BioC 3.2: CHECK report for AllelicImbalance on zin1

Package: AllelicImbalance

Version: 1.7.19

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.7.19.tar.gz

StartedAt: 2015-08-23 21:35:34 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 21:40:49 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 315.0 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_1.7.19.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.7.19’
* 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 ... [22s/23s] 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’
phase,riskVariant : .local: no visible global function definition for
  ‘phaseArray2Matrix’
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 ... OK
* 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 ... [76s/76s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     19.767  0.120  19.921
scanForHeterozygotes-old  9.972  0.004   9.968
import-bam                9.672  0.016   9.700
getAlleleQuality          6.092  0.000   6.089
getAlleleCounts           5.469  0.000   5.465
* 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: 1 NOTE
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 ‘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	0.471	0.000	0.471
ASEset-class	0.286	0.012	0.298
ASEset-gbarplot	0.119	0.000	0.119
ASEset-glocationplot	1.556	0.008	1.562
ASEset-gviztrack	0.456	0.000	0.458
ASEset-scanForHeterozygotes	3.113	0.031	3.187
ASEset.sim	0	0	0
ASEsetFromBam	0.002	0.000	0.002
DetectedAI-class	0.057	0.000	0.063
DetectedAI-plot	1.611	0.000	1.610
DetectedAI-summary	0.077	0.004	0.081
GRvariants	0.002	0.000	0.002
GlobalAnalysis-class	0.002	0.000	0.002
annotation-wrappers	1.834	0.040	1.929
annotationBarplot	0.001	0.000	0.001
barplot-lattice-support	0.134	0.004	0.138
binom.test	0.029	0.000	0.029
chisq.test	0.032	0.000	0.032
cigar-utilities	0.022	0.000	0.022
countAllelesFromBam	0.002	0.000	0.002
coverageMatrixListFromGAL	0.963	0.000	0.962
decorateWithExons	0.001	0.000	0.001
decorateWithGenes	0.002	0.000	0.002
defaultMapBias	0.03	0.00	0.03
defaultPhase	0.001	0.000	0.001
detectAI	0.046	0.000	0.046
fractionPlotDf	0.031	0.000	0.032
gba	0	0	0
genofilters	0.031	0.000	0.032
genomatrix	0	0	0
genotype2phase	0.002	0.004	0.007
getAlleleCounts	5.469	0.000	5.465
getAlleleQuality	6.092	0.000	6.089
getAreaFromGeneNames	0.317	0.004	0.320
getDefaultMapBiasExpMean	0.01	0.00	0.01
getSnpIdFromLocation	19.767	0.120	19.921
histplot	0.000	0.000	0.001
implodeList-old	0.002	0.000	0.001
import-bam-2	0.007	0.000	0.008
import-bam	9.672	0.016	9.700
import-bcf	0.456	0.012	0.480
inferAlleles	0.008	0.000	0.008
inferAltAllele	0.011	0.000	0.011
inferGenotypes	0.019	0.000	0.019
initialize-ASEset	0.03	0.00	0.03
initialize-DetectedAI	0.053	0.000	0.053
initialize-GlobalAnalysis	0.005	0.000	0.005
initialize-riskVariant	0.044	0.000	0.044
legendBarplot	0	0	0
locationplot	0.527	0.020	0.546
lva	0.932	0.000	0.932
lva.internal	0.110	0.000	0.111
makeMaskedFasta	0.454	0.004	0.458
mapBiasRef	0.010	0.000	0.009
phase2genotype	0.015	0.000	0.015
phaseArray2phaseMatrix	0.007	0.000	0.007
phaseMatrix2Array	0.006	0.000	0.005
randomRef	0.012	0.000	0.011
reads	0	0	0
refAllele	0.010	0.004	0.015
regionSummary	0.768	0.000	0.766
riskVariant-class	0	0	0
scanForHeterozygotes-old	9.972	0.004	9.968