Tom Carroll
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/ChIPQC |
| git_branch: devel |
| git_last_commit: a673e8a |
| git_last_commit_date: 2024-10-29 09:51:17 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:15 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| 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 331/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPQC 1.43.0 (landing page) Tom Carroll
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the ChIPQC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPQC.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: 1.43.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPQC.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ChIPQC_1.43.0.tar.gz |
| StartedAt: 2024-11-27 23:04:01 -0500 (Wed, 27 Nov 2024) |
| EndedAt: 2024-11-27 23:11:45 -0500 (Wed, 27 Nov 2024) |
| EllapsedTime: 463.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPQC.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPQC.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ChIPQC_1.43.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/ChIPQC.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ChIPQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPQC' version '1.43.0'
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
ChIPQC-data.Rd: GRanges, DiffBind
ChIPQC-package.Rd: DiffBind
ChIPQC.Rd: DBA-object, DiffBind, dba.peakset, dba, GRanges,
dba.count, bplapply, BiocParallel, register
ChIPQCexperiment-class.Rd: DBA-object, DiffBind
ChIPQCsample-class.Rd: GRanges, GRanges-class
QCdba-methods.Rd: DBA-object, DiffBind, dba
peaks-methods.Rd: GRangesList, GRanges
plotCorHeatmap-methods.Rd: dba.plotHeatmap
plotPrincomp-methods.Rd: dba.plotPCA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChIPQCreport 23.35 1.02 25.38
* 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: 5 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/ChIPQC.Rcheck/00check.log'
for details.
ChIPQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL ChIPQC ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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 | 1.20 | 0.09 | 1.29 | |
| ChIPQC | 0.36 | 0.03 | 0.39 | |
| ChIPQCexperiment-class | 0.36 | 0.03 | 0.39 | |
| ChIPQCreport | 23.35 | 1.02 | 25.38 | |
| ChIPQCsample-class | 1.19 | 0.00 | 1.21 | |
| FragmentLengthCrossCoverage-methods | 0.03 | 0.03 | 0.07 | |
| Normalisedaveragepeaksignal-methods | 0.01 | 0.02 | 0.03 | |
| QCannotation-methods | 0.02 | 0.00 | 0.01 | |
| QCcontrol-methods | 0.24 | 0.00 | 0.23 | |
| QCdba-methods | 0.11 | 0.03 | 0.14 | |
| QCmetadata-methods | 0.11 | 0.00 | 0.11 | |
| QCmetrics-methods | 0.47 | 0.01 | 0.49 | |
| QCsample-methods | 0.06 | 0.00 | 0.06 | |
| ReadLengthCrossCoverage-methods | 0.01 | 0.02 | 0.03 | |
| RelativeCrossCoverage-methods | 0.08 | 0.01 | 0.10 | |
| averagepeaksignal-methods | 0.05 | 0.00 | 0.04 | |
| coveragehistogram-methods | 0.00 | 0.03 | 0.03 | |
| crosscoverage-methods | 0.04 | 0.00 | 0.03 | |
| duplicateRate-methods | 0.01 | 0.02 | 0.03 | |
| duplicates-methods | 0.03 | 0.00 | 0.03 | |
| flagtagcounts-methods | 0.00 | 0.03 | 0.03 | |
| fragmentlength-methods | 0.08 | 0.02 | 0.10 | |
| frip-methods | 0.03 | 0.00 | 0.03 | |
| mapped-methods | 0.03 | 0.00 | 0.03 | |
| peaks-methods | 0.24 | 0.00 | 0.24 | |
| plotCC-methods | 1.22 | 0.03 | 1.25 | |
| plotCorHeatmap-methods | 0.26 | 0.01 | 0.28 | |
| plotCoverageHist-methods | 0.5 | 0.0 | 0.5 | |
| plotFribl-methods | 0.69 | 0.00 | 0.68 | |
| plotFrip-methods | 0.73 | 0.00 | 0.74 | |
| plotPeakProfile-methods | 1.25 | 0.04 | 1.28 | |
| plotPrincomp-methods | 0.32 | 0.00 | 0.31 | |
| plotRap-methods | 0.75 | 0.01 | 0.77 | |
| plotRegi-methods | 1.17 | 0.06 | 1.23 | |
| plotSSD-methods | 1.42 | 0.03 | 1.46 | |
| readlength-methods | 0.00 | 0.02 | 0.01 | |
| reads-methods | 0.03 | 0.00 | 0.03 | |
| regi-methods | 0.05 | 0.00 | 0.05 | |
| ribl-methods | 0.01 | 0.00 | 0.01 | |
| rip-methods | 0.02 | 0.02 | 0.04 | |
| ssd-methods | 0.01 | 0.00 | 0.01 | |