BioC 3.5: CHECK report for AllelicImbalance on veracruz2

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: 2017-08-15 23:34:25 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:41:38 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 433.6 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘1.14.0’
* 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 21.089  1.378  23.075
import-bam           14.946  0.341  15.779
annotation-wrappers   6.717  0.211   7.150
ASEset-glocationplot  5.037  0.018   5.217
getAlleleQuality      4.957  0.012   5.092
getAlleleCounts       4.950  0.015   5.082
* 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

* 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)

name	user	system	elapsed
ASEset-barplot	0.441	0.016	0.471
ASEset-class	0.758	0.006	0.807
ASEset-filters	0.086	0.001	0.099
ASEset-gbarplot	0.036	0.002	0.037
ASEset-glocationplot	5.037	0.018	5.217
ASEset-gviztrack	1.002	0.009	1.027
ASEset-scanForHeterozygotes	3.133	0.062	3.267
ASEset.old	0.001	0.000	0.001
ASEset.sim	0.001	0.000	0.001
ASEsetFromBam	0.003	0.002	0.004
DetectedAI-class	0.066	0.002	0.068
DetectedAI-plot	2.070	0.009	2.170
DetectedAI-summary	0.069	0.003	0.073
GRvariants	0.002	0.001	0.003
GlobalAnalysis-class	0.003	0.001	0.004
LinkVariantAlmlof-class	0.001	0.000	0.001
LinkVariantAlmlof-plot	1.620	0.006	1.673
RegionSummary-class	0.001	0.000	0.000
RiskVariant-class	0.000	0.000	0.001
annotation-wrappers	6.717	0.211	7.150
annotationBarplot	0.000	0.000	0.001
barplot-lattice-support	0.157	0.001	0.166
binom.test	0.030	0.002	0.032
chisq.test	0.100	0.002	0.103
cigar-utilities	0.013	0.000	0.014
countAllelesFromBam	0.003	0.002	0.004
coverageMatrixListFromGAL	0.990	0.011	1.042
decorateWithExons	0.003	0.001	0.003
decorateWithGenes	0.002	0.001	0.003
defaultMapBias	0.058	0.002	0.064
defaultPhase	0.002	0.001	0.002
detectAI	0.046	0.002	0.047
fractionPlotDf	0.029	0.001	0.031
gba	0.001	0.000	0.000
genomatrix	0.000	0.000	0.001
genotype2phase	0.035	0.002	0.038
getAlleleCounts	4.950	0.015	5.082
getAlleleQuality	4.957	0.012	5.092
getAreaFromGeneNames	0.331	0.007	0.339
getDefaultMapBiasExpMean	0.032	0.002	0.035
getSnpIdFromLocation	21.089	1.378	23.075
histplot	0.000	0.000	0.001
implodeList-old	0.007	0.000	0.008
import-bam-2	0.006	0.000	0.006
import-bam	14.946	0.341	15.779
import-bcf	0.697	0.022	0.741
inferAlleles	0.088	0.001	0.098
inferAltAllele	0.013	0.001	0.014
inferGenotypes	0.089	0.001	0.092
initialize-ASEset	0.249	0.001	0.254
initialize-DetectedAI	0.053	0.002	0.055
initialize-GlobalAnalysis	0.006	0.001	0.007
initialize-RiskVariant	0.002	0.001	0.003
legendBarplot	0.001	0.000	0.000
locationplot	1.623	0.018	1.682
lva	4.414	0.012	4.558
lva.internal	0.259	0.002	0.269
makeMaskedFasta	0.667	0.002	0.691
mapBiasRef	0.013	0.001	0.015
minCountFilt	0.032	0.002	0.037
minFreqFilt	0.034	0.002	0.038
multiAllelicFilt	0.013	0.002	0.014
phase2genotype	0.021	0.003	0.024
phaseArray2phaseMatrix	0.008	0.002	0.010
phaseMatrix2Array	0.005	0.001	0.007
randomRef	0.009	0.001	0.010
reads	0	0	0
refAllele	0.016	0.002	0.018
regionSummary	0.403	0.002	0.422
scanForHeterozygotes-old	3.915	0.016	4.011