BioC 3.2: CHECK report for AllelicImbalance on perceval

Package: AllelicImbalance

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.8.0.tar.gz

StartedAt: 2015-11-10 01:50:09 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 02:12:11 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 1322.4 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.8.0’
* 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 ... [30s/224s] 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
countAllelesFromBam,GRanges : .local: no visible binding for global
  variable ‘UserDir’
detectAI,ASEset : .local: no visible binding for global variable
  ‘tf.keep1’
detectAI,ASEset : .local: no visible binding for global variable
  ‘tf.keep2’
detectedAI_vs_threshold_variable_multigraph_plot,DetectedAI : .local:
  no visible binding for global variable ‘grid.arrange’
detectedAI_vs_threshold_variable_plot,DetectedAI : .local :
  <anonymous>: no visible global function definition for
  ‘panel.smoothScatter’
detectedAI_vs_threshold_variable_plot,DetectedAI : .local :
  <anonymous>: no visible global function definition for
  ‘panel.linejoin’
detectedAI_vs_threshold_variable_plot,DetectedAI : .local: no visible
  global function definition for ‘doubleYScale’
frequency_vs_threshold_variable_multigraph_plot,DetectedAI : .local: no
  visible binding for global variable ‘grid.arrange’
frequency_vs_threshold_variable_plot,DetectedAI : .local : <anonymous>:
  no visible global function definition for ‘panel.smoothScatter’
frequency_vs_threshold_variable_plot,DetectedAI : .local : <anonymous>:
  no visible global function definition for ‘panel.linejoin’
frequency_vs_threshold_variable_plot,DetectedAI : .local: no visible
  global function definition for ‘doubleYScale’
getSnpIdFromLocation,GRanges : .local: no visible global function
  definition for ‘getSNPlocs’
reference_frequency_density_vs_threshold_variable_multigraph_plot,DetectedAI
  : .local: no visible binding for global variable ‘grid.arrange’
reference_frequency_density_vs_threshold_variable_plot,DetectedAI :
  .local: no visible global function definition for ‘levelplot’
* 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 ... NOTE
  Error in nrow(x@elementMetadata) : 
    error in evaluating the argument 'x' in selecting a method for function 'nrow': Error: no slot of name "elementMetadata" for this object of class "ASEset"
  Calls: <Anonymous> ... withCallingHandlers -> check_one -> length -> length -> nrow
  Execution halted
* 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 ... [2m/13m] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     23.338  0.678  25.918
import-bam               12.937  0.177  13.114
scanForHeterozygotes-old 13.011  0.023  13.034
annotation-wrappers       8.689  1.681 649.630
getAlleleQuality          7.870  0.007   7.878
getAlleleCounts           7.295  0.011   7.307
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [17s/17s]
 [17s/17s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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 ‘binom.test’ from package ‘stats’ in package ‘AllelicImbalance’
Creating a generic function for ‘chisq.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	0.594	0.002	0.596
ASEset-class	0.369	0.027	0.395
ASEset-gbarplot	0.132	0.003	0.294
ASEset-glocationplot	2.313	0.062	2.878
ASEset-gviztrack	0.475	0.005	0.539
ASEset-scanForHeterozygotes	3.087	0.011	3.099
ASEset.old	0.001	0.000	0.001
ASEset.sim	0.001	0.000	0.001
ASEsetFromBam	0.002	0.000	0.003
DetectedAI-class	0.063	0.001	0.064
DetectedAI-plot	1.616	0.010	2.425
DetectedAI-summary	0.098	0.004	0.101
GRvariants	0.002	0.000	0.003
GlobalAnalysis-class	0.002	0.001	0.002
LinkVariantAlmlof-class	0.000	0.000	0.001
LinkVariantAlmlof-plot	1.196	0.003	1.418
RegionSummary-class	0.001	0.000	0.000
RiskVariant-class	0.001	0.000	0.001
annotation-wrappers	8.689	1.681	649.630
annotationBarplot	0.000	0.000	0.001
barplot-lattice-support	0.179	0.002	0.205
binom.test	0.035	0.002	0.038
chisq.test	0.043	0.003	0.046
cigar-utilities	0.025	0.001	0.025
countAllelesFromBam	0.003	0.000	0.003
coverageMatrixListFromGAL	1.281	0.027	1.309
decorateWithExons	0.002	0.000	0.002
decorateWithGenes	0.002	0.000	0.002
defaultMapBias	0.038	0.001	0.039
defaultPhase	0.001	0.000	0.001
detectAI	0.058	0.001	0.058
fractionPlotDf	0.042	0.001	0.042
gba	0.001	0.000	0.001
genofilters	0.042	0.002	0.043
genomatrix	0.001	0.000	0.000
genotype2phase	0.008	0.001	0.009
getAlleleCounts	7.295	0.011	7.307
getAlleleQuality	7.870	0.007	7.878
getAreaFromGeneNames	0.538	0.007	0.546
getDefaultMapBiasExpMean	0.043	0.002	0.045
getSnpIdFromLocation	23.338	0.678	25.918
histplot	0.001	0.000	0.000
implodeList-old	0.002	0.000	0.002
import-bam-2	0.009	0.000	0.009
import-bam	12.937	0.177	13.114
import-bcf	0.637	0.037	0.691
inferAlleles	0.010	0.001	0.011
inferAltAllele	0.015	0.000	0.015
inferGenotypes	0.027	0.000	0.027
initialize-ASEset	0.04	0.00	0.04
initialize-DetectedAI	0.060	0.001	0.061
initialize-GlobalAnalysis	0.006	0.001	0.006
initialize-RiskVariant	0.002	0.000	0.002
legendBarplot	0.001	0.001	0.000
locationplot	0.657	0.022	0.716
lva	1.691	0.025	1.717
lva.internal	0.315	0.001	0.317
makeMaskedFasta	0.623	0.002	0.625
mapBiasRef	0.013	0.000	0.012
phase2genotype	0.019	0.000	0.020
phaseArray2phaseMatrix	0.009	0.000	0.009
phaseMatrix2Array	0.008	0.001	0.009
randomRef	0.014	0.001	0.015
reads	0	0	0
refAllele	0.018	0.001	0.019
regionSummary	0.646	0.001	0.647
scanForHeterozygotes-old	13.011	0.023	13.034