Multiple platform build/check report for BioC 3.6 - CHECK report for GeneBreak on tokay1

Package: GeneBreak

Version: 1.8.0

Command: rm -rf GeneBreak.buildbin-libdir GeneBreak.Rcheck && mkdir GeneBreak.buildbin-libdir GeneBreak.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneBreak.buildbin-libdir GeneBreak_1.8.0.tar.gz >GeneBreak.Rcheck\00install.out 2>&1 && cp GeneBreak.Rcheck\00install.out GeneBreak-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GeneBreak.buildbin-libdir --install="check:GeneBreak-install.out" --force-multiarch --no-vignettes --timings GeneBreak_1.8.0.tar.gz

StartedAt: 2018-04-12 00:11:52 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:16:39 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 287.2 seconds

RetCode: 0

Status: OK

CheckDir: GeneBreak.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf GeneBreak.buildbin-libdir GeneBreak.Rcheck && mkdir GeneBreak.buildbin-libdir GeneBreak.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneBreak.buildbin-libdir GeneBreak_1.8.0.tar.gz >GeneBreak.Rcheck\00install.out 2>&1 && cp GeneBreak.Rcheck\00install.out GeneBreak-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GeneBreak.buildbin-libdir --install="check:GeneBreak-install.out" --force-multiarch --no-vignettes --timings GeneBreak_1.8.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GeneBreak.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.8.0'
* 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
CopyNumberBreakPointGenes-class                 7.92   0.65    8.57
bpStats-CopyNumberBreakPoints-method            8.07   0.20    8.28
bpPlot-CopyNumberBreakPoints-method             6.53   0.23    6.77
recurrentGenes-CopyNumberBreakPointGenes-method 6.37   0.26    6.65
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                                user system elapsed
CopyNumberBreakPointGenes-class                 8.72   0.19    8.90
bpStats-CopyNumberBreakPoints-method            6.72   0.14    6.86
bpPlot-CopyNumberBreakPoints-method             6.23   0.22    6.45
recurrentGenes-CopyNumberBreakPointGenes-method 5.69   0.17    5.87
* 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-3.6-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
  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
In R CMD INSTALL

install for x64

* installing *source* package 'GeneBreak' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneBreak' as GeneBreak_1.8.0.zip
* DONE (GeneBreak)
In R CMD INSTALL
In R CMD INSTALL

name	user	system	elapsed
CopyNumberBreakPointGenes-class	7.92	0.65	8.57
CopyNumberBreakPoints-class	1.55	0.19	1.74
accessOptions-CopyNumberBreakPoints-method	0.76	0.22	0.98
addGeneAnnotation-CopyNumberBreakPoints-method	3.14	0.23	3.37
bpFilter-CopyNumberBreakPoints-method	1.39	0.22	1.61
bpGenes-CopyNumberBreakPointGenes-method	2.88	0.16	3.03
bpPlot-CopyNumberBreakPoints-method	6.53	0.23	6.77
bpStats-CopyNumberBreakPoints-method	8.07	0.20	8.28
breakpointData-CopyNumberBreakPoints-method	1.08	0.22	1.29
breakpointsPerGene-CopyNumberBreakPointGenes-method	3.02	0.28	3.30
callData-CopyNumberBreakPoints-method	1.45	0.19	1.64
featureChromosomes-CopyNumberBreakPoints-method	0.78	0.11	0.89
featureInfo-CopyNumberBreakPoints-method	2.82	0.14	2.96
featuresPerGene-CopyNumberBreakPointGenes-method	3.03	0.19	3.21
geneChromosomes-CopyNumberBreakPointGenes-method	2.98	0.17	3.16
geneInfo-CopyNumberBreakPointGenes-method	2.56	0.19	2.75
getBreakpoints	1.48	0.26	1.75
namesFeatures-CopyNumberBreakPoints-method	1.02	0.10	1.11
recurrentGenes-CopyNumberBreakPointGenes-method	6.37	0.26	6.65
sampleNames-CopyNumberBreakPoints-method	0.80	0.10	0.89
segmentData-CopyNumberBreakPoints-method	1.18	0.31	1.50

name	user	system	elapsed
CopyNumberBreakPointGenes-class	8.72	0.19	8.90
CopyNumberBreakPoints-class	1.58	0.34	1.93
accessOptions-CopyNumberBreakPoints-method	0.83	0.13	0.95
addGeneAnnotation-CopyNumberBreakPoints-method	2.44	0.19	2.63
bpFilter-CopyNumberBreakPoints-method	1.53	0.26	1.80
bpGenes-CopyNumberBreakPointGenes-method	2.64	0.25	2.89
bpPlot-CopyNumberBreakPoints-method	6.23	0.22	6.45
bpStats-CopyNumberBreakPoints-method	6.72	0.14	6.86
breakpointData-CopyNumberBreakPoints-method	1.0	0.2	1.2
breakpointsPerGene-CopyNumberBreakPointGenes-method	2.77	0.22	2.99
callData-CopyNumberBreakPoints-method	1.11	0.25	1.36
featureChromosomes-CopyNumberBreakPoints-method	0.88	0.07	0.94
featureInfo-CopyNumberBreakPoints-method	3.22	0.20	3.42
featuresPerGene-CopyNumberBreakPointGenes-method	3.17	0.17	3.34
geneChromosomes-CopyNumberBreakPointGenes-method	2.55	0.17	2.72
geneInfo-CopyNumberBreakPointGenes-method	2.53	0.17	2.71
getBreakpoints	1.64	0.15	1.78
namesFeatures-CopyNumberBreakPoints-method	0.75	0.12	0.88
recurrentGenes-CopyNumberBreakPointGenes-method	5.69	0.17	5.87
sampleNames-CopyNumberBreakPoints-method	0.81	0.06	0.88
segmentData-CopyNumberBreakPoints-method	1.13	0.18	1.30

CHECK report for GeneBreak on tokay1

Summary

Command output

Installation output

Tests output

Example timings