Package: ABarray

Version: 1.50.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ABarray.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ABarray_1.50.0.tar.gz

StartedAt: 2019-04-13 00:23:52 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 00:26:18 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 146.6 seconds

RetCode: 0

Status:  OK

CheckDir: ABarray.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ABarray.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ABarray_1.50.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ABarray.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ABarray/DESCRIPTION' ... OK
* this is package 'ABarray' version '1.50.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'ABarray' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
* 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 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
ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow
  = 5000, colClasses = colRead): partial argument match of 'nrow' to
  'nrows'
ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow
  = 36000, colClasses = colRead, as.is = TRUE, check.names = FALSE,
  comment.char = "", na.string = c("NA", "MultipleValues", "Multiple
  Values")): partial argument match of 'na.string' to 'na.strings'
ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow
  = 36000, colClasses = colRead, as.is = TRUE, check.names = FALSE,
  comment.char = "", na.string = c("NA", "MultipleValues", "Multiple
  Values")): partial argument match of 'nrow' to 'nrows'
ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow
  = 36000, colClasses = colRead, check.names = FALSE, comment.char =
  "", na.string = c("NA", "MultipleValues", "Multiple Values")):
  partial argument match of 'na.string' to 'na.strings'
ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow
  = 36000, colClasses = colRead, check.names = FALSE, comment.char =
  "", na.string = c("NA", "MultipleValues", "Multiple Values")):
  partial argument match of 'nrow' to 'nrows'
ABarray: warning in dir.create(dataDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
ABarray: warning in dir.create(pdfDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
ABarray: warning in dir.create(jpgDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
doLPE: warning in dir.create(dataDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
doPlotEset: warning in dir.create(dataDir, showWarning = FALSE):
  partial argument match of 'showWarning' to 'showWarnings'
doPlotEset: warning in dir.create(pdfDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
doPlotEset: warning in dir.create(jpgDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
doPlotFCT: warning in dir.create(dataDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
doPlotFCT: warning in dir.create(pdfDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
doPlotFCT: warning in dir.create(jpgDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
icpPlot: warning in jpeg(file = paste(jpgDir, fname, "_Heatmap.jpg",
  sep = ""), width = fWidth, height = fHeight): partial argument match
  of 'file' to 'filename'
ABarray: no visible binding for global variable 'colSn'
ABarrayGUI : getImputeFunc: no visible binding for global variable
  'knnRbtn'
doLPE: no visible global function definition for 'baseOlig.error'
doLPE: no visible global function definition for 'lpe'
doVennDiagram: no visible global function definition for 'vennCounts'
drawVennDiagram: no visible global function definition for 'vennCounts'
getPantherMap: no visible binding for global variable 'panther'
Undefined global functions or variables:
  baseOlig.error colSn knnRbtn lpe panther vennCounts
* checking Rd files ... NOTE
prepare_Rd: ABarrayGUI.Rd:12-13: Dropping empty section \arguments
prepare_Rd: calcsn.Rd:26-28: Dropping empty section \examples
prepare_Rd: cvv.Rd:22-24: Dropping empty section \examples
prepare_Rd: cvvPlot.Rd:24-26: Dropping empty section \examples
prepare_Rd: doVennDiagram.Rd:33-36: Dropping empty section \examples
prepare_Rd: getMemberEset.Rd:23-25: Dropping empty section \examples
prepare_Rd: getPantherMap.Rd:24-26: Dropping empty section \examples
prepare_Rd: hclusterPlot.Rd:27-29: Dropping empty section \examples
prepare_Rd: matrixPlot.Rd:32-34: Dropping empty section \examples
prepare_Rd: qnNormalize.Rd:52-54: Dropping empty section \examples
prepare_Rd: savejpg.Rd:26-28: Dropping empty section \examples
prepare_Rd: snSummary.Rd:22-25: Dropping empty section \examples
* 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 files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/ABarray.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ABarray_1.50.0.tar.gz && rm -rf ABarray.buildbin-libdir && mkdir ABarray.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ABarray.buildbin-libdir ABarray_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ABarray_1.50.0.zip && rm ABarray_1.50.0.tar.gz ABarray_1.50.0.zip
###
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100  128k  100  128k    0     0  3153k      0 --:--:-- --:--:-- --:--:-- 3571k

install for i386

* installing *source* package 'ABarray' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ABarray'
    finding HTML links ... done
    ABarray                                 html  
    ABarrayGUI                              html  
    calcsn                                  html  
    concord                                 html  
    cvv                                     html  
    cvvPlot                                 html  
    doANOVA                                 html  
    doLPE                                   html  
    doPlotEset                              html  
    doPlotFCT                               html  
    doVennDiagram                           html  
    drawVennDiagram                         html  
    getMemberEset                           html  
    getPantherMap                           html  
    hclusterPlot                            html  
    icpPlot                                 html  
    imputeFlag                              html  
    lpe.fdr.BH                              html  
    mamaplot                                html  
    matrixPlot                              html  
    mvaPair2                                html  
    panel.cor                               html  
    panel.scatter                           html  
    qnNormalize                             html  
    rgcolorsfunc                            html  
    savejpg                                 html  
    scaleColorBar                           html  
    snSummary                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ABarray' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ABarray' as ABarray_1.50.0.zip
* DONE (ABarray)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ABarray' successfully unpacked and MD5 sums checked
In R CMD INSTALL