BioC 3.2: CHECK report for AllelicImbalance on zin1

Package: AllelicImbalance

Version: 1.8.3

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.8.3.tar.gz

StartedAt: 2016-04-22 22:02:59 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:08:51 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 351.6 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.8.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.3’
* 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 ... [25s/25s] 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) : 
    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 ... [81s/81s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     18.888  0.116  19.048
import-bam               11.049  0.012  11.065
scanForHeterozygotes-old  8.491  0.008   8.504
annotation-wrappers       5.949  0.095   6.078
getAlleleQuality          6.014  0.000   6.030
getAlleleCounts           5.230  0.000   5.227
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [13s/13s]
 [14s/14s] 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
  ‘/home/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 ‘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	0.152	0.004	0.156
ASEset-class	0.301	0.000	0.301
ASEset-gbarplot	0.115	0.000	0.115
ASEset-glocationplot	1.594	0.012	1.620
ASEset-gviztrack	0.475	0.004	0.478
ASEset-scanForHeterozygotes	2.805	0.024	2.844
ASEset.old	0.000	0.000	0.001
ASEset.sim	0	0	0
ASEsetFromBam	0.001	0.000	0.002
DetectedAI-class	0.06	0.00	0.06
DetectedAI-plot	1.227	0.004	1.230
DetectedAI-summary	0.085	0.004	0.088
GRvariants	0.000	0.000	0.002
GlobalAnalysis-class	0.003	0.000	0.002
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	1.021	0.004	1.024
RegionSummary-class	0.001	0.000	0.000
RiskVariant-class	0.000	0.000	0.001
annotation-wrappers	5.949	0.095	6.078
annotationBarplot	0	0	0
barplot-lattice-support	0.150	0.004	0.153
binom.test	0.025	0.004	0.029
chisq.test	0.032	0.004	0.036
cigar-utilities	0.013	0.000	0.013
countAllelesFromBam	0.002	0.000	0.003
coverageMatrixListFromGAL	0.965	0.000	0.971
decorateWithExons	0.002	0.000	0.002
decorateWithGenes	0.002	0.000	0.002
defaultMapBias	0.031	0.000	0.031
defaultPhase	0.002	0.000	0.001
detectAI	0.047	0.000	0.047
fractionPlotDf	0.031	0.000	0.030
gba	0.000	0.000	0.001
genofilters	0.034	0.000	0.034
genomatrix	0	0	0
genotype2phase	0.007	0.000	0.008
getAlleleCounts	5.230	0.000	5.227
getAlleleQuality	6.014	0.000	6.030
getAreaFromGeneNames	0.329	0.000	0.329
getDefaultMapBiasExpMean	0.005	0.004	0.009
getSnpIdFromLocation	18.888	0.116	19.048
histplot	0.001	0.000	0.000
implodeList-old	0.001	0.000	0.002
import-bam-2	0.007	0.000	0.007
import-bam	11.049	0.012	11.065
import-bcf	0.513	0.008	0.535
inferAlleles	0.009	0.000	0.009
inferAltAllele	0.012	0.000	0.012
inferGenotypes	0.018	0.000	0.018
initialize-ASEset	0.028	0.000	0.028
initialize-DetectedAI	0.044	0.000	0.044
initialize-GlobalAnalysis	0.005	0.000	0.005
initialize-RiskVariant	0.002	0.000	0.001
legendBarplot	0.000	0.000	0.001
locationplot	0.396	0.000	0.396
lva	1.171	0.020	1.192
lva.internal	0.194	0.000	0.194
makeMaskedFasta	0.511	0.000	0.511
mapBiasRef	0.010	0.000	0.009
phase2genotype	0.011	0.000	0.015
phaseArray2phaseMatrix	0.007	0.000	0.006
phaseMatrix2Array	0.001	0.004	0.006
randomRef	0.012	0.000	0.011
reads	0	0	0
refAllele	0.014	0.000	0.014
regionSummary	0.423	0.000	0.423
scanForHeterozygotes-old	8.491	0.008	8.504