prada 1.47.0
Florian Hahne
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/prada | | 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 | [ ERROR ] | | |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | ERROR | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings prada_1.47.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/prada.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘prada/DESCRIPTION’ ... OK
* this is package ‘prada’ version ‘1.47.0’
* 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 ‘prada’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biobase’ ‘grid’ ‘methods’ ‘RColorBrewer’ ‘rrcov’
A package should be listed in only one of these fields.
* 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 ‘tcltk’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.defaultPlot: no visible global function definition for ‘grid.segments’
analysePlate: no visible binding for global variable ‘dat’
devRes: no visible global function definition for ‘upViewport’
devRes: no visible global function definition for ‘downViewport’
gatePoints: no visible binding for global variable ‘prev’
killProgress: no visible binding for global variable
‘.tkprogress.canceled’
killProgress: no visible global function definition for ‘tkdestroy’
killProgress: no visible binding for global variable
‘.tkprogress.window’
progress: no visible global function definition for ‘tktoplevel’
progress: no visible global function definition for ‘tclVar’
progress: no visible global function definition for ‘tkwm.geometry’
progress: no visible binding for global variable ‘.tkprogress.window’
progress: no visible global function definition for ‘tkwm.title’
progress: no visible global function definition for ‘tkconfigure’
progress: no visible global function definition for ‘tkframe’
progress: no visible global function definition for ‘tkfont.create’
progress: no visible binding for '<<-' assignment to
‘.tkprogress.labelText’
progress: no visible binding for global variable
‘.tkprogress.labelText’
progress: no visible global function definition for ‘tclvalue<-’
progress: no visible global function definition for ‘tklabel’
progress: no visible global function definition for ‘tclvalue’
progress: no visible global function definition for ‘tkgrid’
progress: no visible global function definition for ‘tclRequire’
progress: no visible global function definition for ‘tkwidget’
progress: no visible binding for global variable ‘.tkprogress.iterator’
progress: no visible binding for global variable
‘.tkprogress.fallbackIterator’
progress: no visible global function definition for ‘tkbind’
progress : <anonymous>: no visible binding for '<<-' assignment to
‘.tkprogress.canceled’
updateProgress: no visible binding for '<<-' assignment to
‘.tkprogress.iterator’
updateProgress: no visible binding for global variable
‘.tkprogress.iterator’
updateProgress: no visible global function definition for ‘tclvalue<-’
updateProgress: no visible binding for '<<-' assignment to
‘.tkprogress.fallbackIterator’
updateProgress: no visible binding for global variable
‘.tkprogress.fallbackIterator’
updateProgress: no visible binding for '<<-' assignment to
‘.tkprogress.labelText’
updateProgress: no visible binding for global variable
‘.tkprogress.labelText’
updateProgress: no visible global function definition for ‘tcl’
Undefined global functions or variables:
.tkprogress.canceled .tkprogress.fallbackIterator
.tkprogress.iterator .tkprogress.labelText .tkprogress.window dat
downViewport grid.segments prev tcl tclRequire tclVar tclvalue
tclvalue<- tkbind tkconfigure tkdestroy tkfont.create tkframe tkgrid
tklabel tktoplevel tkwidget tkwm.geometry tkwm.title upViewport
* checking Rd files ... OK
* 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘prada-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotPlate
> ### Title: Plot a well statistic for microtiter plates.
> ### Aliases: plotPlate
> ### Keywords: hplot
>
> ### ** Examples
>
> plotPlate(runif(96), main="example 1", col=c("#0000e0", "#e00000"), desc=c("act", "inh"))
> plotPlate(runif(384), nrow=16, ncol=24, main="example 2", col=c("#0000e0", "white", "#e00000"))
> plotPlate(runif(48), main="example 3", col=c("#0000e0", "#e00000"), ind=c(1:24, 73:96))
> x <- runif(96)
> x[sample(96, 10)] <- NA
> plotPlate(x, main="example 4", col=c("#0000e0", "#e00000"),
+ char=c(rep(NA, 72), LETTERS[1:24]), na.action="xout")
Error in if (!is.vector(char) || length(char) != length(ind) || !all(nchar(char) <= :
missing value where TRUE/FALSE needed
Calls: plotPlate
Execution halted
* 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: 1 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/prada.Rcheck/00check.log’
for details.
* installing *source* package ‘prada’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o prada.so inPolygon.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/prada.Rcheck/prada/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘split’ from package ‘base’ in package ‘prada’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (prada)