missMethyl 1.3.5
Belinda Phipson , Jovana Maksimovic
| Snapshot Date: 2015-10-12 19:24:22 -0400 (Mon, 12 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/missMethyl | | Last Changed Rev: 108707 / Revision: 109549 | | Last Changed Date: 2015-09-22 06:08:22 -0400 (Tue, 22 Sep 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | ERROR | skipped | skipped | |
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### Running command:
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### rm -rf missMethyl.buildbin-libdir missMethyl.Rcheck && mkdir missMethyl.buildbin-libdir missMethyl.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=missMethyl.buildbin-libdir missMethyl_1.3.5.tar.gz >missMethyl.Rcheck\00install.out 2>&1 && cp missMethyl.Rcheck\00install.out missMethyl-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=missMethyl.buildbin-libdir --install="check:missMethyl-install.out" --force-multiarch --no-vignettes --timings missMethyl_1.3.5.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/missMethyl.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'missMethyl/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'missMethyl' version '1.3.5'
* 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 'missMethyl' 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
** 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
SWAN.MethyLumiSet: no visible global function definition for
'phenoData'
SWAN.default: no visible global function definition for 'phenoData'
SWAN.default: no visible global function definition for
'featureNames<-'
SWAN.default: no visible global function definition for 'sampleNames<-'
gometh: no visible binding for global variable
'IlluminaHumanMethylation450kanno.ilmn12.hg19'
gometh: no visible global function definition for 'toTable'
* 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' ... [207s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
gometh 75.61 7.67 103.52
SWAN 32.05 2.25 34.30
RUVadj 16.06 0.70 16.77
densityByProbeType 15.59 1.02 16.61
topRUV 14.20 0.56 14.77
RUVfit 10.79 0.44 11.23
** running examples for arch 'x64' ... [191s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
gometh 50.53 2.60 53.13
SWAN 40.78 2.55 45.26
RUVadj 22.67 1.14 24.08
densityByProbeType 18.48 1.46 19.96
topRUV 19.27 0.65 19.93
RUVfit 14.85 0.72 15.61
* 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 NOTE
See
'C:/biocbld/bbs-3.2-bioc/meat/missMethyl.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'missMethyl' ...
** 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 'missMethyl' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'missMethyl' as missMethyl_1.3.5.zip
* DONE (missMethyl)