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BioC 3.5: CHECK report for AllelicImbalance on tokay2

This page was generated on 2017-10-18 14:22:56 -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: rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.14.0.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.14.0.tar.gz
StartedAt: 2017-10-17 21:58:29 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:09:29 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 659.9 seconds
RetCode: 0
Status:  OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.14.0.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/AllelicImbalance.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
import-bam          13.34   0.07   13.41
annotation-wrappers  8.11   0.25   14.78
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
getSnpIdFromLocation 21.85   1.16   50.70
import-bam           17.49   0.36   17.84
annotation-wrappers   6.28   0.18    6.46
getAlleleCounts       5.26   0.01    5.28
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  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:


install for i386

* 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

install for x64

* installing *source* package 'AllelicImbalance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AllelicImbalance' as AllelicImbalance_1.14.0.zip
* DONE (AllelicImbalance)

AllelicImbalance.Rcheck/examples_i386/AllelicImbalance-Ex.timings:

nameusersystemelapsed
ASEset-barplot0.330.030.36
ASEset-class0.510.000.52
ASEset-filters0.060.000.07
ASEset-gbarplot0.030.000.03
ASEset-glocationplot3.740.083.84
ASEset-gviztrack0.590.020.61
ASEset-scanForHeterozygotes1.860.041.90
ASEset.old000
ASEset.sim000
ASEsetFromBam0.000.020.02
DetectedAI-class0.050.010.06
DetectedAI-plot1.310.001.31
DetectedAI-summary0.070.000.07
GRvariants0.010.000.01
GlobalAnalysis-class000
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot1.360.031.39
RegionSummary-class000
RiskVariant-class000
annotation-wrappers 8.11 0.2514.78
annotationBarplot000
barplot-lattice-support0.130.000.13
binom.test0.030.000.03
chisq.test0.070.000.08
cigar-utilities0.020.000.01
countAllelesFromBam000
coverageMatrixListFromGAL0.670.000.67
decorateWithExons0.000.020.02
decorateWithGenes0.000.020.02
defaultMapBias0.080.010.09
defaultPhase000
detectAI0.090.000.09
fractionPlotDf0.030.020.05
gba000
genomatrix000
genotype2phase0.030.010.04
getAlleleCounts4.350.024.36
getAlleleQuality3.430.003.44
getAreaFromGeneNames0.240.010.25
getDefaultMapBiasExpMean0.040.000.05
getSnpIdFromLocation000
histplot000
implodeList-old000
import-bam-2000
import-bam13.34 0.0713.41
import-bcf0.630.010.64
inferAlleles0.080.000.08
inferAltAllele0.010.000.01
inferGenotypes0.070.000.07
initialize-ASEset0.150.000.15
initialize-DetectedAI0.050.000.05
initialize-GlobalAnalysis000
initialize-RiskVariant0.010.000.01
legendBarplot000
locationplot1.110.001.11
lva3.430.003.69
lva.internal0.150.000.16
makeMaskedFasta0.610.000.67
mapBiasRef0.020.000.01
minCountFilt0.030.020.05
minFreqFilt0.030.000.03
multiAllelicFilt0.010.000.02
phase2genotype0.020.010.03
phaseArray2phaseMatrix0.020.000.02
phaseMatrix2Array0.010.000.01
randomRef0.020.000.02
reads000
refAllele0.010.000.01
regionSummary0.330.000.33
scanForHeterozygotes-old3.090.003.09

AllelicImbalance.Rcheck/examples_x64/AllelicImbalance-Ex.timings:

nameusersystemelapsed
ASEset-barplot0.430.000.42
ASEset-class0.610.000.61
ASEset-filters0.070.000.08
ASEset-gbarplot0.020.020.03
ASEset-glocationplot4.660.004.65
ASEset-gviztrack0.640.040.69
ASEset-scanForHeterozygotes2.110.002.11
ASEset.old000
ASEset.sim000
ASEsetFromBam0.000.020.02
DetectedAI-class0.040.000.04
DetectedAI-plot1.690.001.69
DetectedAI-summary0.080.000.07
GRvariants0.010.000.02
GlobalAnalysis-class000
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot1.630.001.63
RegionSummary-class000
RiskVariant-class000
annotation-wrappers6.280.186.46
annotationBarplot000
barplot-lattice-support0.140.000.14
binom.test0.020.020.04
chisq.test0.090.010.11
cigar-utilities0.020.000.01
countAllelesFromBam000
coverageMatrixListFromGAL0.830.000.82
decorateWithExons000
decorateWithGenes0.000.020.02
defaultMapBias0.050.000.05
defaultPhase000
detectAI0.070.000.08
fractionPlotDf0.040.000.03
gba000
genomatrix000
genotype2phase0.030.020.04
getAlleleCounts5.260.015.28
getAlleleQuality4.710.024.72
getAreaFromGeneNames0.280.000.28
getDefaultMapBiasExpMean0.010.010.04
getSnpIdFromLocation21.85 1.1650.70
histplot0.000.010.01
implodeList-old000
import-bam-20.010.000.02
import-bam17.49 0.3617.84
import-bcf0.680.020.71
inferAlleles0.080.000.08
inferAltAllele0.020.000.01
inferGenotypes0.060.000.06
initialize-ASEset0.150.000.16
initialize-DetectedAI0.030.020.04
initialize-GlobalAnalysis000
initialize-RiskVariant0.010.000.01
legendBarplot000
locationplot1.380.001.38
lva3.720.003.73
lva.internal0.220.000.22
makeMaskedFasta0.760.000.77
mapBiasRef0.020.000.01
minCountFilt0.030.000.03
minFreqFilt0.030.000.04
multiAllelicFilt0.020.000.01
phase2genotype0.010.010.03
phaseArray2phaseMatrix0.020.000.02
phaseMatrix2Array000
randomRef0.000.020.01
reads000
refAllele0.030.000.03
regionSummary0.370.000.38
scanForHeterozygotes-old3.720.003.72