BioC 3.3: CHECK report for AllelicImbalance on windows2.bioconductor.org

Package: AllelicImbalance

Version: 1.9.0

Command: rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.9.0.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.9.0.tar.gz

StartedAt: 2015-10-27 00:33:19 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 00:40:13 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 414.7 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.9.0.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/AllelicImbalance.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '1.9.0'
* 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 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: 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 ...
** running examples for arch 'i386' ... [67s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getSnpIdFromLocation     17.89   0.31   18.42
scanForHeterozygotes-old  7.45   0.00    7.46
import-bam                6.78   0.05    6.83
annotation-wrappers       5.29   0.19    7.78
** running examples for arch 'x64' ... [76s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getSnpIdFromLocation     17.53   0.23   17.77
import-bam                9.71   0.02    9.74
scanForHeterozygotes-old  9.11   0.00    9.11
annotation-wrappers       6.67   0.27    6.94
getAlleleQuality          5.47   0.00    5.47
getAlleleCounts           5.28   0.00    5.28
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R' [8s]
 [8s] OK
** running tests for arch 'x64' ...
  Running 'test-all.R' [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
  'c:/biocbld/bbs-3.3-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 '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

install for x64

* installing *source* package 'AllelicImbalance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AllelicImbalance' as AllelicImbalance_1.9.0.zip
* DONE (AllelicImbalance)

name	user	system	elapsed
ASEset-barplot	0.16	0.00	0.16
ASEset-class	0.56	0.03	0.59
ASEset-gbarplot	0.09	0.00	0.10
ASEset-glocationplot	1.18	0.05	1.21
ASEset-gviztrack	0.32	0.00	0.33
ASEset-scanForHeterozygotes	2.27	0.03	2.30
ASEset.old	0	0	0
ASEset.sim	0	0	0
ASEsetFromBam	0	0	0
DetectedAI-class	0.05	0.00	0.05
DetectedAI-plot	0.90	0.03	0.93
DetectedAI-summary	0.07	0.00	0.07
GRvariants	0	0	0
GlobalAnalysis-class	0.01	0.00	0.01
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	0.70	0.00	0.71
RegionSummary-class	0	0	0
RiskVariant-class	0	0	0
annotation-wrappers	5.29	0.19	7.78
annotationBarplot	0	0	0
barplot-lattice-support	0.11	0.00	0.11
binom.test	0.02	0.00	0.02
chisq.test	0.03	0.00	0.03
cigar-utilities	0.01	0.00	0.01
countAllelesFromBam	0	0	0
coverageMatrixListFromGAL	0.69	0.00	0.69
decorateWithExons	0	0	0
decorateWithGenes	0	0	0
defaultMapBias	0.01	0.00	0.03
defaultPhase	0.02	0.00	0.01
detectAI	0.06	0.00	0.07
fractionPlotDf	0.05	0.00	0.04
gba	0	0	0
genofilters	0.03	0.01	0.05
genomatrix	0	0	0
genotype2phase	0.00	0.02	0.02
getAlleleCounts	4.11	0.00	4.11
getAlleleQuality	4.56	0.00	4.56
getAreaFromGeneNames	0.28	0.02	0.29
getDefaultMapBiasExpMean	0	0	0
getSnpIdFromLocation	17.89	0.31	18.42
histplot	0	0	0
implodeList-old	0	0	0
import-bam-2	0	0	0
import-bam	6.78	0.05	6.83
import-bcf	0.31	0.01	0.38
inferAlleles	0	0	0
inferAltAllele	0.02	0.00	0.01
inferGenotypes	0.01	0.00	0.02
initialize-ASEset	0.03	0.00	0.03
initialize-DetectedAI	0.04	0.00	0.03
initialize-GlobalAnalysis	0.01	0.00	0.02
initialize-RiskVariant	0	0	0
legendBarplot	0	0	0
locationplot	0.39	0.00	0.39
lva	1.03	0.03	1.07
lva.internal	0.18	0.00	0.18
makeMaskedFasta	0.32	0.00	0.32
mapBiasRef	0	0	0
phase2genotype	0.01	0.00	0.02
phaseArray2phaseMatrix	0	0	0
phaseMatrix2Array	0.02	0.00	0.01
randomRef	0.02	0.00	0.02
reads	0	0	0
refAllele	0.01	0.00	0.01
regionSummary	0.36	0.00	0.36
scanForHeterozygotes-old	7.45	0.00	7.46

name	user	system	elapsed
ASEset-barplot	0.15	0.00	0.16
ASEset-class	0.61	0.00	0.61
ASEset-gbarplot	0.10	0.02	0.11
ASEset-glocationplot	1.94	0.01	1.95
ASEset-gviztrack	0.39	0.00	0.39
ASEset-scanForHeterozygotes	2.37	0.00	2.38
ASEset.old	0	0	0
ASEset.sim	0	0	0
ASEsetFromBam	0	0	0
DetectedAI-class	0.04	0.00	0.05
DetectedAI-plot	1.22	0.02	1.23
DetectedAI-summary	0.08	0.00	0.08
GRvariants	0	0	0
GlobalAnalysis-class	0	0	0
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	0.89	0.03	0.92
RegionSummary-class	0	0	0
RiskVariant-class	0	0	0
annotation-wrappers	6.67	0.27	6.94
annotationBarplot	0	0	0
barplot-lattice-support	0.14	0.00	0.14
binom.test	0.02	0.00	0.01
chisq.test	0.03	0.00	0.03
cigar-utilities	0.02	0.00	0.01
countAllelesFromBam	0	0	0
coverageMatrixListFromGAL	0.81	0.04	0.86
decorateWithExons	0.00	0.02	0.02
decorateWithGenes	0	0	0
defaultMapBias	0.03	0.00	0.03
defaultPhase	0	0	0
detectAI	0.05	0.00	0.05
fractionPlotDf	0.01	0.01	0.03
gba	0	0	0
genofilters	0.03	0.00	0.04
genomatrix	0	0	0
genotype2phase	0.02	0.00	0.01
getAlleleCounts	5.28	0.00	5.28
getAlleleQuality	5.47	0.00	5.47
getAreaFromGeneNames	0.28	0.02	0.30
getDefaultMapBiasExpMean	0.00	0.02	0.01
getSnpIdFromLocation	17.53	0.23	17.77
histplot	0	0	0
implodeList-old	0.02	0.00	0.01
import-bam-2	0	0	0
import-bam	9.71	0.02	9.74
import-bcf	0.47	0.00	0.47
inferAlleles	0.00	0.01	0.01
inferAltAllele	0.02	0.00	0.02
inferGenotypes	0.01	0.00	0.01
initialize-ASEset	0.04	0.00	0.04
initialize-DetectedAI	0.04	0.00	0.04
initialize-GlobalAnalysis	0	0	0
initialize-RiskVariant	0.00	0.02	0.02
legendBarplot	0	0	0
locationplot	0.46	0.00	0.45
lva	1.23	0.01	1.25
lva.internal	0.2	0.0	0.2
makeMaskedFasta	0.44	0.00	0.44
mapBiasRef	0.00	0.01	0.01
phase2genotype	0.00	0.02	0.02
phaseArray2phaseMatrix	0.00	0.02	0.01
phaseMatrix2Array	0	0	0
randomRef	0.00	0.01	0.02
reads	0	0	0
refAllele	0.00	0.02	0.02
regionSummary	0.45	0.00	0.45
scanForHeterozygotes-old	9.11	0.00	9.11