BioC 3.4: CHECK report for AllelicImbalance on morelia

Package: AllelicImbalance

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.12.0.tar.gz

StartedAt: 2017-04-14 22:29:44 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:37:37 -0700 (Fri, 14 Apr 2017)

EllapsedTime: 473.6 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.12.0’
* 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 ... 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 69.536  2.417  73.725
import-bam           14.237  0.473  14.722
annotation-wrappers   7.315  0.349   8.100
getAlleleQuality      5.317  0.013   5.334
getAlleleCounts       5.279  0.017   5.300
* 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-3.4-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'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AllelicImbalance)

name	user	system	elapsed
ASEset-barplot	0.198	0.007	0.205
ASEset-class	0.382	0.008	0.390
ASEset-filters	0.475	0.002	0.477
ASEset-gbarplot	0.024	0.001	0.026
ASEset-glocationplot	2.209	0.050	2.261
ASEset-gviztrack	0.529	0.010	0.539
ASEset-scanForHeterozygotes	1.979	0.008	1.987
ASEset.old	0.001	0.000	0.001
ASEset.sim	0.001	0.000	0.000
ASEsetFromBam	0.003	0.001	0.004
DetectedAI-class	0.095	0.002	0.097
DetectedAI-plot	1.496	0.007	1.504
DetectedAI-summary	0.101	0.005	0.105
GRvariants	0.002	0.002	0.003
GlobalAnalysis-class	0.002	0.001	0.003
LinkVariantAlmlof-class	0.000	0.000	0.001
LinkVariantAlmlof-plot	1.235	0.005	1.246
RegionSummary-class	0.000	0.000	0.001
RiskVariant-class	0.001	0.000	0.001
annotation-wrappers	7.315	0.349	8.100
annotationBarplot	0.000	0.000	0.001
barplot-lattice-support	0.257	0.003	0.260
binom.test	0.049	0.004	0.053
chisq.test	0.054	0.004	0.058
cigar-utilities	0.016	0.001	0.018
countAllelesFromBam	0.003	0.001	0.004
coverageMatrixListFromGAL	1.102	0.023	1.127
decorateWithExons	0.002	0.002	0.004
decorateWithGenes	0.002	0.001	0.003
defaultMapBias	0.040	0.002	0.042
defaultPhase	0.001	0.001	0.001
detectAI	0.072	0.005	0.077
fractionPlotDf	0.035	0.002	0.037
gba	0.001	0.001	0.001
genomatrix	0.001	0.000	0.001
genotype2phase	0.010	0.003	0.013
getAlleleCounts	5.279	0.017	5.300
getAlleleQuality	5.317	0.013	5.334
getAreaFromGeneNames	0.550	0.010	0.561
getDefaultMapBiasExpMean	0.012	0.002	0.013
getSnpIdFromLocation	69.536	2.417	73.725
histplot	0.001	0.001	0.001
implodeList-old	0.002	0.000	0.002
import-bam-2	0.008	0.000	0.008
import-bam	14.237	0.473	14.722
import-bcf	0.622	0.019	0.641
inferAlleles	0.009	0.001	0.011
inferAltAllele	0.018	0.002	0.018
inferGenotypes	0.029	0.001	0.031
initialize-ASEset	0.041	0.000	0.043
initialize-DetectedAI	0.062	0.001	0.063
initialize-GlobalAnalysis	0.004	0.001	0.005
initialize-RiskVariant	0.002	0.001	0.002
legendBarplot	0.000	0.000	0.001
locationplot	0.424	0.003	0.428
lva	1.801	0.062	1.864
lva.internal	0.282	0.003	0.285
makeMaskedFasta	0.735	0.074	0.810
mapBiasRef	0.014	0.001	0.016
minCountFilt	0.044	0.002	0.046
minFreqFilt	0.044	0.002	0.046
multiAllelicFilt	0.012	0.002	0.014
phase2genotype	0.017	0.003	0.019
phaseArray2phaseMatrix	0.008	0.001	0.010
phaseMatrix2Array	0.005	0.001	0.006
randomRef	0.014	0.001	0.014
reads	0.000	0.000	0.001
refAllele	0.016	0.001	0.016
regionSummary	0.490	0.003	0.494
scanForHeterozygotes-old	4.900	0.049	4.952