BioC 3.0: CHECK report for AllelicImbalance on perceval

Package: AllelicImbalance

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AllelicImbalance_1.4.2.tar.gz

StartedAt: 2015-04-09 22:34:16 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:44:42 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 626.4 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 --no-multiarch AllelicImbalance_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.2’
* 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 ... [49s/52s] 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 ... NOTE
barplotLatticeCounts: no visible binding for global variable ‘alleles’
barplotLatticeFraction: no visible binding for global variable
  ‘alleles’
getSnpIdFromLocation: no visible global function definition for
  ‘getSNPlocs’
* 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 ... [104s/105s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getSnpIdFromLocation 31.693  1.058  32.929
import-bam           17.794  0.463  18.442
getAlleleCounts       9.916  0.018   9.939
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [24s/24s]
 [24s/25s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.

* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘binom.test’ from package ‘stats’ in package ‘AllelicImbalance’
Creating a generic function for ‘chisq.test’ from package ‘stats’ in package ‘AllelicImbalance’
Creating a generic function for ‘hist’ from package ‘graphics’ 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	0.224	0.008	0.232
ASEset-class	0.130	0.001	0.131
ASEset-glocationplot	4.185	0.049	4.268
ASEset-gviztrack	0.764	0.008	0.773
ASEset-lbarplot	0.124	0.001	0.129
ASEset-locationplot	0.591	0.005	0.617
ASEset.sim	0.000	0.000	0.001
GRvariants	0.003	0.001	0.004
ReferenceBias-class	0.116	0.001	0.117
ReferenceBias-show	0.001	0.000	0.000
annotation-wrappers	3.910	0.255	4.167
barplot-lattice-support	0.228	0.012	0.259
binom.test	0.057	0.001	0.057
boxplot	0.024	0.002	0.040
chisq.test	0.045	0.001	0.045
cigar-utilities	0.038	0.000	0.038
coverageMatrixListFromGAL	1.682	0.003	1.686
decorateWithExons	0.002	0.001	0.003
decorateWithGenes	0.002	0.000	0.002
defaultMapBias	0.059	0.002	0.071
detectAI	0.063	0.000	0.065
genofilters	0.044	0.000	0.046
getAlleleCounts	9.916	0.018	9.939
getAreaFromGeneNames	0.607	0.032	0.639
getDefaultMapBiasExpMean	0.011	0.001	0.012
getSnpIdFromLocation	31.693	1.058	32.929
histplot	0.000	0.000	0.001
implodeList	0.002	0.000	0.003
import-bam	17.794	0.463	18.442
import-bcf	0.975	0.065	1.056
inferAlleles	0.011	0.000	0.011
inferGenotypes	0.028	0.000	0.029
initialize-ASEset	0.042	0.000	0.043
initialize-ReferenceBias	0.102	0.001	0.103
reads	0	0	0
refAllele	0.045	0.002	0.046
refFraction	0.033	0.000	0.034
scanForHeterozygotes	4.537	0.029	4.566