cellHTS 1.38.0
Ligia Bras
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/cellHTS | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings cellHTS_1.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/cellHTS.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellHTS/DESCRIPTION’ ... OK
* this is package ‘cellHTS’ version ‘1.38.0’
* 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 ‘cellHTS’ can be installed ... [8s/10s] OK
* 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
* 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:
‘Biobase’ ‘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’
* 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 ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/7s] 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
‘/home/biocbuild/bbs-3.1-bioc/meat/cellHTS.Rcheck/00check.log’
for details.
* installing *source* package ‘cellHTS’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (cellHTS)