GGBase 3.24.0
VJ Carey
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/GGBase | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/GGBase.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGBase/DESCRIPTION' ... OK
* this is package 'GGBase' version '3.24.0'
* 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 'GGBase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 'snpStats' which was already attached by Depends.
Please remove these calls from your code.
Missing or unexported object: 'snpStats::rbind2'
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
.oldcode : <anonymous>: warning in axis(3, at = genePosition(x@gene,
annlib = x@annotation), col = "red", lwd = 2, label = " "): partial
argument match of 'label' to 'labels'
.oldcode : pedinf2df: warning in read.table(fn, h = FALSE): partial
argument match of 'h' to 'header'
allsnps: warning in dir(system.file("parts", package = packname), full
= TRUE): partial argument match of 'full' to 'full.names'
.oldcode : genePosition: no visible global function definition for
'revmap'
.oldcode : featureFilter: no visible global function definition for
'keys'
.oldcode : sym2pid: no visible global function definition for 'revmap'
.oldcode : <anonymous>: no visible global function definition for
'revmap'
.oldcode : snpLocs.Hsapiens: no visible global function definition for
'getSNPlocs'
sym2pid: no visible global function definition for 'revmap'
plot_EvG,genesym-rsid-smlSet: no visible global function definition for
'revmap'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [32s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MAFfilter 8.27 0.43 10.76
plot_EvG 6.43 0.18 6.75
make_smlSet 5.88 0.18 6.05
** running examples for arch 'x64' ... [31s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MAFfilter 8.52 0.22 8.78
make_smlSet 6.02 0.08 6.10
plot_EvG 5.57 0.15 5.74
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
Running 'MAFfilter.R' [16s]
Running 'make.R' [15s]
Running 'plot_EvG.R' [15s]
[47s] OK
** running tests for arch 'x64'
Running 'MAFfilter.R' [15s]
Running 'make.R' [22s]
Running 'plot_EvG.R' [20s]
[56s] 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
NOTE: There were 2 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/GGBase.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GGBase' ...
** R
** 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
* installing *source* package 'GGBase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GGBase' as GGBase_3.24.0.zip
* DONE (GGBase)