Evert van den Broek
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/GeneBreak |
| Branch: RELEASE_3_11 |
| Last Commit: 622fa51 |
| Last Changed Date: 2020-04-27 14:52:15 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:38 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE GeneBreak PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 676/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneBreak 1.18.0 Evert van den Broek
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: GeneBreak |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneBreak.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GeneBreak_1.18.0.tar.gz |
| StartedAt: 2020-10-17 04:17:46 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:22:55 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 309.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneBreak.Rcheck |
| Warnings: 0 |
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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:GeneBreak.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GeneBreak_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/GeneBreak.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 'GeneBreak/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneBreak' 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 'GeneBreak' 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 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
.glmbreak: no visible global function definition for 'glm'
.glmbreak: no visible global function definition for 'predict'
addGeneAnnotation,CopyNumberBreakPoints: no visible global function
definition for 'head'
bpStats,CopyNumberBreakPoints: no visible global function definition
for 'sd'
bpStats,CopyNumberBreakPoints: no visible global function definition
for 'p.adjust'
Undefined global functions or variables:
glm head p.adjust predict sd
Consider adding
importFrom("stats", "glm", "p.adjust", "predict", "sd")
importFrom("utils", "head")
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 data for ASCII and uncompressed saves ... 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
CopyNumberBreakPointGenes-class 7.72 0.37 8.09
bpPlot-CopyNumberBreakPoints-method 6.13 0.13 6.25
bpStats-CopyNumberBreakPoints-method 5.67 0.16 5.83
recurrentGenes-CopyNumberBreakPointGenes-method 5.42 0.25 5.67
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CopyNumberBreakPointGenes-class 7.78 0.19 7.97
bpStats-CopyNumberBreakPoints-method 6.31 0.27 6.58
bpPlot-CopyNumberBreakPoints-method 5.22 0.11 5.33
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/GeneBreak.Rcheck/00check.log'
for details.
GeneBreak.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/GeneBreak_1.18.0.tar.gz && rm -rf GeneBreak.buildbin-libdir && mkdir GeneBreak.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneBreak.buildbin-libdir GeneBreak_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL GeneBreak_1.18.0.zip && rm GeneBreak_1.18.0.tar.gz GeneBreak_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 4104k 100 4104k 0 0 36.5M 0 --:--:-- --:--:-- --:--:-- 38.5M
install for i386
* installing *source* package 'GeneBreak' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'segmentData' in package 'GeneBreak'
** help
*** installing help indices
converting help for package 'GeneBreak'
finding HTML links ... done
CopyNumberBreakPointGenes-class html
CopyNumberBreakPoints-class html
GeneBreak html
accessOptions-CopyNumberBreakPoints-method
html
addGeneAnnotation-CopyNumberBreakPoints-method
html
bpFilter-CopyNumberBreakPoints-method html
bpGenes-CopyNumberBreakPointGenes-method
html
bpPlot-CopyNumberBreakPoints-method html
bpStats-CopyNumberBreakPoints-method html
breakpointData-CopyNumberBreakPoints-method
html
breakpointsPerGene-CopyNumberBreakPointGenes-method
html
callData-CopyNumberBreakPoints-method html
copynumber.data.chr18 html
copynumber.data.chr20 html
copynumber.data.chr21 html
ens.gene.ann.hg18 html
ens.gene.ann.hg19 html
ens.gene.ann.hg38 html
featureChromosomes-CopyNumberBreakPoints-method
html
featureInfo-CopyNumberBreakPoints-method
html
featuresPerGene-CopyNumberBreakPointGenes-method
html
geneChromosomes-CopyNumberBreakPointGenes-method
html
geneInfo-CopyNumberBreakPointGenes-method
html
getBreakpoints html
namesFeatures-CopyNumberBreakPoints-method
html
recurrentGenes-CopyNumberBreakPointGenes-method
html
sampleNames-CopyNumberBreakPoints-method
html
segmentData-CopyNumberBreakPoints-method
html
** 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
install for x64
* installing *source* package 'GeneBreak' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneBreak' as GeneBreak_1.18.0.zip
* DONE (GeneBreak)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'GeneBreak' successfully unpacked and MD5 sums checked
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GeneBreak.Rcheck/examples_i386/GeneBreak-Ex.timings
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GeneBreak.Rcheck/examples_x64/GeneBreak-Ex.timings
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