MEDIPS 1.16.0
Lukas Chavez
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/MEDIPS | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### rm -rf MEDIPS.buildbin-libdir MEDIPS.Rcheck && mkdir MEDIPS.buildbin-libdir MEDIPS.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEDIPS.buildbin-libdir MEDIPS_1.16.0.tar.gz >MEDIPS.Rcheck\00install.out 2>&1 && cp MEDIPS.Rcheck\00install.out MEDIPS-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=MEDIPS.buildbin-libdir --install="check:MEDIPS-install.out" --force-multiarch --no-vignettes --timings MEDIPS_1.16.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/MEDIPS.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' version '1.16.0'
* 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 'MEDIPS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'BSgenome' 'DNAcopy'
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 ... 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
'GenomicFeatures' 'GenomicRanges'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MEDIPS.CpGenrich: no visible global function definition for 'seqlevels'
MEDIPS.CpGenrich: no visible global function definition for
'seqlengths'
MEDIPS.GenomicCoordinates: no visible global function definition for
'GRanges'
MEDIPS.addCNV: no visible global function definition for 'seqnames'
MEDIPS.couplingVector: no visible global function definition for
'countOverlaps'
MEDIPS.createROIset: no visible global function definition for
'seqlevels'
MEDIPS.createROIset: no visible global function definition for
'seqlengths'
MEDIPS.createROIset: no visible global function definition for
'countOverlaps'
MEDIPS.createSet: no visible global function definition for 'seqlevels'
MEDIPS.createSet: no visible global function definition for
'seqlengths'
MEDIPS.createSet: no visible global function definition for
'countOverlaps'
MEDIPS.exportWIG: no visible global function definition for 'seqnames'
MEDIPS.getPositions: no visible global function definition for
'GRanges'
MEDIPS.meth: no visible global function definition for 'seqnames'
MEDIPS.plotCalibrationPlot: no visible global function definition for
'seqnames'
MEDIPS.saturation: no visible global function definition for
'seqlevels'
MEDIPS.saturation: no visible global function definition for
'seqlengths'
MEDIPS.saturation: no visible global function definition for
'countOverlaps'
MEDIPS.selectROIs: no visible global function definition for 'GRanges'
MEDIPS.selectROIs: no visible global function definition for
'elementMetadata<-'
MEDIPS.selectROIs: no visible global function definition for
'elementMetadata'
MEDIPS.selectROIs: no visible global function definition for
'findOverlaps'
MEDIPS.selectROIs: no visible global function definition for 'seqnames'
MEDIPS.seqCoverage: no visible global function definition for
'seqlevels'
MEDIPS.seqCoverage: no visible global function definition for
'seqlengths'
MEDIPS.seqCoverage: no visible global function definition for
'countOverlaps'
MEDIPS.setAnnotation: no visible global function definition for
'GRanges'
MEDIPS.setAnnotation: no visible global function definition for
'findOverlaps'
bin.ROIs: no visible global function definition for 'GRanges'
getGRange: no visible global function definition for 'GRanges'
getGRange: no visible global function definition for 'strand<-'
getMObjectFromWIG: no visible global function definition for 'GRanges'
getMObjectFromWIG: no visible global function definition for
'seqlengths'
getMObjectFromWIG: no visible global function definition for
'runLength'
getMObjectFromWIG: no visible global function definition for 'seqnames'
getMObjectFromWIG: no visible global function definition for 'runValue'
getPairedGRange: no visible global function definition for 'GRanges'
getPairedGRange: no visible global function definition for 'strand<-'
scanBamToGRanges: no visible global function definition for 'GRanges'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [203s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MEDIPS.meth 63.22 0.25 63.56
MEDIPS.addCNV 42.81 0.44 47.72
MEDIPS.saturation 11.53 0.03 11.56
MEDIPS.plotSaturation 10.67 0.05 10.72
MEDIPS.plotSeqCoverage 7.11 0.08 7.19
MEDIPS.selectROIs 6.49 0.01 6.51
MEDIPS.seqCoverage 5.35 0.15 5.51
MEDIPS.selectSig 4.99 0.13 5.13
MEDIPS.setAnnotation 4.36 0.08 8.17
MEDIPS.getAnnotation 0.50 0.10 7.20
** running examples for arch 'x64' ... [193s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MEDIPS.meth 65.50 0.29 65.79
MEDIPS.addCNV 40.08 0.45 40.53
MEDIPS.saturation 10.78 0.02 10.79
MEDIPS.plotSaturation 10.21 0.02 10.33
MEDIPS.plotSeqCoverage 7.30 0.06 7.36
MEDIPS.selectSig 5.99 0.08 6.07
MEDIPS.seqCoverage 5.34 0.16 5.49
MEDIPS.selectROIs 5.43 0.01 5.45
MEDIPS.setAnnotation 4.80 0.10 8.73
MEDIPS.getAnnotation 0.44 0.04 6.79
* 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
NOTE: There were 3 notes.
See
'D:/biocbld/bbs-3.0-bioc/meat/MEDIPS.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'MEDIPS' ...
** R
** 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 'MEDIPS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MEDIPS' as MEDIPS_1.16.0.zip
* DONE (MEDIPS)