BioC 3.3: CHECK report for AllelicImbalance on morelia

Package: AllelicImbalance

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.9.0.tar.gz

StartedAt: 2015-10-22 03:18:41 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 03:23:19 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 278.5 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_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/AllelicImbalance.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.9.0’
* 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 ... [19s/20s] 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: no visible binding for global variable
  ‘UserDir’
detectAI,ASEset: no visible binding for global variable ‘tf.keep1’
detectAI,ASEset: no visible binding for global variable ‘tf.keep2’
detectedAI_vs_threshold_variable_multigraph_plot,DetectedAI: no visible
  binding for global variable ‘grid.arrange’
detectedAI_vs_threshold_variable_plot,DetectedAI : <anonymous>: no
  visible global function definition for ‘panel.smoothScatter’
detectedAI_vs_threshold_variable_plot,DetectedAI : <anonymous>: no
  visible global function definition for ‘panel.linejoin’
detectedAI_vs_threshold_variable_plot,DetectedAI: no visible global
  function definition for ‘doubleYScale’
frequency_vs_threshold_variable_multigraph_plot,DetectedAI: no visible
  binding for global variable ‘grid.arrange’
frequency_vs_threshold_variable_plot,DetectedAI : <anonymous>: no
  visible global function definition for ‘panel.smoothScatter’
frequency_vs_threshold_variable_plot,DetectedAI : <anonymous>: no
  visible global function definition for ‘panel.linejoin’
frequency_vs_threshold_variable_plot,DetectedAI: no visible global
  function definition for ‘doubleYScale’
getSnpIdFromLocation,GRanges: no visible global function definition for
  ‘getSNPlocs’
reference_frequency_density_vs_threshold_variable_multigraph_plot,DetectedAI:
  no visible binding for global variable ‘grid.arrange’
reference_frequency_density_vs_threshold_variable_plot,DetectedAI: no
  visible global function definition for ‘levelplot’
Undefined global functions or variables:
  UserDir doubleYScale getSNPlocs grid.arrange levelplot panel.linejoin
  panel.smoothScatter tf.keep1 tf.keep2
* 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 ... [71s/72s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     17.543  0.375  18.252
import-bam                8.108  0.145   8.255
scanForHeterozygotes-old  8.142  0.040   8.183
annotation-wrappers       5.382  0.229   5.921
getAlleleCounts           5.433  0.010   5.445
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [10s/10s]
 [10s/10s] 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-3.3-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	0.179	0.001	0.180
ASEset-class	0.615	0.021	0.636
ASEset-gbarplot	0.091	0.002	0.093
ASEset-glocationplot	1.266	0.014	1.281
ASEset-gviztrack	0.342	0.003	0.344
ASEset-scanForHeterozygotes	2.452	0.038	2.491
ASEset.old	0.001	0.000	0.000
ASEset.sim	0.000	0.000	0.001
ASEsetFromBam	0.001	0.000	0.001
DetectedAI-class	0.060	0.001	0.061
DetectedAI-plot	0.989	0.006	1.063
DetectedAI-summary	0.067	0.004	0.070
GRvariants	0.002	0.000	0.003
GlobalAnalysis-class	0.002	0.000	0.003
LinkVariantAlmlof-class	0.001	0.000	0.001
LinkVariantAlmlof-plot	1.095	0.002	1.105
RegionSummary-class	0.001	0.000	0.000
RiskVariant-class	0.001	0.000	0.001
annotation-wrappers	5.382	0.229	5.921
annotationBarplot	0.001	0.000	0.001
barplot-lattice-support	0.164	0.001	0.166
binom.test	0.024	0.001	0.025
chisq.test	0.029	0.000	0.031
cigar-utilities	0.016	0.000	0.015
countAllelesFromBam	0.002	0.000	0.002
coverageMatrixListFromGAL	0.890	0.018	0.909
decorateWithExons	0.001	0.001	0.001
decorateWithGenes	0.001	0.000	0.002
defaultMapBias	0.023	0.001	0.024
defaultPhase	0.001	0.000	0.001
detectAI	0.034	0.000	0.035
fractionPlotDf	0.026	0.001	0.027
gba	0	0	0
genofilters	0.025	0.001	0.025
genomatrix	0	0	0
genotype2phase	0.005	0.001	0.005
getAlleleCounts	5.433	0.010	5.445
getAlleleQuality	4.779	0.015	4.794
getAreaFromGeneNames	0.284	0.004	0.288
getDefaultMapBiasExpMean	0.007	0.000	0.006
getSnpIdFromLocation	17.543	0.375	18.252
histplot	0.001	0.000	0.001
implodeList-old	0.001	0.000	0.001
import-bam-2	0.006	0.000	0.006
import-bam	8.108	0.145	8.255
import-bcf	0.423	0.022	0.445
inferAlleles	0.009	0.000	0.010
inferAltAllele	0.013	0.001	0.014
inferGenotypes	0.024	0.000	0.024
initialize-ASEset	0.038	0.000	0.038
initialize-DetectedAI	0.037	0.001	0.038
initialize-GlobalAnalysis	0.003	0.000	0.004
initialize-RiskVariant	0.002	0.000	0.001
legendBarplot	0	0	0
locationplot	0.552	0.025	0.579
lva	1.322	0.015	1.337
lva.internal	0.187	0.001	0.187
makeMaskedFasta	0.346	0.001	0.347
mapBiasRef	0.009	0.001	0.008
phase2genotype	0.012	0.000	0.013
phaseArray2phaseMatrix	0.005	0.001	0.006
phaseMatrix2Array	0.005	0.000	0.005
randomRef	0.009	0.000	0.009
reads	0.001	0.000	0.001
refAllele	0.013	0.001	0.013
regionSummary	0.383	0.001	0.383
scanForHeterozygotes-old	8.142	0.040	8.183