Gro Nilsen
| Snapshot Date: 2023-04-03 14:00:24 -0400 (Mon, 03 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/copynumber |
| git_branch: devel |
| git_last_commit: 63a78b1 |
| git_last_commit_date: 2023-03-06 11:52:54 -0400 (Mon, 06 Mar 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-04-04 11:06:37 -0400 (Tue, 04 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4554 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4314 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4311 |
| 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 | ||||
|
To the developers/maintainers of the copynumber package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/copynumber.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 422/2200 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Gro Nilsen
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: copynumber |
| Version: 1.39.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:copynumber.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings copynumber_1.39.1.tar.gz |
| StartedAt: 2023-04-04 00:06:47 -0400 (Tue, 04 Apr 2023) |
| EndedAt: 2023-04-04 00:12:00 -0400 (Tue, 04 Apr 2023) |
| EllapsedTime: 313.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: copynumber.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:copynumber.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings copynumber_1.39.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/copynumber.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘copynumber/DESCRIPTION’ ... OK
* this is package ‘copynumber’ version ‘1.39.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘copynumber’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'copynumber' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.17-bioc/meat/copynumber.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘BiocGenerics’
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
addArmlines: no visible global function definition for ‘modifyList’
addArmlines: no visible global function definition for ‘abline’
addChromlines: no visible global function definition for ‘modifyList’
addChromlines: no visible global function definition for ‘abline’
addChromlines: no visible global function definition for ‘mtext’
addToFreqPlot: no visible global function definition for ‘abline’
addToFreqPlot: no visible global function definition for ‘axis’
addToFreqPlot: no visible global function definition for ‘title’
addToPlot: no visible global function definition for ‘axis’
addToPlot: no visible global function definition for ‘mtext’
addToPlot: no visible global function definition for ‘title’
addToPlot: no visible global function definition for ‘abline’
aspcf: no visible global function definition for ‘read.table’
aspcf: no visible global function definition for ‘write.table’
c.lines: no visible global function definition for ‘lines’
chromPattern: no visible global function definition for ‘rect’
chromPattern: no visible global function definition for ‘par’
chromosomeAberration: no visible global function definition for
‘dev.cur’
chromosomeAberration: no visible global function definition for
‘dev.new’
chromosomeAberration: no visible global function definition for ‘par’
chromosomeAberration: no visible global function definition for ‘rect’
chromosomeAberration: no visible global function definition for ‘title’
chromosomeAberration: no visible global function definition for ‘axis’
chromosomeAberration: no visible global function definition for
‘abline’
chromosomeAberration: no visible global function definition for
‘devAskNewPage’
chromosomeFreq: no visible global function definition for ‘dev.cur’
chromosomeFreq: no visible global function definition for ‘dev.new’
chromosomeFreq: no visible global function definition for ‘par’
chromosomeFreq: no visible global function definition for ‘rect’
chromosomeFreq: no visible global function definition for ‘abline’
chromosomeFreq: no visible global function definition for ‘title’
chromosomeFreq: no visible global function definition for
‘devAskNewPage’
chromosomeHeat: no visible global function definition for ‘dev.cur’
chromosomeHeat: no visible global function definition for ‘dev.new’
chromosomeHeat: no visible global function definition for ‘par’
chromosomeHeat: no visible global function definition for ‘rect’
chromosomeHeat: no visible global function definition for ‘title’
chromosomeHeat: no visible global function definition for ‘axis’
chromosomeHeat: no visible global function definition for ‘abline’
chromosomeHeat: no visible global function definition for
‘devAskNewPage’
colorSetup: no visible global function definition for
‘colorRampPalette’
connectSeg: no visible global function definition for ‘segments’
draw.roundEdge: no visible global function definition for ‘polygon’
drawStalk: no visible global function definition for ‘polygon’
filterMarkS4: no visible global function definition for ‘quantile’
genomeAberration: no visible global function definition for ‘dev.cur’
genomeAberration: no visible global function definition for ‘dev.new’
genomeAberration: no visible global function definition for ‘par’
genomeAberration: no visible global function definition for ‘rect’
genomeAberration: no visible global function definition for ‘title’
genomeAberration: no visible global function definition for ‘axis’
genomeAberration: no visible global function definition for ‘abline’
genomeAberration: no visible global function definition for
‘devAskNewPage’
genomeFreq: no visible global function definition for ‘dev.cur’
genomeFreq: no visible global function definition for ‘dev.new’
genomeFreq: no visible global function definition for ‘par’
genomeFreq: no visible global function definition for ‘title’
genomeFreq: no visible global function definition for ‘rect’
genomeFreq: no visible global function definition for ‘abline’
genomeFreq: no visible global function definition for ‘devAskNewPage’
genomeHeat: no visible global function definition for ‘dev.cur’
genomeHeat: no visible global function definition for ‘dev.new’
genomeHeat: no visible global function definition for ‘par’
genomeHeat: no visible global function definition for ‘rect’
genomeHeat: no visible global function definition for ‘title’
genomeHeat: no visible global function definition for ‘axis’
genomeHeat: no visible global function definition for ‘abline’
genomeHeat: no visible global function definition for ‘devAskNewPage’
getFreqPlotParameters: no visible global function definition for
‘modifyList’
getHeatParameters: no visible global function definition for
‘modifyList’
getMad: no visible global function definition for ‘mad’
getPlotParameters: no visible global function definition for ‘rainbow’
getPlotParameters: no visible global function definition for
‘modifyList’
madWins: no visible global function definition for ‘mad’
medianFilter: no visible global function definition for ‘runmed’
multipcf: no visible global function definition for ‘read.table’
multipcf: no visible global function definition for ‘write.table’
pcf: no visible global function definition for ‘read.table’
pcf: no visible global function definition for ‘write.table’
pcfWins: no visible global function definition for ‘mad’
plotAllele: no visible global function definition for ‘modifyList’
plotAllele: no visible global function definition for ‘pdf’
plotAllele: no visible global function definition for ‘dev.cur’
plotAllele: no visible global function definition for ‘dev.new’
plotAllele: no visible global function definition for ‘devAskNewPage’
plotAllele: no visible global function definition for ‘quantile’
plotAllele: no visible global function definition for ‘par’
plotAllele: no visible global function definition for ‘legend’
plotAllele: no visible global function definition for ‘title’
plotAllele: no visible global function definition for ‘graphics.off’
plotChrom: no visible global function definition for ‘pdf’
plotChrom: no visible global function definition for ‘dev.cur’
plotChrom: no visible global function definition for ‘dev.new’
plotChrom: no visible global function definition for ‘devAskNewPage’
plotChrom: no visible global function definition for ‘quantile’
plotChrom: no visible global function definition for ‘par’
plotChrom: no visible global function definition for ‘legend’
plotChrom: no visible global function definition for ‘title’
plotChrom: no visible global function definition for ‘graphics.off’
plotCircle: no visible global function definition for ‘par’
plotCircle: no visible global function definition for ‘text’
plotCircle: no visible global function definition for ‘xspline’
plotCircle: no visible global function definition for ‘lines’
plotGamma: no visible global function definition for ‘quantile’
plotGamma: no visible global function definition for ‘col2rgb’
plotGamma: no visible global function definition for ‘rgb’
plotGamma: no visible global function definition for ‘dev.cur’
plotGamma: no visible global function definition for ‘dev.new’
plotGamma: no visible global function definition for ‘par’
plotGamma: no visible global function definition for ‘axis’
plotGamma: no visible global function definition for ‘box’
plotGamma: no visible global function definition for ‘legend’
plotGamma: no visible global function definition for ‘barplot’
plotGamma: no visible global function definition for ‘abline’
plotGamma: no visible global function definition for ‘mtext’
plotGamma: no visible global function definition for ‘points’
plotGenome: no visible global function definition for ‘quantile’
plotGenome: no visible global function definition for ‘pdf’
plotGenome: no visible global function definition for ‘dev.cur’
plotGenome: no visible global function definition for ‘dev.new’
plotGenome: no visible global function definition for ‘par’
plotGenome: no visible global function definition for ‘legend’
plotGenome: no visible global function definition for ‘title’
plotGenome: no visible global function definition for ‘devAskNewPage’
plotGenome: no visible global function definition for ‘graphics.off’
plotIdeogram: no visible global function definition for ‘rect’
plotIdeogram: no visible global function definition for ‘mtext’
plotObs: no visible global function definition for ‘par’
plotSample: no visible global function definition for ‘pdf’
plotSample: no visible global function definition for ‘dev.cur’
plotSample: no visible global function definition for ‘dev.new’
plotSample: no visible global function definition for ‘devAskNewPage’
plotSample: no visible global function definition for ‘quantile’
plotSample: no visible global function definition for ‘par’
plotSample: no visible global function definition for ‘legend’
plotSample: no visible global function definition for ‘title’
plotSample: no visible global function definition for ‘graphics.off’
plotSegments: no visible global function definition for ‘par’
sawMarkM: no visible global function definition for ‘quantile’
subset.abe: no visible binding for global variable ‘quantile’
subsetData: no visible global function definition for ‘read.table’
subsetSegments: no visible global function definition for ‘read.table’
winsorize: no visible global function definition for ‘read.table’
winsorize: no visible global function definition for ‘write.table’
Undefined global functions or variables:
abline axis barplot box col2rgb colorRampPalette dev.cur dev.new
devAskNewPage graphics.off legend lines mad modifyList mtext par pdf
points polygon quantile rainbow read.table rect rgb runmed segments
text title write.table xspline
Consider adding
importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.cur",
"dev.new", "devAskNewPage", "graphics.off", "pdf",
"rainbow", "rgb")
importFrom("graphics", "abline", "axis", "barplot", "box", "legend",
"lines", "mtext", "par", "points", "polygon", "rect",
"segments", "text", "title", "xspline")
importFrom("stats", "mad", "quantile", "runmed")
importFrom("utils", "modifyList", "read.table", "write.table")
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 ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... 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
plotCircle 9.691 0.387 13.257
plotFreq 5.740 0.080 7.644
plotHeatmap 5.072 0.067 6.779
callAberrations 4.638 0.125 6.395
plotAberration 4.639 0.092 6.278
getGRangesFormat 4.443 0.117 5.969
plotGenome 4.405 0.063 5.868
subsetSegments 4.322 0.069 5.834
plotSample 4.289 0.060 5.794
* 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-3.17-bioc/meat/copynumber.Rcheck/00check.log’
for details.
copynumber.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL copynumber ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’ * installing *source* package ‘copynumber’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 'copynumber' is deprecated and will be removed from Bioconductor version 3.18 ** testing if installed package can be loaded from final location Warning: Package 'copynumber' is deprecated and will be removed from Bioconductor version 3.18 ** testing if installed package keeps a record of temporary installation path * DONE (copynumber)
copynumber.Rcheck/copynumber-Ex.timings
| name | user | system | elapsed | |
| SNPdata | 0.004 | 0.003 | 0.013 | |
| aspcf | 3.377 | 0.158 | 4.791 | |
| callAberrations | 4.638 | 0.125 | 6.395 | |
| getGRangesFormat | 4.443 | 0.117 | 5.969 | |
| imputeMissing | 3.113 | 0.045 | 4.105 | |
| interpolate.pcf | 0.675 | 0.010 | 0.896 | |
| lymphoma | 0.001 | 0.001 | 0.007 | |
| micma | 0.001 | 0.001 | 0.002 | |
| multipcf | 1.353 | 0.024 | 1.843 | |
| pcf | 1.240 | 0.019 | 1.689 | |
| pcfPlain | 0.172 | 0.015 | 0.248 | |
| plotAberration | 4.639 | 0.092 | 6.278 | |
| plotAllele | 3.638 | 0.072 | 4.865 | |
| plotChrom | 3.609 | 0.051 | 4.776 | |
| plotCircle | 9.691 | 0.387 | 13.257 | |
| plotFreq | 5.740 | 0.080 | 7.644 | |
| plotGamma | 1.814 | 0.058 | 2.460 | |
| plotGenome | 4.405 | 0.063 | 5.868 | |
| plotHeatmap | 5.072 | 0.067 | 6.779 | |
| plotSample | 4.289 | 0.060 | 5.794 | |
| selectSegments | 1.214 | 0.010 | 1.607 | |
| subsetData | 0.008 | 0.002 | 0.016 | |
| subsetSegments | 4.322 | 0.069 | 5.834 | |
| winsorize | 0.548 | 0.006 | 0.731 | |