BioC 3.3: CHECK report for AllelicImbalance on morelia

Package: AllelicImbalance

Version: 1.9.21

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.9.21.tar.gz

StartedAt: 2016-04-20 23:11:01 -0700 (Wed, 20 Apr 2016)

EndedAt: 2016-04-20 23:18:11 -0700 (Wed, 20 Apr 2016)

EllapsedTime: 430.6 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_1.9.21.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.9.21’
* 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 ... [26s/27s] 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
.array2MatrixList: no visible global function definition for 'setNames'
.lvaRegressionPvalue : <anonymous>: no visible global function
  definition for 'lm'
.lvaRegressionReturnCommonParamMatrix : <anonymous>: no visible global
  function definition for 'lm'
.lvaRegressionReturnCommonParamMatrixTxSNPspecific: no visible global
  function definition for 'lm'
decorateWithExons: no visible global function definition for 'lines'
decorateWithExons: no visible global function definition for 'text'
decorateWithGenes: no visible global function definition for 'lines'
decorateWithGenes: no visible global function definition for 'text'
legendBarplot: no visible global function definition for 'symbols'
legendBarplot: no visible global function definition for 'text'
barplot,ASEset: no visible global function definition for
  'plot.default'
barplot,ASEset: no visible global function definition for 'symbols'
barplot,ASEset: no visible global function definition for 'lines'
barplot,ASEset : <anonymous>: no visible global function definition for
  'lines'
barplot,ASEset: no visible global function definition for 'text'
barplot,ASEset: no visible global function definition for 'title'
barplot,ASEset: no visible global function definition for 'dist'
locationplot,ASEset: no visible global function definition for
  'plot.default'
locationplot,ASEset: no visible global function definition for 'lines'
locationplot,ASEset: no visible global function definition for 'points'
locationplot,ASEset: no visible global function definition for 'abline'
plot,LinkVariantAlmlof-ANY: no visible global function definition for
  'abline'
plot,LinkVariantAlmlof-ANY: no visible global function definition for
  'mtext'
reference_frequency_density_vs_threshold_variable_plot,DetectedAI: no
  visible global function definition for 'heat.colors'
Undefined global functions or variables:
  abline dist heat.colors lines lm mtext plot.default points setNames
  symbols text title
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "lines", "mtext", "plot.default",
             "points", "symbols", "text", "title")
  importFrom("stats", "dist", "lm", "setNames")
to your NAMESPACE file.
* 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 ... [134s/142s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     67.253  2.159  70.670
import-bam               11.916  0.521  12.457
annotation-wrappers       6.099  0.340  11.173
getAlleleQuality          6.170  0.022   6.199
getAlleleCounts           5.945  0.027   5.988
scanForHeterozygotes-old  5.704  0.144   5.853
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [14s/14s]
 [14s/14s] 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-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 'chisq.test' from package 'stats' in package 'AllelicImbalance'
Creating a generic function for 'binom.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	0.156	0.009	0.165
ASEset-class	0.339	0.016	0.356
ASEset-filters	0.038	0.002	0.039
ASEset-gbarplot	0.042	0.002	0.045
ASEset-glocationplot	2.200	0.066	2.268
ASEset-gviztrack	0.422	0.008	0.430
ASEset-scanForHeterozygotes	2.880	0.015	2.959
ASEset.old	0.001	0.000	0.000
ASEset.sim	0.001	0.000	0.001
ASEsetFromBam	0.002	0.001	0.003
DetectedAI-class	0.068	0.001	0.070
DetectedAI-plot	1.417	0.009	1.627
DetectedAI-summary	0.074	0.004	0.077
GRvariants	0.003	0.001	0.004
GlobalAnalysis-class	0.003	0.002	0.003
LinkVariantAlmlof-class	0.001	0.000	0.001
LinkVariantAlmlof-plot	1.115	0.004	2.193
RegionSummary-class	0.001	0.000	0.000
RiskVariant-class	0.001	0.000	0.000
annotation-wrappers	6.099	0.340	11.173
annotationBarplot	0.001	0.000	0.001
barplot-lattice-support	0.160	0.002	0.162
binom.test	0.024	0.001	0.025
chisq.test	0.031	0.001	0.032
cigar-utilities	0.010	0.000	0.011
countAllelesFromBam	0.002	0.001	0.002
coverageMatrixListFromGAL	0.995	0.023	1.020
decorateWithExons	0.003	0.001	0.003
decorateWithGenes	0.003	0.001	0.003
defaultMapBias	0.042	0.002	0.043
defaultPhase	0.002	0.000	0.002
detectAI	0.071	0.001	0.073
fractionPlotDf	0.031	0.002	0.033
gba	0.000	0.000	0.001
genomatrix	0.001	0.000	0.001
genotype2phase	0.009	0.002	0.011
getAlleleCounts	5.945	0.027	5.988
getAlleleQuality	6.170	0.022	6.199
getAreaFromGeneNames	0.487	0.007	0.495
getDefaultMapBiasExpMean	0.009	0.001	0.010
getSnpIdFromLocation	67.253	2.159	70.670
histplot	0.001	0.000	0.001
implodeList-old	0.002	0.000	0.002
import-bam-2	0.006	0.000	0.006
import-bam	11.916	0.521	12.457
import-bcf	0.559	0.030	0.590
inferAlleles	0.009	0.001	0.010
inferAltAllele	0.014	0.001	0.016
inferGenotypes	0.017	0.001	0.017
initialize-ASEset	0.029	0.001	0.029
initialize-DetectedAI	0.066	0.001	0.067
initialize-GlobalAnalysis	0.005	0.001	0.007
initialize-RiskVariant	0.002	0.002	0.004
legendBarplot	0.001	0.000	0.000
locationplot	0.372	0.003	0.376
lva	1.767	0.107	1.876
lva.internal	0.181	0.002	0.184
makeMaskedFasta	0.664	0.132	0.801
mapBiasRef	0.014	0.002	0.015
minCountFilt	0.044	0.002	0.046
minFreqFilt	0.042	0.001	0.044
multiAllelicFilt	0.013	0.001	0.014
phase2genotype	0.022	0.002	0.025
phaseArray2phaseMatrix	0.009	0.002	0.010
phaseMatrix2Array	0.008	0.001	0.010
randomRef	0.015	0.001	0.017
reads	0.000	0.000	0.001
refAllele	0.015	0.002	0.017
regionSummary	0.486	0.005	0.491
scanForHeterozygotes-old	5.704	0.144	5.853