BioC 3.2: CHECK report for AllelicImbalance on oaxaca

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 01:15:12 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:24:31 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 559.1 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 (2015-08-14)
* 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 ‘1.8.0’
* 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 ... [29s/31s] 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 ... [93s/238s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     20.237  0.482  23.159
scanForHeterozygotes-old 11.414  0.071  11.490
import-bam                9.196  0.182  11.058
getAlleleQuality          7.840  0.024   7.870
getAlleleCounts           6.885  0.020   6.908
annotation-wrappers       5.983  0.572 146.821
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [14s/16s]
 [14s/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	0.554	0.003	0.557
ASEset-class	0.391	0.020	0.411
ASEset-gbarplot	0.128	0.003	0.131
ASEset-glocationplot	2.491	0.054	2.704
ASEset-gviztrack	0.528	0.004	0.531
ASEset-scanForHeterozygotes	3.447	0.017	3.473
ASEset.old	0.000	0.000	0.001
ASEset.sim	0.001	0.000	0.001
ASEsetFromBam	0.003	0.001	0.003
DetectedAI-class	0.047	0.001	0.047
DetectedAI-plot	1.487	0.009	1.677
DetectedAI-summary	0.134	0.006	0.177
GRvariants	0.001	0.001	0.001
GlobalAnalysis-class	0.001	0.000	0.001
LinkVariantAlmlof-class	0.001	0.000	0.001
LinkVariantAlmlof-plot	1.165	0.012	1.190
RegionSummary-class	0.001	0.000	0.001
RiskVariant-class	0.001	0.000	0.001
annotation-wrappers	5.983	0.572	146.821
annotationBarplot	0.001	0.000	0.000
barplot-lattice-support	0.172	0.001	0.193
binom.test	0.034	0.001	0.034
chisq.test	0.039	0.001	0.041
cigar-utilities	0.025	0.000	0.025
countAllelesFromBam	0.002	0.000	0.003
coverageMatrixListFromGAL	1.171	0.014	1.185
decorateWithExons	0.002	0.000	0.003
decorateWithGenes	0.001	0.000	0.002
defaultMapBias	0.034	0.001	0.035
defaultPhase	0.002	0.001	0.002
detectAI	0.052	0.001	0.053
fractionPlotDf	0.045	0.000	0.046
gba	0	0	0
genofilters	0.040	0.001	0.041
genomatrix	0.000	0.000	0.001
genotype2phase	0.007	0.001	0.007
getAlleleCounts	6.885	0.020	6.908
getAlleleQuality	7.840	0.024	7.870
getAreaFromGeneNames	0.498	0.007	0.505
getDefaultMapBiasExpMean	0.011	0.001	0.011
getSnpIdFromLocation	20.237	0.482	23.159
histplot	0.001	0.000	0.001
implodeList-old	0.003	0.000	0.002
import-bam-2	0.009	0.000	0.009
import-bam	9.196	0.182	11.058
import-bcf	0.472	0.022	0.531
inferAlleles	0.010	0.001	0.011
inferAltAllele	0.01	0.00	0.01
inferGenotypes	0.025	0.001	0.026
initialize-ASEset	0.033	0.001	0.034
initialize-DetectedAI	0.061	0.000	0.061
initialize-GlobalAnalysis	0.004	0.000	0.005
initialize-RiskVariant	0.002	0.000	0.002
legendBarplot	0.000	0.001	0.000
locationplot	0.616	0.017	0.679
lva	1.204	0.011	1.216
lva.internal	0.247	0.000	0.247
makeMaskedFasta	0.488	0.001	0.491
mapBiasRef	0.014	0.001	0.014
phase2genotype	0.021	0.001	0.022
phaseArray2phaseMatrix	0.009	0.001	0.009
phaseMatrix2Array	0.009	0.001	0.010
randomRef	0.014	0.000	0.014
reads	0.001	0.001	0.001
refAllele	0.018	0.000	0.018
regionSummary	0.613	0.001	0.616
scanForHeterozygotes-old	11.414	0.071	11.490