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BioC 3.5: CHECK report for AllelicImbalance on tokay2

This page was generated on 2017-08-16 13:22:43 -0400 (Wed, 16 Aug 2017).

Package 35/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.14.0
Jesper R Gadin
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/AllelicImbalance
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -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: 2017-08-15 21:56:35 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:07:29 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 653.6 seconds
RetCode: 0
Status:  OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 3.4.1 (2017-06-30)
* 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          11.28    0.0   11.28
annotation-wrappers  6.45    0.2    8.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
getSnpIdFromLocation 23.00   1.54   61.95
import-bam           18.07   0.25   18.31
annotation-wrappers   8.14   0.22    8.36
getAlleleCounts       5.73   0.02    5.75
ASEset-glocationplot  5.72   0.00    5.72
* 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-barplot0.330.050.38
ASEset-class0.430.000.43
ASEset-filters0.060.000.06
ASEset-gbarplot0.040.000.04
ASEset-glocationplot2.890.022.90
ASEset-gviztrack0.970.000.97
ASEset-scanForHeterozygotes1.400.061.47
ASEset.old000
ASEset.sim000
ASEsetFromBam000
DetectedAI-class0.030.010.05
DetectedAI-plot1.130.021.14
DetectedAI-summary0.060.000.06
GRvariants000
GlobalAnalysis-class000
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot1.010.001.01
RegionSummary-class000
RiskVariant-class000
annotation-wrappers6.450.208.28
annotationBarplot000
barplot-lattice-support0.130.000.12
binom.test0.040.000.05
chisq.test0.100.020.11
cigar-utilities0.010.000.01
countAllelesFromBam000
coverageMatrixListFromGAL0.640.010.66
decorateWithExons0.020.000.02
decorateWithGenes000
defaultMapBias0.030.020.04
defaultPhase000
detectAI0.050.000.05
fractionPlotDf0.010.000.02
gba000
genomatrix000
genotype2phase0.030.000.03
getAlleleCounts3.580.013.60
getAlleleQuality3.610.023.62
getAreaFromGeneNames0.330.000.33
getDefaultMapBiasExpMean0.010.000.02
getSnpIdFromLocation000
histplot000
implodeList-old0.020.000.01
import-bam-2000
import-bam11.28 0.0011.28
import-bcf0.470.000.47
inferAlleles0.060.000.06
inferAltAllele000
inferGenotypes0.050.000.05
initialize-ASEset0.120.000.12
initialize-DetectedAI0.040.000.03
initialize-GlobalAnalysis000
initialize-RiskVariant0.000.020.02
legendBarplot000
locationplot0.920.010.94
lva2.620.002.65
lva.internal0.140.000.14
makeMaskedFasta0.460.000.46
mapBiasRef0.000.020.01
minCountFilt0.030.000.03
minFreqFilt0.030.000.03
multiAllelicFilt000
phase2genotype0.030.000.03
phaseArray2phaseMatrix0.020.000.02
phaseMatrix2Array000
randomRef0.010.000.02
reads000
refAllele0.000.010.01
regionSummary0.250.020.27
scanForHeterozygotes-old2.640.002.64

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

nameusersystemelapsed
ASEset-barplot0.380.030.40
ASEset-class0.70.00.7
ASEset-filters0.100.000.09
ASEset-gbarplot0.030.020.05
ASEset-glocationplot5.720.005.72
ASEset-gviztrack0.780.030.81
ASEset-scanForHeterozygotes3.80.03.8
ASEset.old000
ASEset.sim000
ASEsetFromBam0.010.000.01
DetectedAI-class0.060.000.07
DetectedAI-plot2.140.002.14
DetectedAI-summary0.070.000.06
GRvariants0.010.000.02
GlobalAnalysis-class0.020.000.01
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot1.480.001.49
RegionSummary-class000
RiskVariant-class000
annotation-wrappers8.140.228.36
annotationBarplot000
barplot-lattice-support0.130.010.14
binom.test0.030.000.03
chisq.test0.110.020.12
cigar-utilities0.010.000.02
countAllelesFromBam0.000.010.01
coverageMatrixListFromGAL1.070.001.07
decorateWithExons0.000.020.01
decorateWithGenes000
defaultMapBias0.030.010.05
defaultPhase0.010.000.01
detectAI0.050.000.05
fractionPlotDf0.030.000.03
gba000
genomatrix000
genotype2phase0.020.020.03
getAlleleCounts5.730.025.75
getAlleleQuality4.960.004.96
getAreaFromGeneNames0.400.010.42
getDefaultMapBiasExpMean0.020.020.03
getSnpIdFromLocation23.00 1.5461.95
histplot000
implodeList-old000
import-bam-2000
import-bam18.07 0.2518.31
import-bcf1.040.021.06
inferAlleles0.10.00.1
inferAltAllele0.010.000.01
inferGenotypes0.080.000.08
initialize-ASEset0.190.000.19
initialize-DetectedAI0.040.000.05
initialize-GlobalAnalysis0.000.010.01
initialize-RiskVariant000
legendBarplot000
locationplot2.220.002.22
lva4.050.004.57
lva.internal0.180.000.19
makeMaskedFasta0.950.002.32
mapBiasRef0.020.000.02
minCountFilt0.050.000.04
minFreqFilt0.030.020.05
multiAllelicFilt0.010.000.01
phase2genotype0.030.000.03
phaseArray2phaseMatrix0.000.000.02
phaseMatrix2Array0.020.000.01
randomRef0.020.000.01
reads000
refAllele0.020.020.04
regionSummary0.430.000.43
scanForHeterozygotes-old3.890.013.91