ABarray 1.42.0
Yongming Andrew Sun
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ABarray | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ABarray_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ABarray.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ABarray/DESCRIPTION’ ... OK
* this is package ‘ABarray’ version ‘1.42.0’
* 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 ‘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
* 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
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* checking examples ... 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
‘/Users/biocbuild/bbs-3.4-bioc/meat/ABarray.Rcheck/00check.log’
for details.