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BioC 3.2: CHECK report for SNPhood on linux1.bioconductor.org

This page was generated on 2015-10-27 17:27:31 -0400 (Tue, 27 Oct 2015).

Package 993/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.0.1
Christian Arnold
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/SNPhood
Last Changed Rev: 109647 / Revision: 109947
Last Changed Date: 2015-10-15 08:24:18 -0400 (Thu, 15 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  TIMEOUT  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SNPhood
Version: 1.0.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.0.1.tar.gz
StartedAt: 2015-10-27 08:17:07 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 08:22:25 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 318.5 seconds
RetCode: 0
Status:  OK 
CheckDir: SNPhood.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/SNPhood.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.0.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SNPhood’ can be installed ... [24s/24s] 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
* 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 ... NOTE
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.calcBinomTestVector: no visible binding for global variable ‘pp’
.plotClusterAverage: no visible binding for global variable ‘value’
.plotClusterAverage: no visible binding for global variable ‘Cluster’
.plotRegionFeatures: no visible binding for global variable ‘value’
.plotRegionFeatures: no visible binding for global variable
  ‘datasetAndReadGroup’
plotAllelicBiasResults: no visible binding for global variable ‘bin’
plotAllelicBiasResults: no visible binding for global variable ‘value’
plotAllelicBiasResults: no visible binding for global variable
  ‘confLower’
plotAllelicBiasResults: no visible binding for global variable
  ‘confUpper’
plotAllelicBiasResults: no visible binding for global variable
  ‘valueTransf’
plotBinCounts: no visible binding for global variable ‘bin’
plotBinCounts: no visible binding for global variable ‘value’
plotGenotypesPerCluster: no visible binding for global variable ‘type’
plotGenotypesPerCluster: no visible binding for global variable ‘value’
plotGenotypesPerCluster: no visible binding for global variable
  ‘Genotype’
plotGenotypesPerSNP: no visible binding for global variable ‘SNP’
plotGenotypesPerSNP: no visible binding for global variable ‘value’
plotGenotypesPerSNP: no visible binding for global variable ‘Genotype’
* 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 ... [98s/100s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
analyzeSNPhood     58.753  2.099  61.079
associateGenotypes  6.906  0.012   6.934
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/SNPhood.Rcheck/00check.log’
for details.


SNPhood.Rcheck/00install.out:

* installing *source* package ‘SNPhood’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SNPhood)

SNPhood.Rcheck/SNPhood-Ex.timings:

nameusersystemelapsed
analyzeSNPhood58.753 2.09961.079
annotation-methods0.1540.0160.170
annotationBins0.0440.0040.048
annotationBins20.2640.0000.606
annotationDatasets0.0450.0000.045
annotationReadGroups0.0510.0000.051
annotationRegions0.0590.0000.059
associateGenotypes6.9060.0126.934
bins-methods0.050.000.05
collectFiles0.0320.0000.032
convertToAllelicFractions0.1310.0000.129
counts-method0.1500.0040.154
datasets-methods0.0530.0000.053
deleteDatasets0.080.000.08
deleteReadGroups0.5390.0000.539
deleteRegions0.250.000.25
enrichment-methods0.0280.0000.028
getDefaultParameterList0.0010.0000.002
mergeReadGroups0.3020.0000.303
parameters-methods0.0050.0000.006
plotAllelicBiasResults4.2940.0004.297
plotAllelicBiasResultsOverview2.0660.0402.433
plotAndCalculateCorrelationDatasets0.1970.0040.201
plotAndCalculateWeakAndStrongGenotype0.9020.0000.901
plotAndClusterMatrix1.2680.0001.269
plotBinCounts1.80.01.8
plotClusterAverage0.4610.0040.465
plotGenotypesPerCluster0.8720.0040.877
plotGenotypesPerSNP0.2650.0000.265
plotRegionCounts2.6570.0083.151
readGroups-methods0.0340.0080.042
regions-methods0.0460.0000.046
renameBins0.0790.0000.082
renameDatasets0.4720.0040.477
renameReadGroups0.0840.0000.084
renameRegions0.5560.0000.557
results0.4530.1000.554
testForAllelicBiases1.8320.0081.840