Mike Smith
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/FourCSeq |
| Branch: RELEASE_3_12 |
| Last Commit: 5575105 |
| Last Changed Date: 2020-10-27 10:58:38 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:27:38 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the FourCSeq package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 646/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Mike Smith
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: FourCSeq |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:FourCSeq.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings FourCSeq_1.24.0.tar.gz |
| StartedAt: 2021-05-06 01:39:51 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 01:49:49 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 598.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: FourCSeq.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:FourCSeq.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings FourCSeq_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/FourCSeq.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘1.24.0’
* package encoding: UTF-8
* 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:
Warning: Package 'FourCSeq' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.12-bioc/meat/FourCSeq.Rcheck/00install.out’ for details.
* 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
* 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
Package in Depends field not imported from: 'ggplot2'
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'
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'
getDifferences: no visible global function definition for 'is'
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 'axis'
plotFits: no visible global function definition for 'mtext'
plotFits: no visible global function definition for 'points'
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'
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 abline aes axis blues9
change count differentialInteraction element_blank fit fitDown fitUp
formula geom_path geom_point ggplot is keepSeqlevels labs legend mad
median metadata mid mtext p.adjust par peak pnorm points predict rel
relevel scale_fill_gradient2 scale_y_continuous seqlengths seqlevels
seqlevels<- subjectHits subsetByOverlaps theme theme_bw theme_set
Consider adding
importFrom("grDevices", "blues9")
importFrom("graphics", "abline", "axis", "legend", "mtext", "par",
"points")
importFrom("methods", "is")
importFrom("stats", "formula", "mad", "median", "p.adjust", "pnorm",
"predict", "relevel")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotScatter 56.884 0.780 57.754
getZScores 32.528 0.300 32.873
plotDifferences 8.948 0.008 8.977
getDifferences 5.992 0.004 5.998
plotZScores 5.800 0.024 5.830
getAllResults 5.604 0.012 5.621
* 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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.12-bioc/meat/FourCSeq.Rcheck/00check.log’
for details.
FourCSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL FourCSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘FourCSeq’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: Package 'FourCSeq' is deprecated and will be removed from Bioconductor version 3.13 ** testing if installed package can be loaded from final location Warning: Package 'FourCSeq' is deprecated and will be removed from Bioconductor version 3.13 ** 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 | 0.008 | 1.070 | |
| addFragments | 2.944 | 0.048 | 3.003 | |
| addViewpointFrags | 1.112 | 0.132 | 1.243 | |
| combineFragEnds | 0.316 | 0.004 | 0.319 | |
| countFragmentOverlaps | 2.772 | 0.008 | 2.935 | |
| countFragmentOverlapsSecondCutter | 0 | 0 | 0 | |
| fc | 0.132 | 0.000 | 0.133 | |
| fcf | 0.176 | 0.008 | 0.181 | |
| findViewpointFragments | 0.948 | 0.000 | 0.951 | |
| getAllResults | 5.604 | 0.012 | 5.621 | |
| getDifferences | 5.992 | 0.004 | 5.998 | |
| getDistAroundVp | 1.048 | 0.008 | 1.058 | |
| getNormalizationFactors | 0.412 | 0.020 | 0.430 | |
| getReferenceSeq | 0.528 | 0.016 | 0.544 | |
| getZScores | 32.528 | 0.300 | 32.873 | |
| normalizeRPM | 0.208 | 0.008 | 0.218 | |
| plotDifferences | 8.948 | 0.008 | 8.977 | |
| plotFits | 2.040 | 0.012 | 2.063 | |
| plotNormalizationFactors | 4.336 | 0.000 | 4.342 | |
| plotScatter | 56.884 | 0.780 | 57.754 | |
| plotZScores | 5.800 | 0.024 | 5.830 | |
| smoothCounts | 0.204 | 0.000 | 0.207 | |
| smoothHitPerCent | 1.968 | 0.020 | 1.999 | |
| writeTrackFiles | 1.192 | 0.008 | 1.198 | |