BioC 3.3: CHECK report for iterativeBMA on zin2

Package: iterativeBMA

Version: 1.30.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings iterativeBMA_1.30.0.tar.gz

StartedAt: 2016-10-13 03:37:23 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:38:14 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 51.5 seconds

RetCode: 0

Status:  OK

CheckDir: iterativeBMA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings iterativeBMA_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/iterativeBMA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iterativeBMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iterativeBMA’ version ‘1.30.0’
* 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 ‘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
* 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’
imageplot.bma.mod: no visible global function definition for ‘par’
imageplot.bma.mod: no visible global function definition for ‘image’
imageplot.bma.mod: no visible global function definition for ‘axis’
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’
Undefined global functions or variables:
  axis bic.glm exprs image par
Consider adding
  importFrom("graphics", "axis", "image", "par")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/home/biocbuild/bbs-3.3-bioc/meat/iterativeBMA.Rcheck/00check.log’
for details.

* 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
* DONE (iterativeBMA)

name	user	system	elapsed
BssWssFast	0.113	0.000	0.112
bma_predict	1.4	0.0	1.4
brier_score	1.392	0.004	1.395
imageplot_iterate_bma	1.460	0.012	1.470
iterateBMAglm_train	1.355	0.004	1.358
iterateBMAglm_train_predict	1.443	0.008	1.450
iterateBMAglm_train_predict_test	1.374	0.012	1.386
iterateBMAglm_wrapper	1.389	0.012	1.409
iterativeBMA-package	1.469	0.004	1.479