BioC 3.4: CHECK report for iterativeBMA on zin1

Package: iterativeBMA

Version: 1.31.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iterativeBMA_1.31.0.tar.gz

StartedAt: 2016-09-20 08:25:49 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 08:26:39 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 50.1 seconds

RetCode: 0

Status:  OK

CheckDir: iterativeBMA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iterativeBMA_1.31.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-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 ‘1.31.0’
* 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-3.4-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	0.108	0.004	0.110
bma_predict	1.396	0.012	1.406
brier_score	1.408	0.000	1.408
imageplot_iterate_bma	1.472	0.012	1.483
iterateBMAglm_train	1.388	0.000	1.387
iterateBMAglm_train_predict	1.380	0.016	1.411
iterateBMAglm_train_predict_test	1.408	0.004	1.412
iterateBMAglm_wrapper	1.360	0.012	1.373
iterativeBMA-package	1.428	0.000	1.429