BioC 3.3: CHECK report for AllelicImbalance on linux2.bioconductor.org

Package: AllelicImbalance

Version: 1.9.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.9.0.tar.gz

StartedAt: 2015-10-27 01:37:42 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:42:43 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 300.9 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/AllelicImbalance.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.9.0’
* 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 ... [20s/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 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     20.926  0.124  21.088
import-bam               10.009  0.008  10.026
scanForHeterozygotes-old  9.509  0.000   9.509
annotation-wrappers       6.570  0.107   6.689
getAlleleQuality          5.585  0.000   5.585
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [11s/11s]
 [11s/11s] 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-3.3-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	0.142	0.000	0.143
ASEset-class	0.542	0.011	0.554
ASEset-gbarplot	0.095	0.005	0.098
ASEset-glocationplot	1.621	0.012	1.633
ASEset-gviztrack	0.695	0.000	0.696
ASEset-scanForHeterozygotes	2.143	0.032	2.174
ASEset.old	0.000	0.000	0.001
ASEset.sim	0.000	0.000	0.001
ASEsetFromBam	0.002	0.000	0.003
DetectedAI-class	0.071	0.000	0.071
DetectedAI-plot	1.197	0.007	1.205
DetectedAI-summary	0.089	0.003	0.093
GRvariants	0.002	0.000	0.002
GlobalAnalysis-class	0.002	0.000	0.002
LinkVariantAlmlof-class	0.000	0.000	0.001
LinkVariantAlmlof-plot	0.919	0.000	0.919
RegionSummary-class	0	0	0
RiskVariant-class	0	0	0
annotation-wrappers	6.570	0.107	6.689
annotationBarplot	0.001	0.000	0.000
barplot-lattice-support	0.116	0.000	0.115
binom.test	0.022	0.000	0.021
chisq.test	0.026	0.000	0.027
cigar-utilities	0.015	0.000	0.015
countAllelesFromBam	0.001	0.000	0.002
coverageMatrixListFromGAL	1.145	0.000	1.145
decorateWithExons	0.002	0.000	0.002
decorateWithGenes	0.001	0.000	0.002
defaultMapBias	0.028	0.000	0.028
defaultPhase	0.001	0.000	0.001
detectAI	0.036	0.000	0.035
fractionPlotDf	0.025	0.000	0.026
gba	0.001	0.000	0.000
genofilters	0.026	0.000	0.025
genomatrix	0.000	0.000	0.001
genotype2phase	0.005	0.000	0.005
getAlleleCounts	4.617	0.000	4.618
getAlleleQuality	5.585	0.000	5.585
getAreaFromGeneNames	0.264	0.000	0.265
getDefaultMapBiasExpMean	0.008	0.000	0.007
getSnpIdFromLocation	20.926	0.124	21.088
histplot	0.001	0.000	0.001
implodeList-old	0.002	0.000	0.002
import-bam-2	0.01	0.00	0.01
import-bam	10.009	0.008	10.026
import-bcf	0.529	0.004	0.534
inferAlleles	0.006	0.004	0.011
inferAltAllele	0.012	0.004	0.016
inferGenotypes	0.028	0.000	0.027
initialize-ASEset	0.04	0.00	0.04
initialize-DetectedAI	0.062	0.000	0.062
initialize-GlobalAnalysis	0.007	0.000	0.006
initialize-RiskVariant	0.003	0.000	0.002
legendBarplot	0.001	0.000	0.000
locationplot	0.697	0.000	0.697
lva	1.732	0.000	1.731
lva.internal	0.299	0.000	0.298
makeMaskedFasta	0.6	0.0	0.6
mapBiasRef	0.013	0.000	0.012
phase2genotype	0.02	0.00	0.02
phaseArray2phaseMatrix	0.009	0.000	0.009
phaseMatrix2Array	0.007	0.000	0.008
randomRef	0.014	0.000	0.015
reads	0.000	0.000	0.001
refAllele	0.019	0.000	0.019
regionSummary	0.680	0.000	0.684
scanForHeterozygotes-old	9.509	0.000	9.509