GeneBreak 1.2.0
Evert van den Broek
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/GeneBreak | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf GeneBreak.buildbin-libdir GeneBreak.Rcheck && mkdir GeneBreak.buildbin-libdir GeneBreak.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneBreak.buildbin-libdir GeneBreak_1.2.0.tar.gz >GeneBreak.Rcheck\00install.out 2>&1 && cp GeneBreak.Rcheck\00install.out GeneBreak-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=GeneBreak.buildbin-libdir --install="check:GeneBreak-install.out" --force-multiarch --no-vignettes --timings GeneBreak_1.2.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/GeneBreak.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.2.0'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
recurrentGenes-CopyNumberBreakPointGenes-method 13.51 0.25 13.76
bpPlot-CopyNumberBreakPoints-method 10.95 0.15 11.11
CopyNumberBreakPointGenes-class 10.91 0.14 11.04
bpStats-CopyNumberBreakPoints-method 10.61 0.16 10.77
geneChromosomes-CopyNumberBreakPointGenes-method 5.62 0.17 5.79
geneInfo-CopyNumberBreakPointGenes-method 5.02 0.22 5.24
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
bpStats-CopyNumberBreakPoints-method 12.85 0.16 13.01
CopyNumberBreakPointGenes-class 12.64 0.14 12.99
recurrentGenes-CopyNumberBreakPointGenes-method 12.14 0.22 12.36
bpPlot-CopyNumberBreakPoints-method 10.97 0.12 11.09
breakpointsPerGene-CopyNumberBreakPointGenes-method 5.59 0.35 5.93
addGeneAnnotation-CopyNumberBreakPoints-method 5.47 0.24 5.71
geneInfo-CopyNumberBreakPointGenes-method 5.07 0.18 5.24
featuresPerGene-CopyNumberBreakPointGenes-method 4.95 0.28 5.22
geneChromosomes-CopyNumberBreakPointGenes-method 4.88 0.17 5.06
* 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
'E:/biocbld/bbs-3.3-bioc/meat/GeneBreak.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GeneBreak' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'segmentData' in package 'GeneBreak'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'GeneBreak' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneBreak' as GeneBreak_1.2.0.zip
* DONE (GeneBreak)