cellHTS 1.41.0
Andrzej Oles
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cellHTS | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK | |
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### Running command:
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### rm -rf cellHTS.buildbin-libdir cellHTS.Rcheck && mkdir cellHTS.buildbin-libdir cellHTS.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellHTS.buildbin-libdir cellHTS_1.41.0.tar.gz >cellHTS.Rcheck\00install.out 2>&1 && cp cellHTS.Rcheck\00install.out cellHTS-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=cellHTS.buildbin-libdir --install="check:cellHTS-install.out" --force-multiarch --no-vignettes --timings cellHTS_1.41.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/cellHTS.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 'cellHTS/DESCRIPTION' ... OK
* this is package 'cellHTS' version '1.41.0'
* 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 'cellHTS' can be installed ... WARNING
Found the following significant warnings:
WARNING: omitting pointless dependence on 'R' without a version requirement
See 'c:/biocbld/bbs-3.3-bioc/meat/cellHTS.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' call to 'prada' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'RColorBrewer' 'genefilter' 'prada'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'scaleByPlateMedian'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'cellHTS/R/zzz.R':
.onAttach calls:
message(paste("\n-------------------------------------------------------------------", "\nA note from the 'cellHTS' package:", "\nThe package 'cellHTS2' offers better functionality for working with", "\nmultiple screens and with multi-channel screens. Please consider", "\nusing 'cellHTS2' for new projects. However, 'cellHTS' will be", "\nsupported for a while to help with your existing projects.", "\n-------------------------------------------------------------------\n\n", sep = ""))
Package startup functions should use 'packageStartupMessage' to
generate messages.
See section 'Good practice' in '?.onAttach'.
annotate.cellHTS: warning in read.table(file.path(path, file), sep =
"\t", header = TRUE, as.is = TRUE, na.string = "", quote = "", fill =
TRUE): partial argument match of 'na.string' to 'na.strings'
configure.cellHTS: warning in read.table(file.path(ppath, confFile),
sep = "\t", header = TRUE, as.is = TRUE, na.string = "", fill =
TRUE): partial argument match of 'na.string' to 'na.strings'
configure.cellHTS: warning in read.table(file.path(ppath, logFile), sep
= "\t", header = TRUE, as.is = TRUE, na.string = "", fill = TRUE):
partial argument match of 'na.string' to 'na.strings'
tableOutput: warning in read.table(fn, sep = "\t", header = header,
na.string = "", as.is = TRUE): partial argument match of 'na.string'
to 'na.strings'
.onAttach: no visible global function definition for 'addVigs2WinMenu'
QMbyPlate: no visible global function definition for 'brewer.pal'
QMbyPlate : <anonymous>: no visible global function definition for
'plotPlate'
envisionPlateReader: no visible global function definition for
'listLen'
imageScreen: no visible global function definition for 'brewer.pal'
makePlot: no visible global function definition for 'devDims'
plotPlateLibrary: no visible global function definition for
'brewer.pal'
plotPlateLibrary: no visible global function definition for
'pushViewport'
plotPlateLibrary: no visible global function definition for 'viewport'
plotPlateLibrary: no visible global function definition for
'grid.layout'
plotPlateLibrary: no visible global function definition for 'plotPlate'
plotPlateLibrary: no visible global function definition for
'popViewport'
plotSpatialEffects: no visible global function definition for
'pushViewport'
plotSpatialEffects: no visible global function definition for
'viewport'
plotSpatialEffects: no visible global function definition for
'grid.layout'
plotSpatialEffects: no visible global function definition for
'plotPlate'
plotSpatialEffects: no visible global function definition for
'brewer.pal'
plotSpatialEffects: no visible global function definition for
'popViewport'
scaleByPlateShorth: no visible global function definition for 'shorth'
writeReport: no visible global function definition for 'progress'
writeReport: no visible global function definition for 'killProgress'
writeReport: no visible global function definition for 'updateProgress'
Undefined global functions or variables:
addVigs2WinMenu brewer.pal devDims grid.layout killProgress listLen
plotPlate popViewport progress pushViewport shorth updateProgress
viewport
* checking Rd files ... NOTE
prepare_Rd: oneRowPerId.Rd:19: Dropping empty section \details
* 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 ... OK
* checking data for ASCII and uncompressed saves ... WARNING
Error in if (dep$op != ">=") next : argument is of length zero
Calls: <Anonymous>
Execution halted
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [5s] OK
** running examples for arch 'x64' ... [5s] 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 WARNINGs, 4 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/cellHTS.Rcheck/00check.log'
for details.
install for i386
WARNING: omitting pointless dependence on 'R' without a version requirement
* installing *source* package 'cellHTS' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
WARNING: omitting pointless dependence on 'R' without a version requirement
* installing *source* package 'cellHTS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellHTS' as cellHTS_1.41.0.zip
* DONE (cellHTS)