BioC 3.4: CHECK report for AllelicImbalance on morelia

Package: AllelicImbalance

Version: 1.11.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.11.3.tar.gz

StartedAt: 2016-09-20 03:01:26 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:08:03 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 397.0 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_1.11.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-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 ‘1.11.3’
* 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 64.008  2.047  66.852
import-bam           11.759  0.408  12.172
annotation-wrappers   5.428  0.384  10.224
* 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'
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	0.168	0.004	0.173
ASEset-class	0.305	0.005	0.311
ASEset-filters	0.024	0.001	0.025
ASEset-gbarplot	0.023	0.001	0.025
ASEset-glocationplot	1.980	0.046	2.027
ASEset-gviztrack	0.303	0.003	0.306
ASEset-scanForHeterozygotes	1.402	0.006	1.409
ASEset.old	0.000	0.000	0.001
ASEset.sim	0.001	0.000	0.001
ASEsetFromBam	0.002	0.001	0.003
DetectedAI-class	0.066	0.002	0.067
DetectedAI-plot	1.363	0.006	1.704
DetectedAI-summary	0.059	0.003	0.061
GRvariants	0.001	0.001	0.002
GlobalAnalysis-class	0.002	0.001	0.004
LinkVariantAlmlof-class	0.001	0.000	0.000
LinkVariantAlmlof-plot	0.802	0.012	0.815
RegionSummary-class	0	0	0
RiskVariant-class	0.000	0.001	0.000
annotation-wrappers	5.428	0.384	10.224
annotationBarplot	0.001	0.000	0.001
barplot-lattice-support	0.141	0.001	0.142
binom.test	0.021	0.000	0.022
chisq.test	0.026	0.001	0.027
cigar-utilities	0.01	0.00	0.01
countAllelesFromBam	0.002	0.001	0.004
coverageMatrixListFromGAL	0.565	0.006	0.571
decorateWithExons	0.001	0.001	0.002
decorateWithGenes	0.002	0.001	0.003
defaultMapBias	0.024	0.001	0.025
defaultPhase	0.001	0.000	0.001
detectAI	0.046	0.001	0.047
fractionPlotDf	0.045	0.002	0.046
gba	0.000	0.000	0.001
genomatrix	0	0	0
genotype2phase	0.005	0.002	0.007
getAlleleCounts	3.763	0.021	3.785
getAlleleQuality	3.900	0.008	3.911
getAreaFromGeneNames	0.312	0.005	0.317
getDefaultMapBiasExpMean	0.008	0.001	0.009
getSnpIdFromLocation	64.008	2.047	66.852
histplot	0.001	0.000	0.000
implodeList-old	0.001	0.000	0.002
import-bam-2	0.006	0.000	0.007
import-bam	11.759	0.408	12.172
import-bcf	0.591	0.032	0.654
inferAlleles	0.012	0.002	0.014
inferAltAllele	0.017	0.001	0.019
inferGenotypes	0.030	0.002	0.031
initialize-ASEset	0.041	0.001	0.041
initialize-DetectedAI	0.045	0.001	0.046
initialize-GlobalAnalysis	0.004	0.001	0.005
initialize-RiskVariant	0.001	0.001	0.002
legendBarplot	0.000	0.000	0.001
locationplot	0.325	0.008	0.334
lva	1.352	0.086	1.438
lva.internal	0.238	0.001	0.240
makeMaskedFasta	0.499	0.003	0.503
mapBiasRef	0.013	0.001	0.014
minCountFilt	0.039	0.001	0.040
minFreqFilt	0.046	0.002	0.048
multiAllelicFilt	0.011	0.002	0.012
phase2genotype	0.013	0.001	0.015
phaseArray2phaseMatrix	0.005	0.001	0.006
phaseMatrix2Array	0.005	0.001	0.005
randomRef	0.016	0.001	0.017
reads	0.001	0.000	0.001
refAllele	0.018	0.001	0.020
regionSummary	0.428	0.003	0.430
scanForHeterozygotes-old	3.912	0.018	3.931