Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-24 15:06:04 -0400 (Fri, 24 Sep 2021).

CHECK results for BSgenome on tokay2

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. Pag├Ęs
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BSgenome.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BSgenome_1.60.0.tar.gz
StartedAt: 2021-09-23 19:50:00 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 20:01:11 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 670.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BSgenome.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BSgenome.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BSgenome_1.60.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BSgenome.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'BSgenome' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
SNPlocs-class       35.59   3.11   69.36
BSgenome-utils      25.22   0.62   25.84
BSgenomeViews-class 21.25   3.26   32.04
BSgenome-class      19.34   0.78   33.59
injectSNPs          14.09   0.59   25.77
bsapply             10.42   0.61   11.11
XtraSNPlocs-class    8.41   0.36   11.19
export-methods       7.71   0.58    8.29
getSeq-methods       7.25   0.36    7.61
BSgenomeForge        6.92   0.10    7.20
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
SNPlocs-class       44.62   2.42   49.12
BSgenome-utils      26.25   0.25   26.50
BSgenomeViews-class 19.82   2.22   22.03
BSgenome-class      20.81   0.72   21.54
injectSNPs          16.22   1.59   17.81
bsapply             11.41   0.33   12.78
getSeq-methods       7.44   0.38    7.81
export-methods       6.69   0.73    7.44
XtraSNPlocs-class    5.62   0.34    5.97
BSgenomeForge        5.81   0.06    5.89
* 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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/BSgenome.Rcheck/00check.log'
for details.



Installation output

BSgenome.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BSgenome_1.60.0.tar.gz && rm -rf BSgenome.buildbin-libdir && mkdir BSgenome.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BSgenome.buildbin-libdir BSgenome_1.60.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BSgenome_1.60.0.zip && rm BSgenome_1.60.0.tar.gz BSgenome_1.60.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  5 5490k    5  307k    0     0  1016k      0  0:00:05 --:--:--  0:00:05 1017k
 53 5490k   53 2945k    0     0  2262k      0  0:00:02  0:00:01  0:00:01 2262k
100 5490k  100 5490k    0     0  2663k      0  0:00:02  0:00:02 --:--:-- 2665k

install for i386

* installing *source* package 'BSgenome' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BSgenome'
    finding HTML links ... done
    BSParams-class                          html  
    finding level-2 HTML links ... done

    BSgenome-class                          html  
    BSgenome-utils                          html  
    BSgenomeForge                           html  
    BSgenomeViews-class                     html  
    SNPlocs-class                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/BSgenome.buildbin-libdir/00LOCK-BSgenome/00new/BSgenome/help/snplocs.html
    XtraSNPlocs-class                       html  
    available.genomes                       html  
    bsapply                                 html  
    export-methods                          html  
    getSeq-methods                          html  
    injectSNPs                              html  
** 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

install for x64

* installing *source* package 'BSgenome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BSgenome' as BSgenome_1.60.0.zip
* DONE (BSgenome)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BSgenome' successfully unpacked and MD5 sums checked

Tests output


Example timings

BSgenome.Rcheck/examples_i386/BSgenome-Ex.timings

nameusersystemelapsed
BSgenome-class19.34 0.7833.59
BSgenome-utils25.22 0.6225.84
BSgenomeForge6.920.107.20
BSgenomeViews-class21.25 3.2632.04
SNPlocs-class35.59 3.1169.36
XtraSNPlocs-class 8.41 0.3611.19
available.genomes2.170.222.75
bsapply10.42 0.6111.11
export-methods7.710.588.29
getSeq-methods7.250.367.61
injectSNPs14.09 0.5925.77

BSgenome.Rcheck/examples_x64/BSgenome-Ex.timings

nameusersystemelapsed
BSgenome-class20.81 0.7221.54
BSgenome-utils26.25 0.2526.50
BSgenomeForge5.810.065.89
BSgenomeViews-class19.82 2.2222.03
SNPlocs-class44.62 2.4249.12
XtraSNPlocs-class5.620.345.97
available.genomes1.670.051.98
bsapply11.41 0.3312.78
export-methods6.690.737.44
getSeq-methods7.440.387.81
injectSNPs16.22 1.5917.81