BioC 3.5: CHECK report for AllelicImbalance on toluca2

Package: AllelicImbalance

Version: 1.13.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.13.3.tar.gz

StartedAt: 2017-04-23 00:13:34 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 00:22:02 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 508.1 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

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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_1.13.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/AllelicImbalance.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.13.3’
* 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     23.994  1.544  25.817
import-bam               14.605  0.433  15.483
ASEset-glocationplot      9.220  0.035   9.425
annotation-wrappers       7.994  0.269   8.349
getAlleleCounts           5.749  0.015   5.840
getAlleleQuality          5.721  0.023   5.788
scanForHeterozygotes-old  5.538  0.019   5.614
lva                       5.181  0.013   5.530
* 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	0.551	0.012	0.599
ASEset-class	0.941	0.006	0.987
ASEset-filters	0.124	0.003	0.127
ASEset-gbarplot	0.168	0.002	0.171
ASEset-glocationplot	9.220	0.035	9.425
ASEset-gviztrack	1.061	0.009	1.086
ASEset-scanForHeterozygotes	3.423	0.067	3.516
ASEset.old	0.000	0.000	0.001
ASEset.sim	0.000	0.000	0.001
ASEsetFromBam	0.003	0.002	0.004
DetectedAI-class	0.070	0.002	0.071
DetectedAI-plot	3.381	0.016	3.443
DetectedAI-summary	0.088	0.005	0.095
GRvariants	0.002	0.001	0.004
GlobalAnalysis-class	0.003	0.001	0.003
LinkVariantAlmlof-class	0.001	0.000	0.001
LinkVariantAlmlof-plot	1.998	0.012	2.030
RegionSummary-class	0.000	0.001	0.000
RiskVariant-class	0.001	0.000	0.001
annotation-wrappers	7.994	0.269	8.349
annotationBarplot	0.000	0.000	0.001
barplot-lattice-support	0.186	0.001	0.191
binom.test	0.035	0.002	0.037
chisq.test	0.126	0.002	0.128
cigar-utilities	0.014	0.000	0.014
countAllelesFromBam	0.002	0.002	0.004
coverageMatrixListFromGAL	1.141	0.011	1.157
decorateWithExons	0.002	0.002	0.003
decorateWithGenes	0.002	0.001	0.003
defaultMapBias	0.059	0.003	0.060
defaultPhase	0.001	0.000	0.002
detectAI	0.072	0.004	0.076
fractionPlotDf	0.029	0.001	0.030
gba	0.001	0.001	0.001
genomatrix	0.001	0.000	0.001
genotype2phase	0.042	0.003	0.044
getAlleleCounts	5.749	0.015	5.840
getAlleleQuality	5.721	0.023	5.788
getAreaFromGeneNames	0.449	0.008	0.459
getDefaultMapBiasExpMean	0.027	0.001	0.027
getSnpIdFromLocation	23.994	1.544	25.817
histplot	0.001	0.000	0.001
implodeList-old	0.009	0.000	0.009
import-bam-2	0.008	0.000	0.009
import-bam	14.605	0.433	15.483
import-bcf	0.698	0.023	0.727
inferAlleles	0.110	0.002	0.113
inferAltAllele	0.015	0.001	0.017
inferGenotypes	0.097	0.001	0.100
initialize-ASEset	0.286	0.001	0.291
initialize-DetectedAI	0.060	0.002	0.062
initialize-GlobalAnalysis	0.006	0.002	0.007
initialize-RiskVariant	0.003	0.001	0.004
legendBarplot	0.001	0.000	0.001
locationplot	2.064	0.019	2.099
lva	5.181	0.013	5.530
lva.internal	0.278	0.002	0.281
makeMaskedFasta	0.636	0.007	0.655
mapBiasRef	0.012	0.001	0.013
minCountFilt	0.036	0.002	0.038
minFreqFilt	0.036	0.002	0.038
multiAllelicFilt	0.012	0.002	0.013
phase2genotype	0.020	0.002	0.022
phaseArray2phaseMatrix	0.009	0.001	0.009
phaseMatrix2Array	0.008	0.002	0.009
randomRef	0.016	0.001	0.017
reads	0.001	0.001	0.001
refAllele	0.017	0.001	0.018
regionSummary	0.490	0.002	0.493
scanForHeterozygotes-old	5.538	0.019	5.614