| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:25 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 BBCAnalyzer package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BBCAnalyzer.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 129/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BBCAnalyzer 1.28.0 (landing page) Sarah Sandmann
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: BBCAnalyzer |
| Version: 1.28.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BBCAnalyzer.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings BBCAnalyzer_1.28.0.tar.gz |
| StartedAt: 2023-04-10 23:07:24 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:12:15 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 290.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BBCAnalyzer.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BBCAnalyzer.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings BBCAnalyzer_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/BBCAnalyzer.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BBCAnalyzer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BBCAnalyzer' version '1.28.0'
* 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 'BBCAnalyzer' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer'
See 'F:/biocbuild/bbs-3.16-bioc/meat/BBCAnalyzer.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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
analyzeBases: no visible global function definition for 'read.table'
analyzeBasesPlotOnly: no visible global function definition for
'read.table'
analyzeReads: no visible global function definition for 'path'
analyzeReads: no visible global function definition for 'write.table'
checkBamInput: no visible global function definition for 'path'
checkVcfInput: no visible global function definition for 'path'
frequencyAnalysis: no visible global function definition for
'write.table'
frequencyAnalysisVcf: no visible global function definition for
'read.table'
frequencyAnalysisVcf: no visible global function definition for 'path'
frequencyAnalysisVcf: no visible global function definition for
'write.table'
plotCountsPerSampleRelativeVcf_plot: no visible global function
definition for 'par'
plotCountsPerSampleRelativeVcf_plot: no visible global function
definition for 'barplot'
plotCountsPerSampleRelativeVcf_plot: no visible global function
definition for 'rect'
plotCountsPerSampleRelativeVcf_plot: no visible global function
definition for 'lines'
plotCountsPerSampleRelativeVcf_plot: no visible global function
definition for 'text'
plotCountsPerSampleRelative_plot: no visible global function definition
for 'par'
plotCountsPerSampleRelative_plot: no visible global function definition
for 'barplot'
plotCountsPerSampleRelative_plot: no visible global function definition
for 'rect'
plotCountsPerSampleRelative_plot: no visible global function definition
for 'lines'
plotCountsPerSampleRelative_plot: no visible global function definition
for 'text'
plotCountsPerSampleVcf_plot: no visible global function definition for
'par'
plotCountsPerSampleVcf_plot: no visible global function definition for
'barplot'
plotCountsPerSampleVcf_plot: no visible global function definition for
'rect'
plotCountsPerSampleVcf_plot: no visible global function definition for
'lines'
plotCountsPerSampleVcf_plot: no visible global function definition for
'text'
plotCountsPerSample_plot: no visible global function definition for
'par'
plotCountsPerSample_plot: no visible global function definition for
'barplot'
plotCountsPerSample_plot: no visible global function definition for
'rect'
plotCountsPerSample_plot: no visible global function definition for
'lines'
plotCountsPerSample_plot: no visible global function definition for
'text'
plotCountsPerTargetRelativeVcf_plot: no visible global function
definition for 'par'
plotCountsPerTargetRelativeVcf_plot: no visible global function
definition for 'barplot'
plotCountsPerTargetRelativeVcf_plot: no visible global function
definition for 'rect'
plotCountsPerTargetRelativeVcf_plot: no visible global function
definition for 'lines'
plotCountsPerTargetRelativeVcf_plot: no visible global function
definition for 'text'
plotCountsPerTargetRelative_plot: no visible global function definition
for 'par'
plotCountsPerTargetRelative_plot: no visible global function definition
for 'barplot'
plotCountsPerTargetRelative_plot: no visible global function definition
for 'rect'
plotCountsPerTargetRelative_plot: no visible global function definition
for 'lines'
plotCountsPerTargetRelative_plot: no visible global function definition
for 'text'
plotCountsPerTargetVcf_plot: no visible global function definition for
'par'
plotCountsPerTargetVcf_plot: no visible global function definition for
'barplot'
plotCountsPerTargetVcf_plot: no visible global function definition for
'rect'
plotCountsPerTargetVcf_plot: no visible global function definition for
'lines'
plotCountsPerTargetVcf_plot: no visible global function definition for
'text'
plotCountsPerTarget_plot: no visible global function definition for
'par'
plotCountsPerTarget_plot: no visible global function definition for
'barplot'
plotCountsPerTarget_plot: no visible global function definition for
'rect'
plotCountsPerTarget_plot: no visible global function definition for
'lines'
plotCountsPerTarget_plot: no visible global function definition for
'text'
processVcfFile: no visible global function definition for 'read.table'
reportVariants: no visible global function definition for 'write.table'
reportVariantsVcf: no visible global function definition for
'write.table'
Undefined global functions or variables:
barplot lines par path read.table rect text write.table
Consider adding
importFrom("graphics", "barplot", "lines", "par", "rect", "text")
importFrom("utils", "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 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
analyzeBasesPlotOnly 30.53 0.4 31.18
* 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, 1 NOTE
See
'F:/biocbuild/bbs-3.16-bioc/meat/BBCAnalyzer.Rcheck/00check.log'
for details.
BBCAnalyzer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL BBCAnalyzer ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'BBCAnalyzer' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer' ** testing if installed package can be loaded from final location Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer' ** testing if installed package keeps a record of temporary installation path * DONE (BBCAnalyzer)
BBCAnalyzer.Rcheck/BBCAnalyzer-Ex.timings
| name | user | system | elapsed | |
| BBCAnalyzer-package | 0.18 | 0.09 | 0.30 | |
| analyzeBases | 0.20 | 0.02 | 0.22 | |
| analyzeBasesPlotOnly | 30.53 | 0.40 | 31.18 | |