BioC 3.3: CHECK report for SNPhood on linux2.bioconductor.org
This page was generated on 2015-10-27 12:13:51 -0400 (Tue, 27 Oct 2015).
SNPhood 1.1.1 Christian Arnold
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SNPhood | Last Changed Rev: 109644 / Revision: 109948 | Last Changed Date: 2015-10-15 05:25:21 -0400 (Thu, 15 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
Summary
Package: SNPhood |
Version: 1.1.1 |
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.1.1.tar.gz |
StartedAt: 2015-10-27 08:13:26 -0400 (Tue, 27 Oct 2015) |
EndedAt: 2015-10-27 08:18:23 -0400 (Tue, 27 Oct 2015) |
EllapsedTime: 296.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SNPhood.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.1.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/SNPhood.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.1.1’
* 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 ... [19s/19s] 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’
Undefined global functions or variables:
Cluster Genotype SNP bin confLower confUpper datasetAndReadGroup pp
type value valueTransf
* 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 ... [97s/99s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
analyzeSNPhood 59.021 1.615 60.860
associateGenotypes 5.212 0.000 5.212
* 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-3.3-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:
name | user | system | elapsed
|
analyzeSNPhood | 59.021 | 1.615 | 60.860 |
|
annotation-methods | 0.205 | 0.032 | 0.236 |
|
annotationBins | 0.073 | 0.000 | 0.073 |
|
annotationBins2 | 0.429 | 0.008 | 0.791 |
|
annotationDatasets | 0.075 | 0.000 | 0.076 |
|
annotationReadGroups | 0.451 | 0.000 | 0.452 |
|
annotationRegions | 0.08 | 0.00 | 0.08 |
|
associateGenotypes | 5.212 | 0.000 | 5.212 |
|
bins-methods | 0.389 | 0.004 | 0.392 |
|
collectFiles | 0.021 | 0.004 | 0.025 |
|
convertToAllelicFractions | 0.129 | 0.000 | 0.129 |
|
counts-method | 0.152 | 0.004 | 0.156 |
|
datasets-methods | 0.045 | 0.000 | 0.045 |
|
deleteDatasets | 0.074 | 0.000 | 0.074 |
|
deleteReadGroups | 0.089 | 0.000 | 0.089 |
|
deleteRegions | 0.149 | 0.000 | 0.148 |
|
enrichment-methods | 0.014 | 0.000 | 0.014 |
|
getDefaultParameterList | 0.000 | 0.000 | 0.001 |
|
mergeReadGroups | 0.236 | 0.000 | 0.235 |
|
parameters-methods | 0.003 | 0.000 | 0.004 |
|
plotAllelicBiasResults | 4.983 | 0.004 | 4.993 |
|
plotAllelicBiasResultsOverview | 1.544 | 0.000 | 1.871 |
|
plotAndCalculateCorrelationDatasets | 0.763 | 0.000 | 0.763 |
|
plotAndCalculateWeakAndStrongGenotype | 1.520 | 0.008 | 1.528 |
|
plotAndClusterMatrix | 1.778 | 0.004 | 1.783 |
|
plotBinCounts | 1.761 | 0.004 | 1.765 |
|
plotClusterAverage | 0.435 | 0.004 | 0.440 |
|
plotGenotypesPerCluster | 0.908 | 0.000 | 0.910 |
|
plotGenotypesPerSNP | 0.260 | 0.000 | 0.261 |
|
plotRegionCounts | 3.818 | 0.004 | 4.312 |
|
readGroups-methods | 0.063 | 0.000 | 0.066 |
|
regions-methods | 0.075 | 0.000 | 0.074 |
|
renameBins | 0.139 | 0.000 | 0.139 |
|
renameDatasets | 0.15 | 0.00 | 0.15 |
|
renameReadGroups | 0.137 | 0.000 | 0.137 |
|
renameRegions | 0.775 | 0.000 | 0.775 |
|
results | 0.553 | 0.088 | 0.644 |
|
testForAllelicBiases | 1.097 | 0.000 | 1.097 |
|