ChAMP 1.6.2
Tiffany Morris
| 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/ChAMP | | Last Changed Rev: 108563 / Revision: 109384 | | Last Changed Date: 2015-09-16 05:57:48 -0700 (Wed, 16 Sep 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ChAMP_1.6.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/ChAMP.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.6.2’
* 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 ... [19s/22s] WARNING
Found the following significant warnings:
Warning: replacing previous import by ‘RPMM::ebayes’ when loading ‘ChAMP’
Warning: replacing previous import by ‘IRanges::desc’ when loading ‘ChAMP’
Warning: replacing previous import by ‘IRanges::colnames’ when loading ‘ChAMP’
See ‘/home/biocbuild/bbs-3.1-bioc/meat/ChAMP.Rcheck/00install.out’ for details.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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.CNA: no visible binding for global variable ‘bloodCtl’
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.TrueMethyl: no visible binding for global variable ‘myNorm’
champ.TrueMethyl: no visible binding for global variable ‘myLoad’
champ.TrueMethyl: no visible binding for global variable
‘probe.features’
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 global function definition for ‘sampleNames<-’
champ.load: no visible binding for global variable ‘snp.hit’
champ.load: no visible binding for global variable ‘multi.hit’
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 sizes of PDF files under ‘inst/doc’ ... 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.
The following files look like leftovers/mistakes:
‘Rplots.pdf’
Please remove them from your package.
* checking examples ... [168s/211s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
champ.CNA 31.172 0.341 39.624
champ.load 29.692 0.335 40.367
champ.norm 28.803 0.071 36.182
champ.SVD 21.070 0.161 26.065
champ.runCombat 12.169 0.021 15.037
champ.MVP 11.754 0.079 14.755
champ.TrueMethyl 11.750 0.020 14.457
champ.lasso 11.339 0.031 13.488
* 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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.1-bioc/meat/ChAMP.Rcheck/00check.log’
for details.
* installing *source* package ‘ChAMP’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Warning: replacing previous import by ‘RPMM::ebayes’ when loading ‘ChAMP’
Warning: replacing previous import by ‘IRanges::desc’ when loading ‘ChAMP’
Warning: replacing previous import by ‘IRanges::colnames’ when loading ‘ChAMP’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Warning: replacing previous import by ‘RPMM::ebayes’ when loading ‘ChAMP’
Warning: replacing previous import by ‘IRanges::desc’ when loading ‘ChAMP’
Warning: replacing previous import by ‘IRanges::colnames’ when loading ‘ChAMP’
* DONE (ChAMP)