ChAMP 1.0.7
Tiffany Morris
| 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/ChAMP | | Last Changed Rev: 86170 / Revision: 88450 | | Last Changed Date: 2014-02-06 11:17:26 -0800 (Thu, 06 Feb 2014) |
| 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 ‘/home/biocbuild/bbs-2.13-bioc/meat/ChAMP.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChAMP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMP’ version ‘1.0.7’
* 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 ‘ChAMP’ can be installed ... [17s/17s] 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
* 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’ calls to packages already attached by Depends:
‘ChAMPdata’ ‘Illumina450ProbeVariants.db’
Please remove these calls from your code.
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
champ.CNA: no visible binding for global variable ‘myLoad’
champ.CNA: no visible binding for global variable ‘probe.features’
champ.MVP: no visible binding for global variable ‘myNorm’
champ.MVP: no visible binding for global variable ‘myLoad’
champ.MVP: no visible binding for global variable ‘probe.features’
champ.SVD: no visible binding for global variable ‘myNorm’
champ.SVD: no visible binding for global variable ‘myLoad’
champ.lasso: no visible binding for global variable ‘myNorm’
champ.lasso: no visible binding for global variable ‘myLoad’
champ.lasso: no visible binding for global variable ‘probe.features’
champ.lasso: no visible binding for global variable ‘probe.450K.VCs.af’
champ.load: no visible binding for global variable ‘probe.features’
champ.norm: no visible binding for global variable ‘myLoad’
champ.norm: no visible binding for global variable ‘probe.features’
champ.norm: no visible binding for global variable ‘probeInfoALL.lv’
champ.runCombat: no visible binding for global variable ‘myNorm’
champ.runCombat: no visible binding for global variable ‘myLoad’
plotThreshold: no visible binding for global variable ‘probe.features’
* 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’ ... NOTE
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
* checking examples ... [193s/194s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
champ.load 41.011 0.292 41.405
champ.norm 40.019 0.196 40.383
champ.CNA 29.218 0.376 29.839
champ.SVD 28.234 0.240 28.574
champ.MVP 14.977 0.284 15.304
champ.runCombat 14.528 0.020 14.595
champ.lasso 14.376 0.044 14.444
* 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 3 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/ChAMP.Rcheck/00check.log’
for details.
* installing *source* package ‘ChAMP’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘RPMM::ebayes’ when loading ‘ChAMP’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘RPMM::ebayes’ when loading ‘ChAMP’
* DONE (ChAMP)