BioC 3.3: CHECK report for lmdme on windows2.bioconductor.org

Package: lmdme

Version: 1.13.0

Command: rm -rf lmdme.buildbin-libdir lmdme.Rcheck && mkdir lmdme.buildbin-libdir lmdme.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lmdme.buildbin-libdir lmdme_1.13.0.tar.gz >lmdme.Rcheck\00install.out 2>&1 && cp lmdme.Rcheck\00install.out lmdme-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=lmdme.buildbin-libdir --install="check:lmdme-install.out" --force-multiarch --no-vignettes --timings lmdme_1.13.0.tar.gz

StartedAt: 2015-10-27 03:36:22 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:37:47 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 84.7 seconds

RetCode: 0

Status:  OK

CheckDir: lmdme.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf lmdme.buildbin-libdir lmdme.Rcheck && mkdir lmdme.buildbin-libdir lmdme.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lmdme.buildbin-libdir lmdme_1.13.0.tar.gz >lmdme.Rcheck\00install.out 2>&1 && cp lmdme.Rcheck\00install.out lmdme-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=lmdme.buildbin-libdir --install="check:lmdme-install.out" --force-multiarch --no-vignettes --timings lmdme_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/lmdme.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lmdme/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lmdme' version '1.13.0'
* 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 whether package 'lmdme' 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 ... 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: no visible global function definition for 'pvalues'
Undefined global functions or variables:
  detectCores mclapply plsr 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [27s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lmdme-permutation 5.19   0.44    5.63
** running examples for arch 'x64' ... [30s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lmdme-permutation 6.15   0.39    6.55
* 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:/biocbld/bbs-3.3-bioc/meat/lmdme.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'lmdme' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'lmdme' as lmdme_1.13.0.zip
* DONE (lmdme)

name	user	system	elapsed
lmdme-biplot	2.45	0.10	2.55
lmdme-decomposition	2.25	0.09	2.34
lmdme-getters	2.19	0.19	2.38
lmdme-leverage	2.52	0.15	2.67
lmdme-lmdme	2.00	0.18	2.17
lmdme-loadingplot	1.97	0.15	2.13
lmdme-padjust	2.17	0.15	2.33
lmdme-permutation	5.19	0.44	5.63
lmdme-printshow	2.04	0.13	2.17
lmdme-screeplot	2.11	0.12	2.23

name	user	system	elapsed
lmdme-biplot	2.72	0.06	2.78
lmdme-decomposition	2.45	0.11	2.56
lmdme-getters	2.78	0.17	2.95
lmdme-leverage	2.53	0.14	2.68
lmdme-lmdme	2.47	0.16	2.62
lmdme-loadingplot	2.47	0.11	2.58
lmdme-padjust	2.44	0.12	2.56
lmdme-permutation	6.15	0.39	6.55
lmdme-printshow	2.16	0.16	2.31
lmdme-screeplot	2.22	0.09	2.31