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This page was generated on 2018-04-12 13:37:49 -0400 (Thu, 12 Apr 2018).
Package 562/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GenomicAlignments 1.14.2 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | ![]() |
Package: GenomicAlignments |
Version: 1.14.2 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicAlignments_1.14.2.tar.gz |
StartedAt: 2018-04-12 04:17:23 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 04:22:05 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 281.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicAlignments.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicAlignments_1.14.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.Rcheck’ * using R version 3.4.4 (2018-03-15) * 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 ‘1.14.2’ * 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 ... 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 ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed junctions-methods 17.900 1.102 19.552 readGAlignments 10.655 0.597 11.493 sequenceLayer 8.124 1.038 9.366 summarizeOverlaps-methods 7.958 0.633 9.111 coordinate-mapping-methods 7.638 0.232 8.033 findSpliceOverlaps-methods 5.948 0.406 6.608 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.Rcheck/00check.log’ for details.
GenomicAlignments.Rcheck/00install.out
* installing *source* package ‘GenomicAlignments’ ... ** libs clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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 /Users/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.Rcheck/GenomicAlignments/libs ** R ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On" 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, cbind, colMeans, colSums, colnames, 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 Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following object is masked from 'package:base': 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 -- Thu Apr 12 04:21:57 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 35.330 0.888 37.237
GenomicAlignments.Rcheck/GenomicAlignments-Ex.timings
name | user | system | elapsed | |
GAlignmentPairs-class | 2.077 | 0.044 | 2.178 | |
GAlignments-class | 0.661 | 0.011 | 0.688 | |
GAlignmentsList-class | 3.465 | 0.081 | 3.637 | |
GappedReads-class | 0.160 | 0.021 | 0.188 | |
OverlapEncodings-class | 1.527 | 0.021 | 1.566 | |
cigar-utils | 0.412 | 0.009 | 0.428 | |
coordinate-mapping-methods | 7.638 | 0.232 | 8.033 | |
coverage-methods | 2.491 | 0.119 | 2.693 | |
encodeOverlaps-methods | 0.041 | 0.001 | 0.044 | |
findCompatibleOverlaps-methods | 1.962 | 0.052 | 2.074 | |
findMateAlignment | 0.255 | 0.007 | 0.270 | |
findOverlaps-methods | 0.528 | 0.004 | 0.562 | |
findSpliceOverlaps-methods | 5.948 | 0.406 | 6.608 | |
intra-range-methods | 0.293 | 0.012 | 0.311 | |
junctions-methods | 17.900 | 1.102 | 19.552 | |
pileLettersAt | 0.811 | 0.025 | 0.851 | |
readGAlignments | 10.655 | 0.597 | 11.493 | |
sequenceLayer | 8.124 | 1.038 | 9.366 | |
setops-methods | 0.084 | 0.002 | 0.086 | |
stackStringsFromBam | 1.424 | 0.019 | 1.474 | |
summarizeOverlaps-methods | 7.958 | 0.633 | 9.111 | |