BioC 3.3: CHECK report for FourCSeq on windows2.bioconductor.org
This page was generated on 2015-10-27 12:15:44 -0400 (Tue, 27 Oct 2015).
FourCSeq 1.5.0
Felix A. Klein
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FourCSeq | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
Summary
| Package: FourCSeq
|
| Version: 1.5.0
|
| Command: rm -rf FourCSeq.buildbin-libdir FourCSeq.Rcheck && mkdir FourCSeq.buildbin-libdir FourCSeq.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FourCSeq.buildbin-libdir FourCSeq_1.5.0.tar.gz >FourCSeq.Rcheck\00install.out 2>&1 && cp FourCSeq.Rcheck\00install.out FourCSeq-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=FourCSeq.buildbin-libdir --install="check:FourCSeq-install.out" --force-multiarch --no-vignettes --timings FourCSeq_1.5.0.tar.gz
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| StartedAt: 2015-10-27 02:28:50 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 02:39:14 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 623.5 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: FourCSeq.Rcheck
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| Warnings: 0
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Command output
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### Running command:
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### rm -rf FourCSeq.buildbin-libdir FourCSeq.Rcheck && mkdir FourCSeq.buildbin-libdir FourCSeq.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FourCSeq.buildbin-libdir FourCSeq_1.5.0.tar.gz >FourCSeq.Rcheck\00install.out 2>&1 && cp FourCSeq.Rcheck\00install.out FourCSeq-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=FourCSeq.buildbin-libdir --install="check:FourCSeq-install.out" --force-multiarch --no-vignettes --timings FourCSeq_1.5.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/FourCSeq.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FourCSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FourCSeq' version '1.5.0'
* 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 'FourCSeq' 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:
'DESeq2' 'GenomicRanges'
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
Packages in Depends field not imported from:
'ggplot2' 'methods'
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
FourC: no visible global function definition for 'SimpleList'
addFragments: no visible global function definition for 'metadata'
addFragments: no visible global function definition for 'DataFrame'
addPeaks: no visible global function definition for 'metadata'
addPeaks: no visible global function definition for 'DataFrame'
addViewpointFrags: no visible global function definition for 'metadata'
addViewpointFrags: no visible global function definition for
'DataFrame'
countFragmentOverlaps: no visible global function definition for
'metadata'
countFragmentOverlaps: no visible global function definition for
'DataFrame'
countFragmentOverlaps: no visible global function definition for
'SimpleList'
countFragmentOverlapsSecondCutter: no visible global function
definition for 'metadata'
countFragmentOverlapsSecondCutter: no visible global function
definition for 'DataFrame'
countFragmentOverlapsSecondCutter: no visible global function
definition for 'SimpleList'
findViewpointFragments: no visible global function definition for
'metadata'
findViewpointFragments : <anonymous>: no visible global function
definition for 'Rle'
getDistAroundVp: no visible global function definition for 'DataFrame'
getFragments: no visible global function definition for 'Rle'
getFragments: no visible global function definition for 'IRanges'
getFragments: no visible global function definition for 'seqlengths'
getReferenceSeq: no visible global function definition for 'metadata'
getSites: no visible global function definition for 'seqlevels<-'
getSites: no visible global function definition for 'seqlevels'
getSites: no visible global function definition for 'Seqinfo'
getSites: no visible global function definition for 'Rle'
getZScores: no visible global function definition for 'DataFrame'
getZScores: no visible global function definition for 'metadata'
getZScores: no visible global function definition for 'SimpleList'
plotDifferences: no visible global function definition for 'theme_bw'
plotDifferences: no visible global function definition for 'rel'
plotDifferences: no visible global function definition for 'theme_set'
plotDifferences: no visible global function definition for 'metadata'
plotDifferences: no visible global function definition for 'aes'
plotDifferences: no visible binding for global variable 'change'
plotDifferences: no visible global function definition for
'scale_fill_gradient2'
plotDifferences: no visible global function definition for 'theme'
plotDifferences: no visible global function definition for
'element_blank'
plotDifferences: no visible binding for global variable 'mid'
plotDifferences: no visible global function definition for 'labs'
plotDifferences: no visible global function definition for 'geom_path'
plotDifferences: no visible global function definition for 'geom_point'
plotDifferences: no visible global function definition for
'scale_y_continuous'
plotDifferences: no visible binding for global variable 'peak'
plotDifferences: no visible binding for global variable
'differentialInteraction'
plotFits: no visible global function definition for 'metadata'
plotVp: no visible global function definition for 'aes'
plotVp: no visible binding for global variable 'mid'
plotVp: no visible binding for global variable 'count'
plotVp: no visible global function definition for 'labs'
plotVp: no visible global function definition for 'geom_path'
plotVp: no visible binding for global variable 'fit'
plotVp: no visible binding for global variable 'fitUp'
plotVp: no visible binding for global variable 'fitDown'
plotVp: no visible global function definition for 'geom_point'
plotVp: no visible global function definition for 'scale_y_continuous'
plotVp: no visible binding for global variable 'peak'
plotVp: no visible binding for global variable
'differentialInteraction'
plotZScores: no visible global function definition for 'theme_bw'
plotZScores: no visible global function definition for 'rel'
plotZScores: no visible global function definition for 'theme_set'
plotZScores: no visible global function definition for 'metadata'
saveGR: no visible global function definition for 'metadata'
saveGR: no visible global function definition for 'seqlengths'
smoothCounts: no visible global function definition for 'SimpleList'
smoothHitPerCent: no visible global function definition for
'SimpleList'
writeTrackFiles: no visible global function definition for 'metadata'
writeTrackFiles: no visible global function definition for
'keepSeqlevels'
Undefined global functions or variables:
DataFrame IRanges Rle Seqinfo SimpleList aes change count
differentialInteraction element_blank fit fitDown fitUp geom_path
geom_point keepSeqlevels labs metadata mid peak rel
scale_fill_gradient2 scale_y_continuous seqlengths seqlevels
seqlevels<- theme theme_bw theme_set
* 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' ... [162s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotScatter 52.53 1.83 54.36
getZScores 48.44 1.61 50.08
writeTrackFiles 16.42 0.45 17.07
plotDifferences 7.75 0.03 7.78
** running examples for arch 'x64' ... [163s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getZScores 53.15 1.66 54.81
plotScatter 46.73 1.73 48.49
writeTrackFiles 16.09 0.49 16.64
plotDifferences 8.27 0.00 8.27
plotZScores 5.52 0.02 5.53
* 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 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/FourCSeq.Rcheck/00check.log'
for details.
FourCSeq.Rcheck/00install.out:
install for i386
* installing *source* package 'FourCSeq' ...
** 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 'FourCSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FourCSeq' as FourCSeq_1.5.0.zip
* DONE (FourCSeq)
FourCSeq.Rcheck/examples_i386/FourCSeq-Ex.timings:
| name | user | system | elapsed
|
| FourC | 0.3 | 0.0 | 0.3 |
|
| addFragments | 0.48 | 0.01 | 0.50 |
|
| addViewpointFrags | 0.44 | 0.00 | 0.43 |
|
| combineFragEnds | 0.81 | 0.00 | 0.82 |
|
| countFragmentOverlaps | 1.36 | 0.03 | 1.39 |
|
| countFragmentOverlapsSecondCutter | 0 | 0 | 0 |
|
| fc | 0.13 | 0.00 | 0.12 |
|
| fcf | 0.20 | 0.00 | 0.21 |
|
| findViewpointFragments | 0.55 | 0.04 | 0.57 |
|
| getAllResults | 3.65 | 0.07 | 3.74 |
|
| getDifferences | 3.25 | 0.05 | 3.29 |
|
| getDistAroundVp | 0.16 | 0.00 | 0.16 |
|
| getNormalizationFactors | 0.52 | 0.02 | 0.53 |
|
| getReferenceSeq | 0.06 | 0.01 | 0.08 |
|
| getZScores | 48.44 | 1.61 | 50.08 |
|
| normalizeRPM | 0.18 | 0.03 | 0.22 |
|
| plotDifferences | 7.75 | 0.03 | 7.78 |
|
| plotFits | 0.58 | 0.02 | 0.59 |
|
| plotNormalizationFactors | 2.89 | 0.03 | 2.92 |
|
| plotScatter | 52.53 | 1.83 | 54.36 |
|
| plotZScores | 4.69 | 0.03 | 4.74 |
|
| smoothCounts | 0.2 | 0.0 | 0.2 |
|
| smoothHitPerCent | 1.52 | 0.25 | 1.77 |
|
| writeTrackFiles | 16.42 | 0.45 | 17.07 |
|
FourCSeq.Rcheck/examples_x64/FourCSeq-Ex.timings:
| name | user | system | elapsed
|
| FourC | 0.20 | 0.00 | 0.21 |
|
| addFragments | 0.50 | 0.01 | 0.51 |
|
| addViewpointFrags | 0.53 | 0.02 | 0.55 |
|
| combineFragEnds | 0.62 | 0.01 | 0.64 |
|
| countFragmentOverlaps | 1.66 | 0.02 | 1.67 |
|
| countFragmentOverlapsSecondCutter | 0 | 0 | 0 |
|
| fc | 0.11 | 0.00 | 0.11 |
|
| fcf | 0.16 | 0.02 | 0.17 |
|
| findViewpointFragments | 0.48 | 0.03 | 0.52 |
|
| getAllResults | 3.94 | 0.06 | 4.00 |
|
| getDifferences | 3.86 | 0.00 | 3.86 |
|
| getDistAroundVp | 0.15 | 0.00 | 0.15 |
|
| getNormalizationFactors | 0.21 | 0.00 | 0.21 |
|
| getReferenceSeq | 0.11 | 0.00 | 0.11 |
|
| getZScores | 53.15 | 1.66 | 54.81 |
|
| normalizeRPM | 0.17 | 0.00 | 0.17 |
|
| plotDifferences | 8.27 | 0.00 | 8.27 |
|
| plotFits | 0.53 | 0.00 | 0.53 |
|
| plotNormalizationFactors | 2.64 | 0.00 | 2.64 |
|
| plotScatter | 46.73 | 1.73 | 48.49 |
|
| plotZScores | 5.52 | 0.02 | 5.53 |
|
| smoothCounts | 0.15 | 0.00 | 0.15 |
|
| smoothHitPerCent | 1.35 | 0.11 | 1.45 |
|
| writeTrackFiles | 16.09 | 0.49 | 16.64 |
|