BioC 3.1: CHECK report for iterativeBMA on moscato2

Package: iterativeBMA

Version: 1.26.0

Command: rm -rf iterativeBMA.buildbin-libdir iterativeBMA.Rcheck && mkdir iterativeBMA.buildbin-libdir iterativeBMA.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iterativeBMA.buildbin-libdir iterativeBMA_1.26.0.tar.gz >iterativeBMA.Rcheck\00install.out 2>&1 && cp iterativeBMA.Rcheck\00install.out iterativeBMA-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=iterativeBMA.buildbin-libdir --install="check:iterativeBMA-install.out" --force-multiarch --no-vignettes --timings iterativeBMA_1.26.0.tar.gz

StartedAt: 2015-10-09 03:08:25 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:09:54 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 88.7 seconds

RetCode: 0

Status:  OK

CheckDir: iterativeBMA.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf iterativeBMA.buildbin-libdir iterativeBMA.Rcheck && mkdir iterativeBMA.buildbin-libdir iterativeBMA.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iterativeBMA.buildbin-libdir iterativeBMA_1.26.0.tar.gz >iterativeBMA.Rcheck\00install.out 2>&1 && cp iterativeBMA.Rcheck\00install.out iterativeBMA-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=iterativeBMA.buildbin-libdir --install="check:iterativeBMA-install.out" --force-multiarch --no-vignettes --timings iterativeBMA_1.26.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/iterativeBMA.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-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 '1.26.0'
* 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
** 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
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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
convertSingleName: no visible global function definition for 'exprs'
iterateBMAglm: no visible global function definition for 'bic.glm'
iterateBMAglm.train: no visible global function definition for 'exprs'
iterateBMAglm.train.predict: no visible global function definition for
  'exprs'
iterateBMAglm.train.predict.test: no visible global function definition
  for 'exprs'
iterateBMAglm.wrapper: no visible global function definition for
  'bic.glm'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [15s] OK
** running examples for arch 'x64' ... [17s] 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
* DONE

Status: 3 NOTEs
See
  'E:/biocbld/bbs-3.1-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_1.26.0.zip
* DONE (iterativeBMA)

name	user	system	elapsed
BssWssFast	0.04	0.00	0.03
bma_predict	1.77	0.02	1.79
brier_score	1.67	0.00	1.67
imageplot_iterate_bma	1.81	0.00	1.81
iterateBMAglm_train	1.84	0.01	1.86
iterateBMAglm_train_predict	1.89	0.00	1.88
iterateBMAglm_train_predict_test	1.82	0.00	1.83
iterateBMAglm_wrapper	1.64	0.00	1.63
iterativeBMA-package	1.73	0.02	1.75

name	user	system	elapsed
BssWssFast	0.03	0.00	0.03
bma_predict	1.83	0.01	1.85
brier_score	1.81	0.03	1.84
imageplot_iterate_bma	1.88	0.00	1.88
iterateBMAglm_train	1.91	0.00	1.91
iterateBMAglm_train_predict	1.84	0.00	1.84
iterateBMAglm_train_predict_test	1.85	0.00	1.85
iterateBMAglm_wrapper	1.80	0.02	1.81
iterativeBMA-package	1.78	0.00	2.16