Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-16 11:35:58 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 241/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BSgenome 1.68.0  (landing page)
Hervé Pagès
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/BSgenome
git_branch: RELEASE_3_17
git_last_commit: c546020
git_last_commit_date: 2023-04-25 09:43:43 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for BSgenome on palomino3


To the developers/maintainers of the BSgenome package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BSgenome
Version: 1.68.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BSgenome.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings BSgenome_1.68.0.tar.gz
StartedAt: 2023-10-16 00:09:35 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 00:20:44 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 669.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BSgenome.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BSgenome.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings BSgenome_1.68.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/BSgenome.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BSgenome/DESCRIPTION' ... OK
* this is package 'BSgenome' version '1.68.0'
* 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 whether package 'BSgenome' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.7Mb
  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 ... 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:
  '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 ... WARNING
checkRd: (5) BSgenomeViews-class.Rd:155-161: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:162-165: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:172-176: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:177-181: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:182-184: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:185-187: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:188-193: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:194-197: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:198-200: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:201-206: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:213-218: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:219-222: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:223-225: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:231-233: \item in \describe must have non-empty label
checkRd: (5) BSgenomeViews-class.Rd:234-236: \item in \describe must have non-empty label
* 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'
  'getRowsByIndexFromOnDiskLongTable_old' 'getRowsFromOnDiskLongTable'
  'saveAsOnDiskLongTable_old' 'saveRowidsForOnDiskLongTable_old'
  'spatialIndex' 'writeOnDiskLongTable' 'writeOnDiskLongTableRowids'
Undocumented S4 classes:
  'OnDiskLongTable_old' 'GRanges_OR_NULL' 'MaskedBSgenome'
  'OnDiskLongTable'
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 '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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
SNPlocs-class       58.58   3.96  174.78
BSgenome-class      35.94   0.31   37.46
injectSNPs          33.18   0.81   41.79
BSgenome-utils      30.73   0.22   31.07
BSgenomeViews-class 23.42   4.85   80.39
bsapply             26.98   0.28   27.86
export-methods      16.91   0.75   17.66
getSeq-methods      11.22   0.33   11.55
XtraSNPlocs-class    7.59   0.59   24.97
BSgenomeForge        5.70   0.05    7.58
* 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 WARNINGs, 6 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/BSgenome.Rcheck/00check.log'
for details.



Installation output

BSgenome.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL BSgenome
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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-class35.94 0.3137.46
BSgenome-utils30.73 0.2231.07
BSgenomeForge5.700.057.58
BSgenomeViews-class23.42 4.8580.39
SNPlocs-class 58.58 3.96174.78
XtraSNPlocs-class 7.59 0.5924.97
available.genomes3.330.133.83
bsapply26.98 0.2827.86
export-methods16.91 0.7517.66
getSeq-methods11.22 0.3311.55
injectSNPs33.18 0.8141.79