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: 2015-10-27 05:19:37 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:28:42 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 544.9 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

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


* 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 ... [34s/36s] 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 ... [112s/168s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     24.582  1.659  69.835
import-bam               13.718  0.310  14.063
scanForHeterozygotes-old 13.810  0.027  13.838
annotation-wrappers       8.491  0.692  20.845
getAlleleQuality          7.845  0.008   7.853
getAlleleCounts           7.390  0.014   7.404
* 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	0.647	0.002	0.650
ASEset-class	0.401	0.032	0.433
ASEset-gbarplot	0.145	0.002	0.147
ASEset-glocationplot	2.577	0.076	2.653
ASEset-gviztrack	0.537	0.005	0.558
ASEset-scanForHeterozygotes	3.440	0.013	3.454
ASEset.old	0.000	0.000	0.001
ASEset.sim	0.000	0.000	0.001
ASEsetFromBam	0.003	0.001	0.002
DetectedAI-class	0.074	0.001	0.075
DetectedAI-plot	1.774	0.011	1.808
DetectedAI-summary	0.107	0.004	0.111
GRvariants	0.002	0.000	0.002
GlobalAnalysis-class	0.002	0.001	0.002
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	1.310	0.002	1.313
RegionSummary-class	0	0	0
RiskVariant-class	0.001	0.001	0.001
annotation-wrappers	8.491	0.692	20.845
annotationBarplot	0.001	0.000	0.001
barplot-lattice-support	0.207	0.002	0.222
binom.test	0.035	0.001	0.036
chisq.test	0.044	0.003	0.046
cigar-utilities	0.027	0.001	0.027
countAllelesFromBam	0.002	0.000	0.003
coverageMatrixListFromGAL	1.324	0.025	1.348
decorateWithExons	0.002	0.001	0.003
decorateWithGenes	0.002	0.000	0.002
defaultMapBias	0.042	0.001	0.043
defaultPhase	0.001	0.001	0.002
detectAI	0.062	0.001	0.063
fractionPlotDf	0.049	0.001	0.050
gba	0.001	0.000	0.000
genofilters	0.043	0.002	0.045
genomatrix	0.000	0.000	0.001
genotype2phase	0.008	0.001	0.009
getAlleleCounts	7.390	0.014	7.404
getAlleleQuality	7.845	0.008	7.853
getAreaFromGeneNames	0.535	0.008	0.543
getDefaultMapBiasExpMean	0.013	0.001	0.014
getSnpIdFromLocation	24.582	1.659	69.835
histplot	0	0	0
implodeList-old	0.002	0.000	0.002
import-bam-2	0.011	0.001	0.010
import-bam	13.718	0.310	14.063
import-bcf	0.673	0.040	0.737
inferAlleles	0.011	0.000	0.012
inferAltAllele	0.016	0.000	0.017
inferGenotypes	0.026	0.001	0.027
initialize-ASEset	0.041	0.001	0.041
initialize-DetectedAI	0.063	0.000	0.063
initialize-GlobalAnalysis	0.006	0.000	0.007
initialize-RiskVariant	0.002	0.001	0.002
legendBarplot	0.001	0.000	0.001
locationplot	0.690	0.022	0.714
lva	1.789	0.029	1.819
lva.internal	0.338	0.002	0.340
makeMaskedFasta	0.670	0.003	0.672
mapBiasRef	0.015	0.001	0.015
phase2genotype	0.022	0.001	0.023
phaseArray2phaseMatrix	0.010	0.001	0.011
phaseMatrix2Array	0.009	0.001	0.009
randomRef	0.016	0.001	0.017
reads	0	0	0
refAllele	0.021	0.001	0.022
regionSummary	0.756	0.001	0.758
scanForHeterozygotes-old	13.810	0.027	13.838