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BioC 3.6: CHECK report for AllelicImbalance on veracruz1

This page was generated on 2017-08-16 13:44:29 -0400 (Wed, 16 Aug 2017).

Package 35/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.15.3
Jesper R Gadin
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AllelicImbalance
Last Changed Rev: 130713 / Revision: 131943
Last Changed Date: 2017-06-27 13:05:27 -0400 (Tue, 27 Jun 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AllelicImbalance
Version: 1.15.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.15.3.tar.gz
StartedAt: 2017-08-15 23:48:34 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:55:37 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 422.8 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_1.15.3.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.15.3’
* 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 18.894  1.287  20.696
import-bam           13.238  0.262  13.892
lva                   6.302  0.016   6.509
annotation-wrappers   5.769  0.177   6.079
ASEset-glocationplot  5.728  0.067   5.924
* 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-barplot0.4420.0080.465
ASEset-class0.8290.0060.848
ASEset-filters0.1170.0020.120
ASEset-gbarplot0.0330.0020.035
ASEset-glocationplot5.7280.0675.924
ASEset-gviztrack0.8380.0110.874
ASEset-scanForHeterozygotes2.2230.0162.309
ASEset.old0.0010.0010.001
ASEset.sim000
ASEsetFromBam0.0020.0020.004
DetectedAI-class0.0680.0020.071
DetectedAI-plot2.0400.0092.115
DetectedAI-summary0.0700.0040.074
GRvariants0.0020.0010.003
GlobalAnalysis-class0.0030.0010.004
LinkVariantAlmlof-class0.0010.0000.000
LinkVariantAlmlof-plot1.7480.0051.802
RegionSummary-class0.0010.0000.001
RiskVariant-class0.0000.0000.001
annotation-wrappers5.7690.1776.079
annotationBarplot000
barplot-lattice-support0.7440.0060.778
binom.test0.0290.0020.033
chisq.test0.0880.0010.092
cigar-utilities0.010.000.01
countAllelesFromBam0.0030.0010.004
coverageMatrixListFromGAL0.9540.0090.985
decorateWithExons0.0020.0010.003
decorateWithGenes0.0020.0020.003
defaultMapBias0.0460.0020.049
defaultPhase0.0010.0000.002
detectAI0.0550.0020.057
fractionPlotDf0.0230.0020.024
gba0.0000.0000.001
genomatrix0.0000.0000.001
genotype2phase0.0360.0030.038
getAlleleCounts4.4340.0164.553
getAlleleQuality4.8740.0094.929
getAreaFromGeneNames0.3070.0040.327
getDefaultMapBiasExpMean0.0240.0020.025
getSnpIdFromLocation18.894 1.28720.696
histplot0.0010.0000.000
implodeList-old0.0050.0000.005
import-bam-20.0080.0000.009
import-bam13.238 0.26213.892
import-bcf0.5900.0160.622
inferAlleles0.0680.0010.072
inferAltAllele0.0130.0010.013
inferGenotypes0.0620.0020.064
initialize-ASEset0.1970.0010.209
initialize-DetectedAI0.0400.0010.041
initialize-GlobalAnalysis0.0050.0000.006
initialize-RiskVariant0.0020.0010.003
legendBarplot0.0010.0000.001
locationplot1.3140.0171.367
lva6.3020.0166.509
lva.internal0.2350.0020.245
makeMaskedFasta0.6550.0030.685
mapBiasRef0.0080.0010.009
minCountFilt0.0390.0010.040
minFreqFilt0.0290.0010.034
multiAllelicFilt0.0110.0010.013
phase2genotype0.0170.0030.020
phaseArray2phaseMatrix0.0080.0020.010
phaseMatrix2Array0.0080.0020.009
randomRef0.0150.0010.016
reads0.0010.0000.000
refAllele0.0150.0010.016
regionSummary0.4420.0020.454
scanForHeterozygotes-old4.0940.0164.193