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This page was generated on 2018-04-12 13:11:44 -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: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GenomicAlignments_1.14.2.tar.gz |
StartedAt: 2018-04-11 23:48:22 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 23:52:30 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 248.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicAlignments.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GenomicAlignments_1.14.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-pc-linux-gnu (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 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 16.208 0.220 17.317 readGAlignments 9.732 0.376 10.130 summarizeOverlaps-methods 7.168 0.152 7.742 coordinate-mapping-methods 7.132 0.092 7.574 sequenceLayer 6.564 0.304 6.919 findSpliceOverlaps-methods 4.904 0.084 5.026 * 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 ‘/home/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.Rcheck/00check.log’ for details.
GenomicAlignments.Rcheck/00install.out
* installing *source* package ‘GenomicAlignments’ ... ** libs gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I/usr/local/include -fpic -g -O2 -Wall -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I/usr/local/include -fpic -g -O2 -Wall -c cigar_utils.c -o cigar_utils.o cigar_utils.c: In function ‘cigar_ranges’: cigar_utils.c:676:9: warning: ‘f_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized] f_elt++; ^ cigar_utils.c:658:27: warning: ‘range_buf2’ may be used uninitialized in this function [-Wmaybe-uninitialized] range_buf1 = range_buf2->elts[*f_elt - 1]; ^ cigar_utils.c:674:22: warning: ‘range_buf1’ may be used uninitialized in this function [-Wmaybe-uninitialized] *(breakpoint++) = IntPairAE_get_nelt(range_buf1); ^ cigar_utils.c:674:16: warning: ‘breakpoint’ may be used uninitialized in this function [-Wmaybe-uninitialized] *(breakpoint++) = IntPairAE_get_nelt(range_buf1); ^ cigar_utils.c:670:12: warning: ‘flag_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized] flag_elt++; ^ cigar_utils.c: In function ‘cigar_width’: cigar_utils.c:734:12: warning: ‘flag_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized] flag_elt++; ^ cigar_utils.c: In function ‘cigar_narrow’: cigar_utils.c:880:6: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized] if (offset == Roffset) ^ cigar_utils.c:852:15: note: ‘Roffset’ was declared here int Loffset, Roffset, buf_offset; ^ cigar_utils.c:878:6: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized] if (offset == Loffset) ^ cigar_utils.c:852:6: note: ‘Loffset’ was declared here int Loffset, Roffset, buf_offset; ^ cigar_utils.c: In function ‘cigar_qnarrow’: cigar_utils.c:1064:6: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized] if (offset == Roffset) ^ cigar_utils.c:1036:15: note: ‘Roffset’ was declared here int Loffset, Roffset, buf_offset; ^ cigar_utils.c:1062:6: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized] if (offset == Loffset) ^ cigar_utils.c:1036:6: note: ‘Loffset’ was declared here int Loffset, Roffset, buf_offset; ^ gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I/usr/local/include -fpic -g -O2 -Wall -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I/usr/local/include -fpic -g -O2 -Wall -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o encodeOverlaps_methods.c: In function ‘overlap_encoding’: encodeOverlaps_methods.c:182:2: warning: ‘out_nelt0’ may be used uninitialized in this function [-Wmaybe-uninitialized] CharAE_delete_at(out, out_nelt0, j1 * nrow); ^ encodeOverlaps_methods.c:99:6: note: ‘out_nelt0’ was declared here int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej, ^ g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/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 -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR installing to /home/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-pc-linux-gnu (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 -- Wed Apr 11 23:52:25 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 33.844 0.532 34.734
GenomicAlignments.Rcheck/GenomicAlignments-Ex.timings
name | user | system | elapsed | |
GAlignmentPairs-class | 1.860 | 0.024 | 1.896 | |
GAlignments-class | 0.620 | 0.000 | 0.619 | |
GAlignmentsList-class | 3.436 | 0.032 | 3.540 | |
GappedReads-class | 0.116 | 0.000 | 0.115 | |
OverlapEncodings-class | 1.280 | 0.000 | 1.278 | |
cigar-utils | 0.384 | 0.008 | 0.705 | |
coordinate-mapping-methods | 7.132 | 0.092 | 7.574 | |
coverage-methods | 2.216 | 0.020 | 2.237 | |
encodeOverlaps-methods | 0.028 | 0.000 | 0.026 | |
findCompatibleOverlaps-methods | 1.048 | 0.016 | 1.067 | |
findMateAlignment | 0.176 | 0.000 | 0.178 | |
findOverlaps-methods | 0.364 | 0.000 | 0.367 | |
findSpliceOverlaps-methods | 4.904 | 0.084 | 5.026 | |
intra-range-methods | 0.204 | 0.012 | 0.217 | |
junctions-methods | 16.208 | 0.220 | 17.317 | |
pileLettersAt | 0.628 | 0.004 | 0.631 | |
readGAlignments | 9.732 | 0.376 | 10.130 | |
sequenceLayer | 6.564 | 0.304 | 6.919 | |
setops-methods | 0.064 | 0.004 | 0.069 | |
stackStringsFromBam | 1.048 | 0.004 | 1.055 | |
summarizeOverlaps-methods | 7.168 | 0.152 | 7.742 | |