Back to Multiple platform build/check report for BioC 3.13
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-09-22 15:04:47 -0400 (Wed, 22 Sep 2021).

CHECK results for BSgenome on nebbiolo1

To the developers/maintainers of the BSgenome package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BSgenome.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 217/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BSgenome 1.60.0  (landing page)
H. Pagès
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/BSgenome
git_branch: RELEASE_3_13
git_last_commit: 6643064
git_last_commit_date: 2021-05-19 11:37:32 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: BSgenome
Version: 1.60.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BSgenome_1.60.0.tar.gz
StartedAt: 2021-09-21 09:05:48 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 09:13:57 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 489.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BSgenome.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BSgenome_1.60.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/BSgenome.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.60.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  'GenomicRanges', '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 ... NOTE
Found the following non-portable file path:
  BSgenome/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-tools/fasta_to_sorted_2bit.R

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BSgenome’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/extdata/GentlemanLab/BSgenome.Creinhardtii.JGI.v5.6-tools/CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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
':::' calls which should be '::':
  ‘S4Vectors:::makeClassinfoRowForCompactPrinting’
  ‘S4Vectors:::makePrettyMatrixForCompactPrinting’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘GenomeInfoDb:::compactPrintNamedAtomicVector’
  ‘GenomicRanges:::get_out_of_bound_index’ ‘IRanges:::.normargSEW’
  ‘IRanges:::unlist_as_integer’ ‘S4Vectors:::anyMissing’
  ‘S4Vectors:::anyMissingOrOutside’ ‘S4Vectors:::decodeRle’
  ‘S4Vectors:::diffWithInitialZero’
  ‘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 ... WARNING
Missing link or links in documentation object 'export-methods.Rd':
  ‘[rtracklayer]{export}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 'batchsizes' and siglist 'OnDiskLongTable'
  generic 'blocksizes' and siglist 'OnDiskLongTable_old'
  generic 'breakpoints' and siglist 'OnDiskLongTable'
  generic 'breakpoints' and siglist 'OnDiskLongTable_old'
  generic 'coerce' and siglist 'RdsCollection,RdsNamedSequences'
  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 'RdsNamedSequences'
  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
SNPlocs-class       64.516  3.633  69.095
BSgenomeViews-class 21.045  5.295  26.589
BSgenome-utils      23.059  0.347  23.418
BSgenome-class      17.779  1.831  19.838
getSeq-methods       9.830  9.391  19.223
injectSNPs          12.824  2.949  15.926
XtraSNPlocs-class    7.057  0.335   7.445
bsapply              5.720  0.432   6.167
export-methods       5.040  0.644   5.684
* 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, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/BSgenome.Rcheck/00check.log’
for details.



Installation output

BSgenome.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BSgenome
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* 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)

Tests output


Example timings

BSgenome.Rcheck/BSgenome-Ex.timings

nameusersystemelapsed
BSgenome-class17.779 1.83119.838
BSgenome-utils23.059 0.34723.418
BSgenomeForge4.2140.0854.300
BSgenomeViews-class21.045 5.29526.589
SNPlocs-class64.516 3.63369.095
XtraSNPlocs-class7.0570.3357.445
available.genomes1.1140.1441.517
bsapply5.7200.4326.167
export-methods5.0400.6445.684
getSeq-methods 9.830 9.39119.223
injectSNPs12.824 2.94915.926