Tom Carroll
| Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 2024) |
| git_url: https://git.bioconductor.org/packages/ChIPQC |
| git_branch: devel |
| git_last_commit: 448ae73 |
| git_last_commit_date: 2024-04-30 10:35:54 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-13 11:32:01 -0400 (Mon, 13 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 330/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPQC 1.41.0 (landing page) Tom Carroll
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the ChIPQC package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ChIPQC |
| Version: 1.41.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPQC_1.41.0.tar.gz |
| StartedAt: 2024-05-12 08:23:55 -0400 (Sun, 12 May 2024) |
| EndedAt: 2024-05-12 08:31:57 -0400 (Sun, 12 May 2024) |
| EllapsedTime: 482.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChIPQC.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPQC_1.41.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/ChIPQC.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPQC’ version ‘1.41.0’
* 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 ‘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 code 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: ‘BiocParallel’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
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
ChIPQC: no visible global function definition for ‘is’
ChIPQC: no visible global function definition for ‘multicoreWorkers’
ChIPQC: no visible global function definition for ‘snowWorkers’
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 is log10_bp log2_Enrichment multicoreWorkers seqlengths
seqlengths<- seqlevels<- snowWorkers
Consider adding
importFrom("methods", "is")
importFrom("stats", "SSD")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) ChIPQC.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:29-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:56-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:59-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:62-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:65-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:68-70: Lost braces in \itemize; meant \describe ?
* 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 ... 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 Depends/Imports.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChIPQCreport 25.822 0.6 26.589
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/ChIPQC.Rcheck/00check.log’
for details.
ChIPQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPQC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘ChIPQC’ ... ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ChIPQC)
ChIPQC.Rcheck/ChIPQC-Ex.timings
| name | user | system | elapsed | |
| ChIPQC-data | 1.202 | 0.066 | 1.273 | |
| ChIPQC | 0.403 | 0.013 | 0.416 | |
| ChIPQCexperiment-class | 0.501 | 0.019 | 0.524 | |
| ChIPQCreport | 25.822 | 0.600 | 26.589 | |
| ChIPQCsample-class | 0.944 | 0.043 | 0.995 | |
| FragmentLengthCrossCoverage-methods | 0.060 | 0.007 | 0.067 | |
| Normalisedaveragepeaksignal-methods | 0.034 | 0.010 | 0.044 | |
| QCannotation-methods | 0.020 | 0.007 | 0.027 | |
| QCcontrol-methods | 0.223 | 0.010 | 0.234 | |
| QCdba-methods | 0.149 | 0.010 | 0.159 | |
| QCmetadata-methods | 0.149 | 0.012 | 0.162 | |
| QCmetrics-methods | 0.418 | 0.020 | 0.443 | |
| QCsample-methods | 0.056 | 0.008 | 0.065 | |
| ReadLengthCrossCoverage-methods | 0.021 | 0.008 | 0.028 | |
| RelativeCrossCoverage-methods | 0.055 | 0.006 | 0.062 | |
| averagepeaksignal-methods | 0.037 | 0.010 | 0.047 | |
| coveragehistogram-methods | 0.034 | 0.010 | 0.045 | |
| crosscoverage-methods | 0.029 | 0.009 | 0.038 | |
| duplicateRate-methods | 0.018 | 0.007 | 0.025 | |
| duplicates-methods | 0.020 | 0.008 | 0.028 | |
| flagtagcounts-methods | 0.021 | 0.008 | 0.030 | |
| fragmentlength-methods | 0.059 | 0.008 | 0.067 | |
| frip-methods | 0.020 | 0.007 | 0.027 | |
| mapped-methods | 0.022 | 0.007 | 0.029 | |
| peaks-methods | 0.149 | 0.008 | 0.158 | |
| plotCC-methods | 0.971 | 0.023 | 1.005 | |
| plotCorHeatmap-methods | 0.235 | 0.015 | 0.254 | |
| plotCoverageHist-methods | 0.472 | 0.013 | 0.487 | |
| plotFribl-methods | 0.469 | 0.011 | 0.484 | |
| plotFrip-methods | 0.516 | 0.013 | 0.530 | |
| plotPeakProfile-methods | 1.160 | 0.035 | 1.196 | |
| plotPrincomp-methods | 0.263 | 0.014 | 0.277 | |
| plotRap-methods | 0.730 | 0.026 | 0.771 | |
| plotRegi-methods | 0.647 | 0.021 | 0.674 | |
| plotSSD-methods | 0.953 | 0.022 | 0.982 | |
| readlength-methods | 0.022 | 0.007 | 0.029 | |
| reads-methods | 0.022 | 0.007 | 0.030 | |
| regi-methods | 0.047 | 0.008 | 0.056 | |
| ribl-methods | 0.022 | 0.008 | 0.029 | |
| rip-methods | 0.022 | 0.008 | 0.030 | |
| ssd-methods | 0.020 | 0.007 | 0.027 | |