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BioC 3.5: CHECK report for AllelicImbalance on veracruz2

This page was generated on 2017-10-18 14:31:25 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.14.0.tar.gz
StartedAt: 2017-10-18 00:18:32 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 00:26:01 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 449.3 seconds
RetCode: 0
Status:  OK 
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 sizes of PDF files under ‘inst/doc’ ... 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 21.663  1.477  23.835
import-bam           15.028  0.384  15.878
annotation-wrappers   7.020  0.234   7.478
ASEset-glocationplot  5.368  0.037   5.572
getAlleleCounts       5.292  0.031   5.471
getAlleleQuality      5.227  0.028   5.405
* 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-barplot0.4650.0190.495
ASEset-class0.8610.0080.907
ASEset-filters0.1110.0020.115
ASEset-gbarplot0.0390.0030.043
ASEset-glocationplot5.3680.0375.572
ASEset-gviztrack0.9070.0120.945
ASEset-scanForHeterozygotes3.2330.0783.414
ASEset.old0.0010.0000.001
ASEset.sim0.0010.0000.001
ASEsetFromBam0.0020.0010.003
DetectedAI-class0.0630.0020.066
DetectedAI-plot2.0490.0192.121
DetectedAI-summary0.0860.0050.092
GRvariants0.0020.0020.003
GlobalAnalysis-class0.0020.0010.003
LinkVariantAlmlof-class0.0010.0000.000
LinkVariantAlmlof-plot1.7260.0101.799
RegionSummary-class0.0010.0000.001
RiskVariant-class0.0010.0000.000
annotation-wrappers7.0200.2347.478
annotationBarplot0.0000.0000.001
barplot-lattice-support0.1600.0010.180
binom.test0.0260.0010.027
chisq.test0.0900.0020.095
cigar-utilities0.0130.0000.013
countAllelesFromBam0.0020.0010.003
coverageMatrixListFromGAL1.0460.0071.093
decorateWithExons0.0020.0010.003
decorateWithGenes0.0030.0010.003
defaultMapBias0.0820.0030.087
defaultPhase0.0020.0000.002
detectAI0.0520.0020.056
fractionPlotDf0.0290.0010.030
gba0.0010.0000.001
genomatrix0.0010.0000.001
genotype2phase0.0370.0030.040
getAlleleCounts5.2920.0315.471
getAlleleQuality5.2270.0285.405
getAreaFromGeneNames0.3180.0070.335
getDefaultMapBiasExpMean0.0270.0010.030
getSnpIdFromLocation21.663 1.47723.835
histplot0.0010.0000.001
implodeList-old0.0080.0000.009
import-bam-20.0090.0000.010
import-bam15.028 0.38415.878
import-bcf0.6690.0230.729
inferAlleles0.0860.0020.094
inferAltAllele0.0130.0010.014
inferGenotypes0.0800.0020.083
initialize-ASEset0.1920.0010.195
initialize-DetectedAI0.0480.0020.050
initialize-GlobalAnalysis0.0050.0010.006
initialize-RiskVariant0.0020.0020.003
legendBarplot0.0000.0000.001
locationplot1.6190.0211.694
lva4.6310.0264.819
lva.internal0.2570.0030.291
makeMaskedFasta0.6970.0040.744
mapBiasRef0.0110.0010.013
minCountFilt0.0350.0010.038
minFreqFilt0.0320.0020.034
multiAllelicFilt0.0110.0020.012
phase2genotype0.0190.0030.022
phaseArray2phaseMatrix0.0090.0020.010
phaseMatrix2Array0.0080.0010.009
randomRef0.0140.0020.015
reads0.0010.0000.001
refAllele0.0160.0020.018
regionSummary0.4250.0030.437
scanForHeterozygotes-old4.4840.0294.714