| Back to Multiple platform build/check report for BioC 3.11 (small subset of software packages ONLY) |
This page was generated on 2020-01-24 03:57:03 -0500 (Fri, 24 Jan 2020).
| Package 15/41 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| BSgenome 1.55.2 H. Pagès
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | [ WARNINGS ] | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK |
| Package: BSgenome |
| Version: 1.55.2 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BSgenome_1.55.2.tar.gz |
| StartedAt: 2020-01-24 03:06:04 -0500 (Fri, 24 Jan 2020) |
| EndedAt: 2020-01-24 03:15:09 -0500 (Fri, 24 Jan 2020) |
| EllapsedTime: 544.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BSgenome.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BSgenome_1.55.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc-testing/meat/BSgenome.Rcheck’
* using R Under development (unstable) (2019-12-14 r77569)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* this is package ‘BSgenome’ version ‘1.55.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
'GenomicRanges', 'Biostrings', 'rtracklayer'
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 ‘BSgenome’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.8Mb
sub-directories of 1Mb or more:
R 1.7Mb
extdata 5.9Mb
* 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’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘Biostrings’ ‘rtracklayer’
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
':::' call which should be '::': ‘S4Vectors:::makePrettyMatrixForCompactPrinting’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘GenomeInfoDb:::compactPrintNamedAtomicVector’
‘GenomeInfoDb:::showGenomeDescription’
‘GenomicRanges:::get_out_of_bound_index’ ‘IRanges:::.normargSEW’
‘IRanges:::unlist_as_integer’ ‘S4Vectors:::anyMissing’
‘S4Vectors:::anyMissingOrOutside’ ‘S4Vectors:::decodeRle’
‘S4Vectors:::diffWithInitialZero’
‘S4Vectors:::makeClassinfoRowForCompactPrinting’
‘S4Vectors:::make_zero_col_DataFrame’ ‘S4Vectors:::quick_unlist’
‘S4Vectors:::quick_unsplit’ ‘S4Vectors:::recycleVector’
‘rtracklayer:::.DNAString_to_twoBit’ ‘rtracklayer:::.TwoBits_export’
‘rtracklayer:::checkArgFormat’ ‘rtracklayer:::twoBitPath’
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 code objects:
‘MaskedBSgenome’ ‘OnDiskLongTable’ ‘OnDiskLongTable_old’
‘as.data.frame.BSgenomeViews’ ‘batchsizes’ ‘blocksizes’ ‘breakpoints’
‘forgeMaskedBSgenomeDataPkg’
‘getBatchesByOverlapsFromOnDiskLongTable’
‘getBatchesBySeqnameFromOnDiskLongTable’
‘getBatchesFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable_old’
‘getRowsByIdFromOnDiskLongTable’ ‘getRowsByIdFromOnDiskLongTable_old’
‘getRowsByIndexFromOnDiskLongTable_old’ ‘getRowsFromOnDiskLongTable’
‘rowids’ ‘saveAsOnDiskLongTable_old’
‘saveRowidsForOnDiskLongTable_old’ ‘spatialIndex’
‘writeOnDiskLongTable’ ‘writeOnDiskLongTableRowids’
Undocumented S4 classes:
‘OnDiskLongTable_old’ ‘OnDiskLongTable’ ‘MaskedBSgenome’
‘GRanges_OR_NULL’
Undocumented S4 methods:
generic '[' and siglist 'XStringSet,GRangesList,ANY,ANY'
generic '[' and siglist 'XStringSet,GenomicRanges,ANY,ANY'
generic '[[' and siglist 'BSgenome,ANY,ANY'
generic '[[' and siglist 'FastaNamedSequences,ANY,ANY'
generic '[[' and siglist 'RdaNamedSequences,ANY,ANY'
generic '[[' and siglist 'TwobitNamedSequences,ANY,ANY'
generic 'batchsizes' and siglist 'OnDiskLongTable'
generic 'blocksizes' and siglist 'OnDiskLongTable_old'
generic 'breakpoints' and siglist 'OnDiskLongTable'
generic 'breakpoints' and siglist 'OnDiskLongTable_old'
generic 'dim' and siglist 'OnDiskLongTable'
generic 'dim' and siglist 'OnDiskLongTable_old'
generic 'dimnames' and siglist 'OnDiskLongTable'
generic 'dimnames' and siglist 'OnDiskLongTable_old'
generic 'dimnames' and siglist 'XtraSNPlocs'
generic 'extractAt' and siglist 'BSgenome'
generic 'forgeMaskedBSgenomeDataPkg' and siglist
'MaskedBSgenomeDataPkgSeed'
generic 'forgeMaskedBSgenomeDataPkg' and siglist 'character'
generic 'forgeMaskedBSgenomeDataPkg' and siglist 'list'
generic 'length' and siglist 'OnDiskNamedSequences'
generic 'names' and siglist 'FastaNamedSequences'
generic 'names' and siglist 'TwobitNamedSequences'
generic 'rowids' and siglist 'OnDiskLongTable'
generic 'rowids' and siglist 'OnDiskLongTable_old'
generic 'seqinfo' and siglist 'FastaNamedSequences'
generic 'seqinfo' and siglist 'RdaNamedSequences'
generic 'seqinfo' and siglist 'TwobitNamedSequences'
generic 'seqnames' and siglist 'OnDiskNamedSequences'
generic 'show' and siglist 'OnDiskLongTable'
generic 'show' and siglist 'OnDiskLongTable_old'
generic 'show' and siglist 'OnDiskNamedSequences'
generic 'spatialIndex' and siglist 'OnDiskLongTable'
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
XtraSNPlocs-class 103.526 2.383 106.942
SNPlocs-class 70.103 1.842 72.112
BSgenome-utils 27.231 0.204 27.447
BSgenomeViews-class 23.708 1.622 30.899
injectSNPs 12.850 1.802 16.808
BSgenome-class 13.375 0.684 14.103
getSeq-methods 8.228 0.015 8.249
bsapply 6.833 0.036 7.493
export-methods 5.323 0.281 5.603
BSgenomeForge 5.100 0.064 5.165
* 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: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.11-bioc-testing/meat/BSgenome.Rcheck/00check.log’
for details.
BSgenome.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL BSgenome ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc-testing/Rlibs’ * installing *source* package ‘BSgenome’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BSgenome)
BSgenome.Rcheck/BSgenome-Ex.timings
| name | user | system | elapsed | |
| BSgenome-class | 13.375 | 0.684 | 14.103 | |
| BSgenome-utils | 27.231 | 0.204 | 27.447 | |
| BSgenomeForge | 5.100 | 0.064 | 5.165 | |
| BSgenomeViews-class | 23.708 | 1.622 | 30.899 | |
| SNPlocs-class | 70.103 | 1.842 | 72.112 | |
| XtraSNPlocs-class | 103.526 | 2.383 | 106.942 | |
| available.genomes | 1.107 | 0.048 | 3.004 | |
| bsapply | 6.833 | 0.036 | 7.493 | |
| export-methods | 5.323 | 0.281 | 5.603 | |
| getSeq-methods | 8.228 | 0.015 | 8.249 | |
| injectSNPs | 12.850 | 1.802 | 16.808 | |