| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:05 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the GeneBreak package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneBreak.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 710/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneBreak 1.22.0 (landing page) Evert van den Broek
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneBreak.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneBreak_1.22.0.tar.gz |
| StartedAt: 2021-10-14 23:29:05 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:33:38 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 273.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneBreak.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneBreak.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneBreak_1.22.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GeneBreak.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.22.0'
* 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 5.58 0.42 6.00
recurrentGenes-CopyNumberBreakPointGenes-method 5.41 0.27 5.67
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CopyNumberBreakPointGenes-class 6.00 0.15 6.15
bpPlot-CopyNumberBreakPoints-method 4.98 0.16 5.14
* 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-3.13-bioc/meat/GeneBreak.Rcheck/00check.log'
for details.
GeneBreak.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GeneBreak_1.22.0.tar.gz && rm -rf GeneBreak.buildbin-libdir && mkdir GeneBreak.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneBreak.buildbin-libdir GeneBreak_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GeneBreak_1.22.0.zip && rm GeneBreak_1.22.0.tar.gz GeneBreak_1.22.0.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
3 4105k 3 162k 0 0 709k 0 0:00:05 --:--:-- 0:00:05 708k
76 4105k 76 3137k 0 0 2572k 0 0:00:01 0:00:01 --:--:-- 2571k
100 4105k 100 4105k 0 0 2764k 0 0:00:01 0:00:01 --:--:-- 2764k
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_1.22.0.zip
* DONE (GeneBreak)
* installing to library 'C:/Users/biocbuild/bbs-3.13-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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