BioC 3.0: CHECK report for FourCSeq on oaxaca
This page was generated on 2015-04-10 10:09:14 -0700 (Fri, 10 Apr 2015).
FourCSeq 1.0.0
Felix A. Klein
| 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/FourCSeq | | 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 |
Summary
| Package: FourCSeq |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch FourCSeq_1.0.0.tar.gz |
| StartedAt: 2015-04-09 23:35:07 -0700 (Thu, 09 Apr 2015) |
| EndedAt: 2015-04-09 23:45:30 -0700 (Thu, 09 Apr 2015) |
| EllapsedTime: 622.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FourCSeq.Rcheck |
| Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch FourCSeq_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/FourCSeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FourCSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FourCSeq’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘FourCSeq’ can be installed ... [43s/44s] 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
* 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 ‘DataFrame’
addPeaks: no visible global function definition for ‘DataFrame’
addViewpointFrags: no visible global function definition for
‘DataFrame’
countFragmentOverlaps: no visible global function definition for
‘DataFrame’
countFragmentOverlaps: no visible global function definition for
‘SimpleList’
countFragmentOverlapsSecondCutter: no visible global function
definition for ‘DataFrame’
countFragmentOverlapsSecondCutter: no visible global function
definition for ‘SimpleList’
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’
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 ‘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 ‘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’
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’
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
‘keepSeqlevels’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [161s/166s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getZScores 72.108 10.105 82.686
plotDifferences 11.364 0.075 11.742
plotZScores 7.545 0.055 7.782
plotScatter 6.118 0.320 9.553
getAllResults 6.090 0.078 6.182
getDifferences 5.081 0.041 5.140
* 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
‘/Users/biocbuild/bbs-3.0-bioc/meat/FourCSeq.Rcheck/00check.log’
for details.
FourCSeq.Rcheck/00install.out:
* 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
* DONE (FourCSeq)
FourCSeq.Rcheck/FourCSeq-Ex.timings:
| name | user | system | elapsed
|
| FourC | 0.310 | 0.011 | 0.321 |
|
| addFragments | 1.392 | 0.009 | 1.403 |
|
| addViewpointFrags | 0.977 | 0.010 | 0.989 |
|
| combineFragEnds | 1.014 | 0.021 | 1.036 |
|
| countFragmentOverlaps | 3.309 | 0.050 | 3.363 |
|
| countFragmentOverlapsSecondCutter | 0.000 | 0.000 | 0.001 |
|
| fc | 0.135 | 0.012 | 0.147 |
|
| fcf | 0.231 | 0.018 | 0.250 |
|
| findViewpointFragments | 0.928 | 0.007 | 0.935 |
|
| getAllResults | 6.090 | 0.078 | 6.182 |
|
| getDifferences | 5.081 | 0.041 | 5.140 |
|
| getDistAroundVp | 0.215 | 0.015 | 0.230 |
|
| getNormalizationFactors | 0.297 | 0.017 | 0.316 |
|
| getReferenceSeq | 0.128 | 0.002 | 0.131 |
|
| getZScores | 72.108 | 10.105 | 82.686 |
|
| normalizeRPM | 0.211 | 0.043 | 0.254 |
|
| plotDifferences | 11.364 | 0.075 | 11.742 |
|
| plotFits | 0.635 | 0.035 | 0.732 |
|
| plotNormalizationFactors | 4.222 | 0.068 | 4.674 |
|
| plotScatter | 6.118 | 0.320 | 9.553 |
|
| plotZScores | 7.545 | 0.055 | 7.782 |
|
| smoothCounts | 0.272 | 0.051 | 0.325 |
|
| smoothHitPerCent | 3.801 | 0.319 | 4.225 |
|
| writeTrackFiles | 1.272 | 0.078 | 1.477 |
|