BioC 2.13: CHECK report for iterativeBMA on moscato1

Package: iterativeBMA

Version: 1.20.0

Command: rm -rf iterativeBMA.buildbin-libdir && mkdir iterativeBMA.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iterativeBMA.buildbin-libdir iterativeBMA_1.20.0.tar.gz >iterativeBMA-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=iterativeBMA.buildbin-libdir --install="check:iterativeBMA-install.out" --force-multiarch --no-vignettes --timings iterativeBMA_1.20.0.tar.gz && mv iterativeBMA.buildbin-libdir/* iterativeBMA.Rcheck/ && rmdir iterativeBMA.buildbin-libdir

StartedAt: 2014-04-05 04:45:38 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:47:10 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 91.7 seconds

RetCode: 0

Status:  OK

CheckDir: iterativeBMA.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/iterativeBMA.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iterativeBMA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iterativeBMA' version '1.20.0'
* 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 'iterativeBMA' 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
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'BMA' 'Biobase' 'leaps'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: BssWssFast.Rd:39: Dropping empty section \note
prepare_Rd: bma_predict.Rd:36: Dropping empty section \note
prepare_Rd: brier_score.Rd:34: Dropping empty section \note
prepare_Rd: testClass.Rd:13-14: Dropping empty section \details
prepare_Rd: trainClass.Rd:13-14: Dropping empty section \details
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'iterativeBMA.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [19s] OK
** running examples for arch 'x64' ... [23s] OK
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/iterativeBMA.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'iterativeBMA' ...
** 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 'iterativeBMA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iterativeBMA' as iterativeBMA_1.20.0.zip
* DONE (iterativeBMA)

name	user	system	elapsed
BssWssFast	0.03	0.00	0.03
bma_predict	2.13	0.03	2.17
brier_score	2	0	2
imageplot_iterate_bma	1.95	0.00	1.95
iterateBMAglm_train	2.03	0.00	2.03
iterateBMAglm_train_predict	1.99	0.04	2.03
iterateBMAglm_train_predict_test	2.03	0.01	2.04
iterateBMAglm_wrapper	2.14	0.00	2.17
iterativeBMA-package	2.73	0.02	3.04

name	user	system	elapsed
BssWssFast	0.03	0.00	0.03
bma_predict	2.42	0.00	2.42
brier_score	2.65	0.02	2.67
imageplot_iterate_bma	2.23	0.00	2.23
iterateBMAglm_train	2.37	0.00	2.37
iterateBMAglm_train_predict	3.26	0.01	3.80
iterateBMAglm_train_predict_test	2.50	0.00	2.49
iterateBMAglm_wrapper	2.54	0.02	2.56
iterativeBMA-package	2.59	0.00	2.60