BioC 3.4: CHECK report for AllelicImbalance on zin1

Package: AllelicImbalance

Version: 1.11.3

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.11.3.tar.gz

StartedAt: 2016-09-20 03:03:39 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:09:36 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 356.3 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.11.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.11.3’
* 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 ... 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 62.628  1.256  64.040
import-bam           11.696  0.032  11.731
annotation-wrappers   5.468  0.072   5.547
* 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
  ‘/home/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'
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	0.132	0.000	0.129
ASEset-class	0.256	0.004	0.263
ASEset-filters	0.032	0.000	0.029
ASEset-gbarplot	0.024	0.004	0.027
ASEset-glocationplot	1.920	0.032	1.954
ASEset-gviztrack	0.328	0.000	0.328
ASEset-scanForHeterozygotes	1.576	0.000	1.577
ASEset.old	0.004	0.000	0.001
ASEset.sim	0	0	0
ASEsetFromBam	0.004	0.000	0.002
DetectedAI-class	0.052	0.000	0.051
DetectedAI-plot	1.504	0.008	1.510
DetectedAI-summary	0.060	0.004	0.065
GRvariants	0.000	0.000	0.001
GlobalAnalysis-class	0.004	0.000	0.002
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	0.844	0.004	0.846
RegionSummary-class	0	0	0
RiskVariant-class	0.000	0.000	0.001
annotation-wrappers	5.468	0.072	5.547
annotationBarplot	0.004	0.000	0.001
barplot-lattice-support	0.132	0.000	0.133
binom.test	0.028	0.000	0.027
chisq.test	0.036	0.000	0.033
cigar-utilities	0.008	0.000	0.010
countAllelesFromBam	0.000	0.000	0.002
coverageMatrixListFromGAL	1.040	0.024	1.062
decorateWithExons	0.000	0.004	0.002
decorateWithGenes	0.000	0.000	0.002
defaultMapBias	0.024	0.000	0.026
defaultPhase	0.000	0.000	0.002
detectAI	0.048	0.000	0.046
fractionPlotDf	0.020	0.004	0.022
gba	0.000	0.000	0.001
genomatrix	0	0	0
genotype2phase	0.004	0.000	0.006
getAlleleCounts	3.476	0.000	3.473
getAlleleQuality	3.624	0.024	3.649
getAreaFromGeneNames	0.316	0.000	0.313
getDefaultMapBiasExpMean	0.008	0.000	0.009
getSnpIdFromLocation	62.628	1.256	64.040
histplot	0	0	0
implodeList-old	0.000	0.000	0.002
import-bam-2	0.008	0.000	0.006
import-bam	11.696	0.032	11.731
import-bcf	0.556	0.000	0.556
inferAlleles	0.008	0.000	0.009
inferAltAllele	0.012	0.000	0.011
inferGenotypes	0.020	0.000	0.019
initialize-ASEset	0.024	0.000	0.026
initialize-DetectedAI	0.044	0.000	0.045
initialize-GlobalAnalysis	0.004	0.000	0.004
initialize-RiskVariant	0.000	0.000	0.002
legendBarplot	0.000	0.000	0.001
locationplot	0.300	0.000	0.301
lva	1.192	0.000	1.190
lva.internal	0.156	0.016	0.171
makeMaskedFasta	0.564	0.000	0.563
mapBiasRef	0.012	0.000	0.008
minCountFilt	0.024	0.000	0.027
minFreqFilt	0.024	0.000	0.026
multiAllelicFilt	0.012	0.000	0.008
phase2genotype	0.012	0.000	0.015
phaseArray2phaseMatrix	0.004	0.000	0.006
phaseMatrix2Array	0.008	0.000	0.005
randomRef	0.012	0.000	0.011
reads	0	0	0
refAllele	0.012	0.000	0.012
regionSummary	0.332	0.000	0.333
scanForHeterozygotes-old	3.228	0.000	3.228