Felix A. Klein
| Snapshot Date: 2020-01-08 16:46:10 -0500 (Wed, 08 Jan 2020) |
| URL: https://git.bioconductor.org/packages/FourCSeq |
| Branch: master |
| Last Commit: a0cd899 |
| Last Changed Date: 2019-10-29 13:38:02 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-09 13:48:06 -0500 (Thu, 09 Jan 2020).
| Package 608/1813 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| FourCSeq 1.21.0 Felix A. Klein
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: FourCSeq |
| Version: 1.21.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FourCSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FourCSeq_1.21.0.tar.gz |
| StartedAt: 2020-01-09 04:14:09 -0500 (Thu, 09 Jan 2020) |
| EndedAt: 2020-01-09 04:26:35 -0500 (Thu, 09 Jan 2020) |
| EllapsedTime: 745.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: FourCSeq.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FourCSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FourCSeq_1.21.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/FourCSeq.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.21.0’
* 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 ... WARNING
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/FourCSeq.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 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'
FourC: no visible global function definition for 'formula'
FourC: no visible global function definition for 'new'
addFragments: no visible global function definition for 'metadata'
addFragments: no visible global function definition for
'subsetByOverlaps'
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'
distFitMonotone: no visible global function definition for 'predict'
distFitMonotoneSymmetric: no visible global function definition for
'predict'
findViewpointFragments: no visible global function definition for
'metadata'
findViewpointFragments : <anonymous>: no visible global function
definition for 'Rle'
findViewpointFragments: no visible global function definition for
'subjectHits'
findViewpointFragments: no visible global function definition for
'write.table'
getDifferences: no visible global function definition for 'relevel'
getDifferences: no visible global function definition for 'formula'
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 binding for global variable 'mad'
getZScores: no visible binding for global variable 'median'
getZScores: no visible global function definition for 'DataFrame'
getZScores: no visible binding for global variable 'pnorm'
getZScores: no visible binding for global variable 'p.adjust'
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 'ggplot'
plotDifferences: no visible global function definition for
'subsetByOverlaps'
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'
plotFits: no visible global function definition for 'par'
plotFits: no visible global function definition for 'plot'
plotFits: no visible global function definition for 'axis'
plotFits: no visible global function definition for 'mtext'
plotFits: no visible global function definition for 'points'
plotNormalizationFactors: no visible global function definition for
'plot'
plotNormalizationFactors: no visible global function definition for
'points'
plotNormalizationFactors: no visible global function definition for
'legend'
plotNormalizationFactors: no visible global function definition for
'abline'
plotSmoothScatter: no visible binding for global variable 'blues9'
plotSmoothScatter: no visible global function definition for 'axis'
plotVp: no visible global function definition for 'ggplot'
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'
plotZScores: no visible global function definition for 'ggplot'
plotZScores: no visible global function definition for
'subsetByOverlaps'
saveGR: no visible global function definition for 'metadata'
saveGR: no visible global function definition for 'seqlengths'
saveGR: no visible global function definition for 'write.table'
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'
updateObject,FourC: no visible global function definition for
'callNextMethod'
Undefined global functions or variables:
DataFrame IRanges Rle Seqinfo SimpleList abline aes axis blues9
callNextMethod change count differentialInteraction element_blank fit
fitDown fitUp formula geom_path geom_point ggplot keepSeqlevels labs
legend mad median metadata mid mtext new p.adjust par peak plot pnorm
points predict rel relevel scale_fill_gradient2 scale_y_continuous
seqlengths seqlevels seqlevels<- subjectHits subsetByOverlaps theme
theme_bw theme_set write.table
Consider adding
importFrom("grDevices", "blues9")
importFrom("graphics", "abline", "axis", "legend", "mtext", "par",
"plot", "points")
importFrom("methods", "callNextMethod", "new")
importFrom("stats", "formula", "mad", "median", "p.adjust", "pnorm",
"predict", "relevel")
importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getZScores 46.136 17.071 63.232
plotScatter 48.380 4.541 52.996
plotDifferences 13.570 0.343 13.914
getDifferences 8.028 0.235 8.267
plotZScores 7.929 0.291 8.226
getAllResults 7.746 0.302 8.058
plotNormalizationFactors 6.376 0.111 6.490
* 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: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/FourCSeq.Rcheck/00check.log’
for details.
FourCSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FourCSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘FourCSeq’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: break used in wrong context: no loop is visible ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (FourCSeq)
FourCSeq.Rcheck/FourCSeq-Ex.timings
| name | user | system | elapsed | |
| FourC | 1.060 | 0.121 | 1.182 | |
| addFragments | 1.950 | 0.130 | 2.083 | |
| addViewpointFrags | 2.987 | 0.193 | 3.186 | |
| combineFragEnds | 0.267 | 0.029 | 0.296 | |
| countFragmentOverlaps | 3.409 | 0.028 | 3.449 | |
| countFragmentOverlapsSecondCutter | 0.000 | 0.000 | 0.001 | |
| fc | 0.108 | 0.008 | 0.116 | |
| fcf | 0.199 | 0.032 | 0.230 | |
| findViewpointFragments | 1.287 | 0.011 | 1.298 | |
| getAllResults | 7.746 | 0.302 | 8.058 | |
| getDifferences | 8.028 | 0.235 | 8.267 | |
| getDistAroundVp | 1.244 | 0.056 | 1.301 | |
| getNormalizationFactors | 0.571 | 0.045 | 0.616 | |
| getReferenceSeq | 0.547 | 0.003 | 0.550 | |
| getZScores | 46.136 | 17.071 | 63.232 | |
| normalizeRPM | 0.333 | 0.049 | 0.382 | |
| plotDifferences | 13.570 | 0.343 | 13.914 | |
| plotFits | 0.938 | 0.063 | 1.008 | |
| plotNormalizationFactors | 6.376 | 0.111 | 6.490 | |
| plotScatter | 48.380 | 4.541 | 52.996 | |
| plotZScores | 7.929 | 0.291 | 8.226 | |
| smoothCounts | 0.312 | 0.065 | 0.377 | |
| smoothHitPerCent | 1.156 | 0.401 | 1.557 | |
| writeTrackFiles | 1.295 | 0.184 | 1.481 | |