version ‘1.16.0’ * 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 'library' or 'require' call to ‘BSgenome’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. 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 ... WARNING Undocumented S4 methods: generic 'updateObject' and siglist 'GAlignments' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Objects in \usage without \alias in documentation object 'intra-range-methods': ‘\S4method{narrow}{GAlignmentsList}’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 or elapsed time > 5s user system elapsed junctions-methods 18.507 1.355 20.011 readGAlignments 13.182 0.832 14.134 sequenceLayer 9.202 1.373 10.669 summarizeOverlaps-methods 9.155 1.085 9.959 coordinate-mapping-methods 7.095 0.290 7.443 findSpliceOverlaps-methods 6.745 0.546 7.391 * 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: 2 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.7-bioc/meat/GenomicAlignments.Rcheck/00check.log’ for details.
GenomicAlignments.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GenomicAlignments ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘GenomicAlignments’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cigar_utils.c -o cigar_utils.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o clang -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/3.5/Resources/library/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 * DONE (GenomicAlignments)
GenomicAlignments.Rcheck/tests/run_unitTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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 Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb 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")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:DelayedArray': type The following object is masked from 'package:base': strsplit Loading required package: Rsamtools [1] TRUE > GenomicAlignments:::.test() RUNIT TEST PROTOCOL -- Tue Oct 16 21:42:53 2018 *********************************************** Number of test functions: 41 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicAlignments RUnit Tests - 41 test functions, 0 errors, 0 failures Number of test functions: 41 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 28.785 1.523 30.177
GenomicAlignments.Rcheck/GenomicAlignments-Ex.timings
name | user | system | elapsed | |
GAlignmentPairs-class | 1.565 | 0.110 | 1.694 | |
GAlignments-class | 0.475 | 0.013 | 0.493 | |
GAlignmentsList-class | 3.470 | 0.102 | 3.604 | |
GappedReads-class | 0.139 | 0.002 | 0.143 | |
OverlapEncodings-class | 1.514 | 0.037 | 1.562 | |
cigar-utils | 0.245 | 0.009 | 0.257 | |
coordinate-mapping-methods | 7.095 | 0.290 | 7.443 | |
coverage-methods | 3.235 | 0.172 | 3.432 | |
encodeOverlaps-methods | 0.047 | 0.001 | 0.048 | |
findCompatibleOverlaps-methods | 1.567 | 0.079 | 1.658 | |
findMateAlignment | 0.135 | 0.002 | 0.137 | |
findOverlaps-methods | 0.536 | 0.032 | 0.572 | |
findSpliceOverlaps-methods | 6.745 | 0.546 | 7.391 | |
intra-range-methods | 0.390 | 0.016 | 0.408 | |
junctions-methods | 18.507 | 1.355 | 20.011 | |
pileLettersAt | 0.704 | 0.011 | 0.715 | |
readGAlignments | 13.182 | 0.832 | 14.134 | |
sequenceLayer | 9.202 | 1.373 | 10.669 | |
setops-methods | 0.134 | 0.002 | 0.137 | |
stackStringsFromBam | 2.480 | 0.188 | 2.704 | |
summarizeOverlaps-methods | 9.155 | 1.085 | 9.959 | |