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BioC 3.5: CHECK report for AllelicImbalance on malbec2

This page was generated on 2017-10-18 14:15:29 -0400 (Wed, 18 Oct 2017).

Package 35/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.14.0
Jesper R Gadin
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/AllelicImbalance
Branch: RELEASE_3_5
Last Commit: 3595853
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AllelicImbalance
Version: 1.14.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.14.0.tar.gz
StartedAt: 2017-10-17 21:06:30 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 21:13:04 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 393.6 seconds
RetCode: 0
Status:  OK 
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.14.0’
* package encoding: UTF-8
* 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 ‘AllelicImbalance’ 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
* 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 ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getSnpIdFromLocation 17.264  4.656  25.436
import-bam           15.044  0.096  15.151
annotation-wrappers   5.652  0.048   6.022
getAlleleCounts       5.536  0.012   5.553
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* 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: OK

AllelicImbalance.Rcheck/00install.out:

* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'chisq.test' from package 'stats' in package 'AllelicImbalance'
Creating a generic function for 'binom.test' from package 'stats' in package 'AllelicImbalance'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AllelicImbalance)

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings:

nameusersystemelapsed
ASEset-barplot0.3280.0120.341
ASEset-class0.5840.0000.583
ASEset-filters0.0760.0000.077
ASEset-gbarplot0.0320.0000.034
ASEset-glocationplot4.5720.0364.612
ASEset-gviztrack0.6240.0040.629
ASEset-scanForHeterozygotes1.8600.0001.861
ASEset.old000
ASEset.sim000
ASEsetFromBam0.0040.0000.002
DetectedAI-class0.0440.0000.046
DetectedAI-plot1.6600.0001.747
DetectedAI-summary0.060.000.06
GRvariants0.0000.0040.002
GlobalAnalysis-class0.0000.0000.002
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot1.2760.0001.278
RegionSummary-class000
RiskVariant-class000
annotation-wrappers5.6520.0486.022
annotationBarplot000
barplot-lattice-support0.1720.0000.173
binom.test0.040.000.04
chisq.test0.1160.0000.118
cigar-utilities0.0160.0000.015
countAllelesFromBam0.0040.0000.004
coverageMatrixListFromGAL0.7640.0000.765
decorateWithExons0.0040.0000.001
decorateWithGenes0.0000.0000.002
defaultMapBias0.0320.0000.034
defaultPhase0.0040.0000.001
detectAI0.0600.0000.059
fractionPlotDf0.0240.0000.023
gba000
genomatrix000
genotype2phase0.0240.0000.024
getAlleleCounts5.5360.0125.553
getAlleleQuality4.1920.0164.210
getAreaFromGeneNames0.3640.0040.368
getDefaultMapBiasExpMean0.020.000.02
getSnpIdFromLocation17.264 4.65625.436
histplot0.0000.0000.001
implodeList-old0.0040.0000.005
import-bam-20.0040.0000.006
import-bam15.044 0.09615.151
import-bcf0.7240.0040.727
inferAlleles0.0680.0000.067
inferAltAllele0.0120.0000.012
inferGenotypes0.0600.0040.062
initialize-ASEset0.1520.0000.154
initialize-DetectedAI0.0400.0000.039
initialize-GlobalAnalysis0.0040.0000.004
initialize-RiskVariant0.0000.0000.002
legendBarplot000
locationplot1.3000.0001.301
lva3.5000.0003.498
lva.internal0.1880.0000.188
makeMaskedFasta0.7360.0000.736
mapBiasRef0.0080.0000.009
minCountFilt0.0240.0000.026
minFreqFilt0.0240.0000.025
multiAllelicFilt0.0080.0000.009
phase2genotype0.0160.0000.015
phaseArray2phaseMatrix0.0080.0000.006
phaseMatrix2Array0.0080.0000.006
randomRef0.0120.0000.010
reads000
refAllele0.0120.0000.012
regionSummary0.3160.0000.314
scanForHeterozygotes-old3.5400.0003.543