manta 1.6.1
Chris Berthiaume , Adrian Marchetti
| Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/manta | | Last Changed Rev: 81080 / Revision: 81334 | | Last Changed Date: 2013-10-02 11:05:25 -0700 (Wed, 02 Oct 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | WARNINGS | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/manta.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘manta/DESCRIPTION’ ... OK
* this is package ‘manta’ version ‘1.6.1’
* 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 ‘manta’ can be installed ... [6s/6s] OK
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 1.4Mb
extdata 4.0Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 for unstated dependencies in R code ... WARNING
‘library’ or ‘require’ calls not declared from:
‘MASS’ ‘grid’ ‘sm’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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
.as.manta: no visible binding for global variable ‘samples’
.as.manta: no visible binding for global variable ‘counts’
.calcTMMvar: no visible binding for global variable ‘x’
.checkMetaLev: no visible binding for global variable ‘meta.sum’
.heatmap.2: no visible global function definition for ‘invalid’
.heatmap.2: no visible global function definition for ‘heatmap.2.key’
compbiasPlot: no visible binding for global variable ‘RAy’
counts2manta: no visible binding for global variable ‘agg’
dbWriteTable2: no visible binding for global variable ‘db.nchars’
hyperplot: no visible binding for global variable ‘out’
nr: no visible binding for global variable ‘x’
outGenes: no visible binding for global variable ‘PValue’
outGenes: no visible binding for global variable ‘R’
spie: no visible global function definition for ‘grid.newpage’
spie: no visible global function definition for ‘pushViewport’
spie: no visible global function definition for ‘viewport’
spie: no visible global function definition for ‘grid.layout’
spie: no visible global function definition for ‘dataViewport’
spie: no visible global function definition for ‘grid.circle’
spie: no visible global function definition for ‘gpar’
spie: no visible global function definition for ‘grid.polygon’
spie: no visible global function definition for ‘grid.rect’
spie: no visible global function definition for ‘stringWidth’
spie: no visible global function definition for ‘stringHeight’
spie: no visible global function definition for ‘grid.text’
spie: no visible global function definition for ‘grid.lines’
spie: no visible global function definition for ‘unit’
spie: no visible global function definition for ‘upViewport’
stats: no visible global function definition for ‘recode’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘addFactLevs’ ‘bestBy’ ‘cmdArgsToVariables’ ‘dbWriteTable2’ ‘delist’
‘geomean’ ‘groupBy’ ‘heatmatrix’ ‘hyperplot’ ‘labsegs’ ‘leghead’ ‘m’
‘makeElipseCoords’ ‘mvlabs’ ‘nerge’ ‘nv’ ‘pad’ ‘parseArgString’ ‘pct’
‘pies’ ‘plotClock’ ‘raAddArms’ ‘raAddAxLabs’ ‘raAddSigLines’ ‘raPlot’
‘read.tab’ ‘regroup’ ‘rerowname’ ‘spie’ ‘sstable’ ‘stats’ ‘tab2df’
‘textplot’ ‘usr2lims’ ‘vennMatrix’ ‘violins’ ‘wjitter’ ‘write.delim’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'summary.manta':
‘summary.manta’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [48s/49s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
in2manta 32.55 0 33.124
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 2 warnings.
NOTE: There were 4 notes.
See
‘/home/biocbuild/bbs-2.12-bioc/meat/manta.Rcheck/00check.log’
for details.