BioC 3.1: CHECK report for prada on petty
This page was generated on 2015-10-09 09:32:38 -0700 (Fri, 09 Oct 2015).
prada 1.44.0 Florian Hahne
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/prada | 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 |  |
Summary
Package: prada |
Version: 1.44.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings prada_1.44.0.tar.gz |
StartedAt: 2015-10-09 01:10:37 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 01:12:01 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 83.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: prada.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings prada_1.44.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/prada.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘prada/DESCRIPTION’ ... OK
* this is package ‘prada’ version ‘1.44.0’
* 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 ... [7s/9s] 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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/prada.Rcheck/00check.log’
for details.
prada.Rcheck/00install.out:
* installing *source* package ‘prada’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c inPolygon.c -o inPolygon.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o prada.so inPolygon.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-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)
prada.Rcheck/prada-Ex.timings:
name | user | system | elapsed
|
analysePlate | 0.001 | 0.000 | 0.001 |
|
as.all | 0.001 | 0.001 | 0.001 |
|
barploterrbar | 0.012 | 0.001 | 0.014 |
|
combineFrames | 0.240 | 0.009 | 0.249 |
|
csApply | 0.038 | 0.003 | 0.042 |
|
cytoFrame-class | 0.059 | 0.007 | 0.066 |
|
cytoSet-class | 0.060 | 0.002 | 0.063 |
|
data-cytoFrame | 0.041 | 0.005 | 0.083 |
|
data-cytoSet | 0.005 | 0.000 | 0.007 |
|
devDims | 0.002 | 0.000 | 0.002 |
|
devRes | 0.004 | 0.001 | 0.005 |
|
fitNorm2 | 0.303 | 0.007 | 0.310 |
|
gate-class | 0.025 | 0.003 | 0.027 |
|
gateSet-class | 0.031 | 0.002 | 0.033 |
|
getAlphaNumeric | 0.002 | 0.001 | 0.002 |
|
getPradaPar | 0.003 | 0.000 | 0.003 |
|
plotNorm2 | 0.196 | 0.005 | 0.210 |
|
plotPlate | 1.358 | 0.035 | 1.394 |
|
readCytoSet | 0 | 0 | 0 |
|
readFCS | 0.050 | 0.004 | 0.054 |
|
removeCensored | 0.009 | 0.001 | 0.009 |
|
tcltkProgress | 0.002 | 0.000 | 0.002 |
|
threePanelPlot | 0.434 | 0.015 | 0.459 |
|
thresholds | 0.001 | 0.000 | 0.002 |
|
vpLocation | 0.002 | 0.000 | 0.003 |
|