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CHECK report for Genominator on tokay1

This page was generated on 2020-04-15 12:19:03 -0400 (Wed, 15 Apr 2020).

Package 688/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Genominator 1.40.0
James Bullard
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/Genominator
Branch: RELEASE_3_10
Last Commit: 475c8da
Last Changed Date: 2019-10-29 13:08:11 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Genominator
Version: 1.40.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Genominator.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Genominator_1.40.0.tar.gz
StartedAt: 2020-04-15 03:28:08 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:32:54 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 286.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Genominator.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Genominator.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Genominator_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Genominator.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Genominator/DESCRIPTION' ... OK
* this is package 'Genominator' version '1.40.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 whether package 'Genominator' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'GenomeGraphs' is deprecated and will be removed from
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Genominator.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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
'library' or 'require' calls to packages already attached by Depends:
  'GenomeGraphs' 'IRanges'
  Please remove these calls from your code.
'library' or 'require' call to 'ShortRead' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'GenomeGraphs' 'RSQLite'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.genominator.coverage plot.genominator.goodness.of.fit
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addPrimingWeights: no visible global function definition for
  'varLabels'
addPrimingWeights: no visible global function definition for
  'alignData'
addPrimingWeights: no visible global function definition for 'subseq'
addPrimingWeights: no visible global function definition for 'sread'
addPrimingWeights: no visible global function definition for
  'AlignedDataFrame'
addPrimingWeights: no visible global function definition for 'pData'
addPrimingWeights: no visible global function definition for
  'varMetadata'
computePrimingWeights: no visible global function definition for
  'mkAllStrings'
computePrimingWeights : p.compute: no visible global function
  definition for 'tables'
computePrimingWeights : p.compute: no visible global function
  definition for 'subseq'
computePrimingWeights : p.compute: no visible global function
  definition for 'sread'
importFromAlignedReads : weights.AlignedRead: no visible global
  function definition for 'varLabels'
importFromAlignedReads : weights.AlignedRead: no visible global
  function definition for 'alignData'
importFromAlignedReads : importObject: no visible global function
  definition for 'position'
importFromAlignedReads : importObject: no visible global function
  definition for 'chromosome'
importFromAlignedReads : importObject: no visible global function
  definition for 'varLabels'
importFromAlignedReads : importObject: no visible global function
  definition for 'alignData'
importFromAlignedReads: no visible global function definition for
  'readAligned'
makeAnnoFactory: no visible global function definition for
  'DisplayPars'
makeAnnoFactory : regionAnno.Biomart: no visible global function
  definition for 'geneRegionBiomart'
makeAnnoFactory : regionAnno.AnnoData: no visible global function
  definition for 'makeAnnotationTrack'
makeRegionPlotter : <anonymous>: no visible global function definition
  for 'DisplayPars'
makeRegionPlotter : <anonymous> : <anonymous>: no visible global
  function definition for 'makeBaseTrack'
makeRegionPlotter : <anonymous> : <anonymous>: no visible global
  function definition for 'makeGenericArray'
makeRegionPlotter : <anonymous>: no visible global function definition
  for 'makeGenomeAxis'
makeRegionPlotter : <anonymous>: no visible global function definition
  for 'gdPlot'
plot.genominator.goodness.of.fit : <anonymous>: no visible global
  function definition for 'qchisq'
plot.genominator.goodness.of.fit : <anonymous>: no visible global
  function definition for 'ppoints'
plot.genominator.goodness.of.fit : <anonymous>: no visible global
  function definition for 'qunif'
plot.genominator.goodness.of.fit : <anonymous>: no visible global
  function definition for 'qqplot'
Undefined global functions or variables:
  AlignedDataFrame DisplayPars alignData chromosome gdPlot
  geneRegionBiomart makeAnnotationTrack makeBaseTrack makeGenericArray
  makeGenomeAxis mkAllStrings pData position ppoints qchisq qqplot
  qunif readAligned sread subseq tables varLabels varMetadata
Consider adding
  importFrom("stats", "ppoints", "qchisq", "qqplot", "qunif")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'ExpData,ANY,ANY'
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
joinExpData               13.94   0.03   14.00
addPrimingWeights          7.92   1.12    9.11
plot.genominator.coverage  6.97   0.03    7.00
aggregateExpData           5.31   0.02    5.34
computeCoverage            2.20   0.07    5.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
joinExpData               13.61   0.04   16.88
addPrimingWeights          8.42   0.72    9.17
plot.genominator.coverage  7.39   0.05    7.63
aggregateExpData           5.75   0.01    5.89
collapseExpData            5.11   0.02    5.13
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/Genominator.Rcheck/00check.log'
for details.



Installation output

Genominator.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/Genominator_1.40.0.tar.gz && rm -rf Genominator.buildbin-libdir && mkdir Genominator.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Genominator.buildbin-libdir Genominator_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Genominator_1.40.0.zip && rm Genominator_1.40.0.tar.gz Genominator_1.40.0.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
100 1478k  100 1478k    0     0  24.4M      0 --:--:-- --:--:-- --:--:-- 26.2M

install for i386

* installing *source* package 'Genominator' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'GenomeGraphs' is deprecated and will be removed from
  Bioconductor version 3.11 
** help
*** installing help indices
  converting help for package 'Genominator'
    finding HTML links ... done
    ExpData                                 html  
    Genominator                             html  
    addPrimingWeights                       html  
    aggregateExpData                        html  
    applyMapped                             html  
    collapseExpData                         html  
    computeCoverage                         html  
    computePrimingWeights                   html  
    getRegion                               html  
    importFromAlignedReads                  html  
    importToExpData                         html  
    joinExpData                             html  
    makeGeneRepresentation                  html  
    mergeWithAnnotation                     html  
    plot.genominator.coverage               html  
    plot.genominator.goodness.of.fit        html  
    regionGoodnessOfFit-methods             html  
    splitByAnnotation                       html  
    summarizeByAnnotation                   html  
    summarizeExpData                        html  
    validAnnotation                         html  
    yeastAnno                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'GenomeGraphs' is deprecated and will be removed from
  Bioconductor version 3.11
** testing if installed package can be loaded from final location
Warning: Package 'GenomeGraphs' is deprecated and will be removed from
  Bioconductor version 3.11
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'Genominator' ...
** testing if installed package can be loaded
Warning: Package 'GenomeGraphs' is deprecated and will be removed from
  Bioconductor version 3.11
* MD5 sums
packaged installation of 'Genominator' as Genominator_1.40.0.zip
* DONE (Genominator)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Genominator' successfully unpacked and MD5 sums checked

Tests output


Example timings

Genominator.Rcheck/examples_i386/Genominator-Ex.timings

nameusersystemelapsed
ExpData000
addPrimingWeights7.921.129.11
aggregateExpData5.310.025.34
applyMapped2.960.083.89
collapseExpData4.440.014.49
computeCoverage2.200.075.33
computePrimingWeights0.550.451.00
getRegion0.710.000.71
importFromAlignedReads000
importToExpData1.380.001.38
joinExpData13.94 0.0314.00
makeGeneRepresentation0.220.020.23
mergeWithAnnotation1.420.001.43
plot.genominator.coverage6.970.037.00
plot.genominator.goodness.of.fit1.650.041.70
regionGoodnessOfFit-methods1.520.051.56
splitByAnnotation2.950.002.95
summarizeByAnnotation1.520.021.54
summarizeExpData1.370.001.37
validAnnotation0.030.000.03
yeastAnno0.160.030.19

Genominator.Rcheck/examples_x64/Genominator-Ex.timings

nameusersystemelapsed
ExpData000
addPrimingWeights8.420.729.17
aggregateExpData5.750.015.89
applyMapped3.590.063.84
collapseExpData5.110.025.13
computeCoverage2.810.032.84
computePrimingWeights0.680.501.17
getRegion0.850.000.84
importFromAlignedReads000
importToExpData1.710.021.73
joinExpData13.61 0.0416.88
makeGeneRepresentation0.140.020.16
mergeWithAnnotation1.460.011.46
plot.genominator.coverage7.390.057.63
plot.genominator.goodness.of.fit1.970.011.98
regionGoodnessOfFit-methods1.980.032.02
splitByAnnotation3.580.003.60
summarizeByAnnotation1.810.001.82
summarizeExpData1.750.001.75
validAnnotation0.020.020.03
yeastAnno0.230.030.26