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BioC 3.2: CHECK report for lmdme on oaxaca

This page was generated on 2015-10-27 17:40:12 -0400 (Tue, 27 Oct 2015).

Package 567/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lmdme 1.12.0
Cristobal Fresno
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/lmdme
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: lmdme
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lmdme_1.12.0.tar.gz
StartedAt: 2015-10-27 05:04:19 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:05:56 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 97.1 seconds
RetCode: 0
Status:  OK 
CheckDir: lmdme.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lmdme_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/lmdme.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lmdme/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lmdme’ version ‘1.12.0’
* 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 ‘lmdme’ can be installed ... [2s/3s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
decomposition,lmdme : <anonymous>: no visible global function
  definition for ‘plsr’
permutation,formula-data.frame-data.frame: no visible binding for
  global variable ‘mclapply’
permutation,formula-data.frame-data.frame: no visible global function
  definition for ‘detectCores’
print,lmdme : .local: no visible global function definition for
  ‘pvalues’
* 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’ ... OK
* checking examples ... [43s/48s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
lmdme-permutation 3.888  0.688   5.334
lmdme-biplot      3.732  0.261   6.129
lmdme-leverage    3.676  0.287   5.589
lmdme-screeplot   3.099  0.314   5.046
lmdme-lmdme       3.023  0.219   5.328
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/lmdme.Rcheck/00check.log’
for details.


lmdme.Rcheck/00install.out:

* installing *source* package ‘lmdme’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘fitted.values’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘fitted’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘coef’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘coefficients’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘resid’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘residuals’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘print’ from package ‘base’ in package ‘lmdme’
Creating a generic function for ‘summary’ from package ‘base’ in package ‘lmdme’
Creating a new generic function for ‘p.adjust’ in package ‘lmdme’
Creating a generic function for ‘biplot’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘screeplot’ from package ‘stats’ in package ‘lmdme’
Creating a generic function for ‘loadingplot’ from package ‘pls’ in package ‘lmdme’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (lmdme)

lmdme.Rcheck/lmdme-Ex.timings:

nameusersystemelapsed
lmdme-biplot3.7320.2616.129
lmdme-decomposition2.9990.3024.004
lmdme-getters2.9200.2333.549
lmdme-leverage3.6760.2875.589
lmdme-lmdme3.0230.2195.328
lmdme-loadingplot3.1360.2524.430
lmdme-padjust3.7390.3034.419
lmdme-permutation3.8880.6885.334
lmdme-printshow2.6340.3473.805
lmdme-screeplot3.0990.3145.046