ChAMP 1.8.2
Tiffany Morris
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ChAMP | | Last Changed Rev: 116669 / Revision: 116712 | | Last Changed Date: 2016-04-21 12:55:18 -0700 (Thu, 21 Apr 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf ChAMP.buildbin-libdir ChAMP.Rcheck && mkdir ChAMP.buildbin-libdir ChAMP.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChAMP.buildbin-libdir ChAMP_1.8.2.tar.gz >ChAMP.Rcheck\00install.out 2>&1 && cp ChAMP.Rcheck\00install.out ChAMP-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ChAMP.buildbin-libdir --install="check:ChAMP-install.out" --force-multiarch --no-vignettes --timings ChAMP_1.8.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/ChAMP.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChAMP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChAMP' version '1.8.2'
* 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 whether package 'ChAMP' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'limma::ebayes' by 'RPMM::ebayes' when loading 'ChAMP'
Warning: replacing previous import 'wateRmelon::colnames' by 'IRanges::colnames' when loading 'ChAMP'
Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'ChAMP'
See 'D:/biocbld/bbs-3.2-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
* 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
** checking loading without being on the library search path ... 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 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 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 ...
** running examples for arch 'i386' ... [340s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
champ.load 55.27 0.92 80.01
champ.norm 50.42 0.99 51.42
champ.CNA 44.05 0.43 81.81
champ.SVD 35.32 0.95 36.63
champ.runCombat 19.83 0.22 20.04
champ.TrueMethyl 18.86 0.14 19.01
champ.MVP 18.11 0.31 18.42
champ.lasso 17.41 0.25 17.66
** running examples for arch 'x64' ... [271s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
champ.norm 59.52 1.93 61.48
champ.load 51.38 1.45 52.88
champ.CNA 44.30 0.56 45.40
champ.SVD 27.05 0.87 28.00
champ.runCombat 19.00 0.31 19.31
champ.MVP 15.72 0.32 16.03
champ.lasso 14.98 0.14 15.12
champ.TrueMethyl 14.45 0.33 14.77
* 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
'D:/biocbld/bbs-3.2-bioc/meat/ChAMP.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'ChAMP' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'limma::ebayes' by 'RPMM::ebayes' when loading 'ChAMP'
Warning: replacing previous import 'wateRmelon::colnames' by 'IRanges::colnames' when loading 'ChAMP'
Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'ChAMP'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'limma::ebayes' by 'RPMM::ebayes' when loading 'ChAMP'
Warning: replacing previous import 'wateRmelon::colnames' by 'IRanges::colnames' when loading 'ChAMP'
Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'ChAMP'
install for x64
* installing *source* package 'ChAMP' ...
** testing if installed package can be loaded
Warning: replacing previous import 'limma::ebayes' by 'RPMM::ebayes' when loading 'ChAMP'
Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'ChAMP'
Warning: replacing previous import 'wateRmelon::colnames' by 'IRanges::colnames' when loading 'ChAMP'
* MD5 sums
packaged installation of 'ChAMP' as ChAMP_1.8.2.zip
* DONE (ChAMP)