BioC 3.3: CHECK report for AllelicImbalance on oaxaca

Package: AllelicImbalance

Version: 1.10.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.10.2.tar.gz

StartedAt: 2016-10-12 23:11:18 -0700 (Wed, 12 Oct 2016)

EndedAt: 2016-10-12 23:19:04 -0700 (Wed, 12 Oct 2016)

EllapsedTime: 466.3 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_1.10.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.10.2’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     71.523  2.578  76.055
import-bam               12.414  0.473  12.909
getAlleleQuality          7.577  0.016   7.628
annotation-wrappers       6.740  0.271   7.041
getAlleleCounts           6.472  0.017   6.497
scanForHeterozygotes-old  6.168  0.150   6.329
* 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: 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	0.474	0.004	0.479
ASEset-class	0.235	0.019	0.253
ASEset-filters	0.038	0.002	0.041
ASEset-gbarplot	0.025	0.002	0.026
ASEset-glocationplot	1.946	0.023	2.008
ASEset-gviztrack	0.926	0.006	0.933
ASEset-scanForHeterozygotes	3.065	0.066	3.136
ASEset.old	0	0	0
ASEset.sim	0.001	0.000	0.001
ASEsetFromBam	0.003	0.001	0.004
DetectedAI-class	0.068	0.002	0.069
DetectedAI-plot	1.560	0.008	1.571
DetectedAI-summary	0.093	0.005	0.098
GRvariants	0.002	0.001	0.003
GlobalAnalysis-class	0.002	0.001	0.003
LinkVariantAlmlof-class	0.000	0.000	0.001
LinkVariantAlmlof-plot	1.322	0.005	1.340
RegionSummary-class	0.001	0.001	0.000
RiskVariant-class	0.000	0.000	0.001
annotation-wrappers	6.740	0.271	7.041
annotationBarplot	0.000	0.000	0.001
barplot-lattice-support	0.190	0.002	0.193
binom.test	0.036	0.001	0.037
chisq.test	0.048	0.001	0.049
cigar-utilities	0.015	0.001	0.014
countAllelesFromBam	0.003	0.001	0.004
coverageMatrixListFromGAL	1.009	0.024	1.035
decorateWithExons	0.002	0.002	0.003
decorateWithGenes	0.003	0.001	0.003
defaultMapBias	0.033	0.002	0.034
defaultPhase	0.002	0.000	0.001
detectAI	0.059	0.002	0.060
fractionPlotDf	0.027	0.002	0.028
gba	0	0	0
genomatrix	0.000	0.000	0.001
genotype2phase	0.007	0.002	0.009
getAlleleCounts	6.472	0.017	6.497
getAlleleQuality	7.577	0.016	7.628
getAreaFromGeneNames	0.459	0.009	0.468
getDefaultMapBiasExpMean	0.013	0.002	0.015
getSnpIdFromLocation	71.523	2.578	76.055
histplot	0	0	0
implodeList-old	0.002	0.000	0.002
import-bam-2	0.007	0.000	0.008
import-bam	12.414	0.473	12.909
import-bcf	0.552	0.029	0.581
inferAlleles	0.012	0.001	0.013
inferAltAllele	0.015	0.001	0.017
inferGenotypes	0.022	0.000	0.022
initialize-ASEset	0.035	0.000	0.035
initialize-DetectedAI	0.050	0.002	0.051
initialize-GlobalAnalysis	0.006	0.001	0.007
initialize-RiskVariant	0.002	0.002	0.004
legendBarplot	0	0	0
locationplot	0.397	0.005	0.403
lva	1.819	0.121	1.945
lva.internal	0.249	0.002	0.252
makeMaskedFasta	0.634	0.127	0.762
mapBiasRef	0.012	0.001	0.013
minCountFilt	0.042	0.002	0.044
minFreqFilt	0.041	0.002	0.043
multiAllelicFilt	0.011	0.002	0.013
phase2genotype	0.021	0.002	0.023
phaseArray2phaseMatrix	0.009	0.001	0.011
phaseMatrix2Array	0.008	0.001	0.009
randomRef	0.015	0.002	0.017
reads	0.001	0.000	0.001
refAllele	0.014	0.001	0.015
regionSummary	0.517	0.009	0.526
scanForHeterozygotes-old	6.168	0.150	6.329