genphen 1.4.0
Simo Kitanovski
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/genphen | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf genphen.buildbin-libdir genphen.Rcheck && mkdir genphen.buildbin-libdir genphen.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genphen.buildbin-libdir genphen_1.4.0.tar.gz >genphen.Rcheck\00install.out 2>&1 && cp genphen.Rcheck\00install.out genphen-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=genphen.buildbin-libdir --install="check:genphen-install.out" --force-multiarch --no-vignettes --timings genphen_1.4.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/genphen.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genphen/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genphen' version '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'randomForest' 'e1071' 'ggplot2' 'effsize' 'Biostrings' 'rjags'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'genphen' 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
getBayesianTtest : getDataList: no visible global function definition
for 'sd'
getBayesianTtest : getEss: no visible global function definition for
'effectiveSize'
getBayesianTtest: no visible global function definition for 'update'
getTTestScore: no visible global function definition for 't.test'
plotGenphenBayes: no visible binding for global variable 'g.1'
plotGenphenBayes: no visible binding for global variable 'site'
plotGenphenBayes: no visible binding for global variable 'g.2'
plotGenphenRfSvm: no visible binding for global variable 'ca.hdi.H'
plotGenphenRfSvm: no visible binding for global variable 'ca.hdi.L'
plotGenphenRfSvm: no visible global function definition for
'terrain.colors'
plotManhattan: no visible binding for global variable 't.test.pvalue'
Undefined global functions or variables:
ca.hdi.H ca.hdi.L effectiveSize g.1 g.2 sd site t.test t.test.pvalue
terrain.colors update
Consider adding
importFrom("grDevices", "terrain.colors")
importFrom("stats", "sd", "t.test", "update")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runGenphenBayes 20.58 0.03 20.61
plotGenphenBayes 19.98 0.04 23.86
runGenphenRf 15.97 0.69 16.65
plotGenphenRfSvm 13.08 0.17 14.89
plotManhattan 10.35 0.04 10.37
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runGenphenRf 14.07 0.37 14.45
plotGenphenBayes 13.78 0.02 42.37
runGenphenBayes 13.46 0.02 13.47
plotGenphenRfSvm 9.73 0.03 9.77
plotManhattan 8.30 0.06 8.36
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/genphen.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'genphen' ...
** R
** data
** 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 'genphen' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genphen' as genphen_1.4.0.zip
* DONE (genphen)