Genominator 1.30.0
James Bullard
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/Genominator | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf Genominator.buildbin-libdir Genominator.Rcheck && mkdir Genominator.buildbin-libdir Genominator.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Genominator.buildbin-libdir Genominator_1.30.0.tar.gz >Genominator.Rcheck\00install.out 2>&1 && cp Genominator.Rcheck\00install.out Genominator-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Genominator.buildbin-libdir --install="check:Genominator-install.out" --force-multiarch --no-vignettes --timings Genominator_1.30.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/Genominator.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.30.0'
* 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 ... OK
* 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 ... OK
* 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 ... OK
* 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 installed files from 'inst/doc' ... 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 6.45 0.05 6.55
addPrimingWeights 4.48 1.03 16.76
aggregateExpData 3.21 0.00 13.96
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
joinExpData 8.74 0.04 8.83
addPrimingWeights 6.67 0.90 9.06
* 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 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/Genominator.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'Genominator' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'Genominator' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Genominator' as Genominator_1.30.0.zip
* DONE (Genominator)