BioC 3.2: CHECK report for AllelicImbalance on moscato1

Package: AllelicImbalance

Version: 1.8.3

Command: rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.8.3.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.8.3.tar.gz

StartedAt: 2016-04-22 23:28:47 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 23:47:35 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 1127.3 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.8.3.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.8.3.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/AllelicImbalance.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'AllelicImbalance' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [477s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getSnpIdFromLocation     22.94   0.26   37.52
import-bam               10.36   0.03   10.38
scanForHeterozygotes-old  9.36   0.01    9.57
annotation-wrappers       9.11   0.22  370.29
getAlleleQuality          8.66   0.02    8.68
getAlleleCounts           5.95   0.03    6.00
** running examples for arch 'x64' ... [114s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getSnpIdFromLocation     22.45   0.31   22.78
import-bam               16.77   0.01   16.79
scanForHeterozygotes-old 13.46   0.00   13.47
annotation-wrappers       8.30   0.25    8.58
getAlleleQuality          7.30   0.00    7.30
getAlleleCounts           6.27   0.00    6.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R' [15s]
 [16s] OK
** running tests for arch 'x64' ...
  Running 'test-all.R' [18s]
 [18s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/AllelicImbalance.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'AllelicImbalance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AllelicImbalance' as AllelicImbalance_1.8.3.zip
* DONE (AllelicImbalance)

name	user	system	elapsed
ASEset-barplot	0.25	0.00	0.25
ASEset-class	0.47	0.00	0.47
ASEset-gbarplot	0.14	0.02	0.16
ASEset-glocationplot	2.08	0.00	2.85
ASEset-gviztrack	0.93	0.00	0.94
ASEset-scanForHeterozygotes	2.69	0.00	2.68
ASEset.old	0	0	0
ASEset.sim	0	0	0
ASEsetFromBam	0.02	0.00	0.01
DetectedAI-class	0.08	0.01	0.10
DetectedAI-plot	1.68	0.02	1.70
DetectedAI-summary	0.09	0.00	0.09
GRvariants	0.00	0.01	0.02
GlobalAnalysis-class	0.00	0.00	0.01
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	1.09	0.00	1.09
RegionSummary-class	0	0	0
RiskVariant-class	0	0	0
annotation-wrappers	9.11	0.22	370.29
annotationBarplot	0	0	0
barplot-lattice-support	0.17	0.00	0.17
binom.test	0.03	0.00	0.03
chisq.test	0.05	0.00	0.05
cigar-utilities	0.01	0.00	0.01
countAllelesFromBam	0	0	0
coverageMatrixListFromGAL	1.38	0.00	1.37
decorateWithExons	0	0	0
decorateWithGenes	0.01	0.00	0.02
defaultMapBias	0.02	0.02	0.06
defaultPhase	0	0	0
detectAI	0.09	0.00	0.10
fractionPlotDf	0.05	0.00	0.04
gba	0	0	0
genofilters	0.07	0.00	0.06
genomatrix	0	0	0
genotype2phase	0.00	0.01	0.02
getAlleleCounts	5.95	0.03	6.00
getAlleleQuality	8.66	0.02	8.68
getAreaFromGeneNames	0.50	0.02	0.51
getDefaultMapBiasExpMean	0.01	0.00	0.01
getSnpIdFromLocation	22.94	0.26	37.52
histplot	0	0	0
implodeList-old	0	0	0
import-bam-2	0	0	0
import-bam	10.36	0.03	10.38
import-bcf	0.56	0.00	1.00
inferAlleles	0.01	0.00	0.01
inferAltAllele	0.02	0.02	0.03
inferGenotypes	0.03	0.00	0.04
initialize-ASEset	0.03	0.00	0.03
initialize-DetectedAI	0.06	0.00	0.06
initialize-GlobalAnalysis	0.02	0.00	0.02
initialize-RiskVariant	0	0	0
legendBarplot	0	0	0
locationplot	0.56	0.01	0.57
lva	1.53	0.00	1.53
lva.internal	0.25	0.00	0.25
makeMaskedFasta	0.50	0.00	0.56
mapBiasRef	0.01	0.00	0.02
phase2genotype	0.02	0.02	0.03
phaseArray2phaseMatrix	0.01	0.00	0.01
phaseMatrix2Array	0	0	0
randomRef	0.02	0.00	0.02
reads	0	0	0
refAllele	0.01	0.00	0.01
regionSummary	0.52	0.00	0.52
scanForHeterozygotes-old	9.36	0.01	9.57

name	user	system	elapsed
ASEset-barplot	0.69	0.00	0.68
ASEset-class	0.33	0.06	0.39
ASEset-gbarplot	0.14	0.00	0.14
ASEset-glocationplot	2.82	0.03	2.86
ASEset-gviztrack	0.53	0.02	0.88
ASEset-scanForHeterozygotes	3.50	0.01	3.51
ASEset.old	0	0	0
ASEset.sim	0	0	0
ASEsetFromBam	0.00	0.02	0.02
DetectedAI-class	0.07	0.00	0.08
DetectedAI-plot	2.03	0.01	2.04
DetectedAI-summary	0.11	0.00	0.11
GRvariants	0.72	0.02	0.73
GlobalAnalysis-class	0.01	0.00	0.02
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	1.90	0.01	1.92
RegionSummary-class	0	0	0
RiskVariant-class	0	0	0
annotation-wrappers	8.30	0.25	8.58
annotationBarplot	0	0	0
barplot-lattice-support	0.18	0.00	0.17
binom.test	0.04	0.00	0.04
chisq.test	0.03	0.00	0.03
cigar-utilities	0.02	0.00	0.02
countAllelesFromBam	0.00	0.02	0.02
coverageMatrixListFromGAL	1.12	0.00	1.12
decorateWithExons	0	0	0
decorateWithGenes	0.00	0.01	0.01
defaultMapBias	0.03	0.00	1.10
defaultPhase	0	0	0
detectAI	0.06	0.00	0.06
fractionPlotDf	0.05	0.02	0.07
gba	0	0	0
genofilters	0.06	0.02	0.08
genomatrix	0	0	0
genotype2phase	0.00	0.03	0.03
getAlleleCounts	6.27	0.00	6.27
getAlleleQuality	7.3	0.0	7.3
getAreaFromGeneNames	0.46	0.00	0.56
getDefaultMapBiasExpMean	0.02	0.00	0.01
getSnpIdFromLocation	22.45	0.31	22.78
histplot	0	0	0
implodeList-old	0	0	0
import-bam-2	0	0	0
import-bam	16.77	0.01	16.79
import-bcf	0.78	0.00	0.78
inferAlleles	0.00	0.02	0.01
inferAltAllele	0.03	0.00	0.03
inferGenotypes	0.03	0.00	0.03
initialize-ASEset	0.03	0.00	0.04
initialize-DetectedAI	0.05	0.02	0.06
initialize-GlobalAnalysis	0.00	0.01	0.01
initialize-RiskVariant	0	0	0
legendBarplot	0	0	0
locationplot	0.54	0.00	0.55
lva	1.64	0.00	1.63
lva.internal	0.27	0.00	0.27
makeMaskedFasta	0.84	0.00	3.13
mapBiasRef	0.01	0.02	0.04
phase2genotype	0.04	0.01	0.04
phaseArray2phaseMatrix	0.01	0.00	0.02
phaseMatrix2Array	0.01	0.00	0.02
randomRef	0.03	0.00	0.03
reads	0	0	0
refAllele	0.03	0.02	0.05
regionSummary	0.69	0.00	0.68
scanForHeterozygotes-old	13.46	0.00	13.47