Sarah Sandmann
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/BBCAnalyzer |
| Branch: RELEASE_3_11 |
| Last Commit: b9621dc |
| Last Changed Date: 2020-04-27 14:50:41 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:07 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE BBCAnalyzer PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 125/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BBCAnalyzer 1.18.0 Sarah Sandmann
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: BBCAnalyzer |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BBCAnalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BBCAnalyzer_1.18.0.tar.gz |
| StartedAt: 2020-10-17 01:47:13 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 01:55:42 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 508.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BBCAnalyzer.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:BBCAnalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BBCAnalyzer_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/BBCAnalyzer.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 'BBCAnalyzer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BBCAnalyzer' version '1.18.0'
* 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 'C:/Users/biocbuild/bbs-3.11-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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
analyzeBasesPlotOnly 24.73 0.75 25.51
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
analyzeBasesPlotOnly 39.75 0.28 40.04
* 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
'C:/Users/biocbuild/bbs-3.11-bioc/meat/BBCAnalyzer.Rcheck/00check.log'
for details.
BBCAnalyzer.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/BBCAnalyzer_1.18.0.tar.gz && rm -rf BBCAnalyzer.buildbin-libdir && mkdir BBCAnalyzer.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BBCAnalyzer.buildbin-libdir BBCAnalyzer_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL BBCAnalyzer_1.18.0.zip && rm BBCAnalyzer_1.18.0.tar.gz BBCAnalyzer_1.18.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1798k 100 1798k 0 0 17.0M 0 --:--:-- --:--:-- --:--:-- 18.1M
install for i386
* 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
converting help for package 'BBCAnalyzer'
finding HTML links ... done
BBCAnalyzer-package html
analyzeBases html
analyzeBasesPlotOnly html
** 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
install for x64
* installing *source* package 'BBCAnalyzer' ...
** testing if installed package can be loaded
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer'
* MD5 sums
packaged installation of 'BBCAnalyzer' as BBCAnalyzer_1.18.0.zip
* DONE (BBCAnalyzer)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'BBCAnalyzer' successfully unpacked and MD5 sums checked
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BBCAnalyzer.Rcheck/examples_i386/BBCAnalyzer-Ex.timings
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BBCAnalyzer.Rcheck/examples_x64/BBCAnalyzer-Ex.timings
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