Back to Build/check report for BioC 3.17
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-01-02 09:00:17 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ABarray on palomino5


To the developers/maintainers of the ABarray package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 7/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ABarray 1.67.0  (landing page)
Yongming Andrew Sun
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/ABarray
git_branch: master
git_last_commit: 5c3fdf9
git_last_commit_date: 2022-11-01 10:41:39 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: ABarray
Version: 1.67.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ABarray.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ABarray_1.67.0.tar.gz
StartedAt: 2022-12-28 21:27:10 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 21:28:10 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 59.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ABarray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ABarray.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ABarray_1.67.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ABarray.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ABarray/DESCRIPTION' ... OK
* this is package 'ABarray' version '1.67.0'
* 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 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 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 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ABarray.Rcheck/00check.log'
for details.



Installation output

ABarray.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL ABarray
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'ABarray' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ABarray)

Tests output


Example timings

ABarray.Rcheck/ABarray-Ex.timings

nameusersystemelapsed
ABarray000
ABarrayGUI000
concord000
doANOVA000
doLPE000
doPlotEset000
doPlotFCT000
drawVennDiagram000
icpPlot000
imputeFlag000
lpe.fdr.BH000
mamaplot000
mvaPair2000
panel.cor000
panel.scatter000
rgcolorsfunc000
scaleColorBar000