Tom Carroll
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/ChIPQC |
| Branch: RELEASE_3_11 |
| Last Commit: 0b035f0 |
| Last Changed Date: 2020-07-18 12:35:57 -0400 (Sat, 18 Jul 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:15 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE ChIPQC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 283/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ChIPQC 1.24.1 Tom Carroll
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: ChIPQC |
| Version: 1.24.1 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ChIPQC_1.24.1.tar.gz |
| StartedAt: 2020-10-17 02:30:55 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:44:44 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 829.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChIPQC.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ChIPQC_1.24.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ChIPQC.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPQC' version '1.24.1'
* 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 'ChIPQC' can be installed ... OK
* 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
* 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
* 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'S4Vectors:::tabulate2'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call("rle_sum_any", ..., PACKAGE = "chipseq")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
GetGRanges: no visible global function definition for 'seqlevels<-'
findCovMaxPos: no visible global function definition for 'seqlengths'
findCovMaxPos: no visible global function definition for 'seqlengths<-'
getAnnotation: no visible binding for global variable
'TxDb.Hsapiens.UCSC.hg38.knownGene'
getAnnotation: no visible global function definition for 'seqlengths'
makeCCplot: no visible binding for global variable 'Shift_Size'
makeCCplot: no visible binding for global variable 'CC_Score'
makeCoveragePlot: no visible binding for global variable 'Depth'
makeCoveragePlot: no visible binding for global variable 'log10_bp'
makeCoveragePlot: no visible binding for global variable 'Sample'
makeFriblPlot: no visible binding for global variable 'Sample'
makeFriblPlot: no visible binding for global variable 'FRIBL'
makeFriblPlot: no visible binding for global variable 'Reads'
makeFripPlot: no visible binding for global variable 'Sample'
makeFripPlot: no visible binding for global variable 'FRIP'
makeFripPlot: no visible binding for global variable 'Reads'
makePeakProfilePlot: no visible binding for global variable 'Distance'
makePeakProfilePlot: no visible binding for global variable 'Signal'
makeRapPlot: no visible binding for global variable 'Sample'
makeRapPlot: no visible binding for global variable 'CountsInPeaks'
makeRegiPlot: no visible binding for global variable 'Sample'
makeRegiPlot: no visible binding for global variable 'GenomicIntervals'
makeRegiPlot: no visible binding for global variable 'log2_Enrichment'
makeSSDPlot: no visible binding for global variable 'Sample'
makeSSDPlot: no visible binding for global variable 'SSD'
makeSSDPlot: no visible global function definition for 'geom_point'
sampleQC: no visible global function definition for 'seqlevels<-'
plotCC,ChIPQCexperiment: no visible binding for global variable
'Sample'
plotCC,list: no visible binding for global variable 'Sample'
plotPeakProfile,ChIPQCexperiment: no visible binding for global
variable 'Sample'
plotPeakProfile,list: no visible binding for global variable 'Sample'
Undefined global functions or variables:
CC_Score CountsInPeaks Depth Distance FRIBL FRIP GenomicIntervals
Reads SSD Sample Shift_Size Signal TxDb.Hsapiens.UCSC.hg38.knownGene
geom_point log10_bp log2_Enrichment seqlengths seqlengths<-
seqlevels<-
Consider adding
importFrom("stats", "SSD")
to your NAMESPACE file.
* 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 ... NOTE
Output for data("tamoxifen_QC", package = "ChIPQC"):
* checking data for non-ASCII characters ... WARNING
Error loading dataset 'exampleExp':
Error in .requirePackage(package) :
unable to find required package 'ChIPQC'
Error loading dataset 'tamoxifen':
Error in .requirePackage(package) :
unable to find required package 'ChIPQC'
The dataset(s) may use package(s) not declared in the DESCRIPTION file.
* 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' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChIPQCreport 21.62 2.98 24.61
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChIPQCreport 23.52 2.16 26.27
* 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, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/ChIPQC.Rcheck/00check.log'
for details.
ChIPQC.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ChIPQC_1.24.1.tar.gz && rm -rf ChIPQC.buildbin-libdir && mkdir ChIPQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPQC.buildbin-libdir ChIPQC_1.24.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ChIPQC_1.24.1.zip && rm ChIPQC_1.24.1.tar.gz ChIPQC_1.24.1.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1073k 100 1073k 0 0 15.0M 0 --:--:-- --:--:-- --:--:-- 16.6M
install for i386
* installing *source* package 'ChIPQC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ChIPQC'
finding HTML links ... done
ChIPQC-data html
finding level-2 HTML links ... done
ChIPQC-package html
ChIPQC html
ChIPQCexperiment-class html
ChIPQCreport html
ChIPQCsample-class html
FragmentLengthCrossCoverage-methods html
Normalisedaveragepeaksignal-methods html
QCannotation-methods html
QCcontrol-methods html
QCdba-methods html
QCmetadata-methods html
QCmetrics-methods html
QCsample-methods html
ReadLengthCrossCoverage-methods html
RelativeCrossCoverage-methods html
averagepeaksignal-methods html
coveragehistogram-methods html
crosscoverage-methods html
duplicateRate-methods html
duplicates-methods html
flagtagcounts-methods html
fragmentlength-methods html
frip-methods html
mapped-methods html
peaks-methods html
plotCC-methods html
plotCorHeatmap-methods html
plotCoverageHist-methods html
plotFribl-methods html
plotFrip-methods html
plotPeakProfile-methods html
plotPrincomp-methods html
plotRap-methods html
plotRegi-methods html
plotSSD-methods html
readlength-methods html
reads-methods html
regi-methods html
ribl-methods html
rip-methods html
ssd-methods html
** building package indices
** installing vignettes
'ChIPQC.Rnw'
** 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
install for x64
* installing *source* package 'ChIPQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPQC' as ChIPQC_1.24.1.zip
* DONE (ChIPQC)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ChIPQC' successfully unpacked and MD5 sums checked
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ChIPQC.Rcheck/examples_i386/ChIPQC-Ex.timings
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ChIPQC.Rcheck/examples_x64/ChIPQC-Ex.timings
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