BioC 3.3: CHECK report for erma on zin2

Package: erma

Version: 0.4.2

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings erma_0.4.2.tar.gz

StartedAt: 2016-10-13 01:47:41 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 01:51:19 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 218.4 seconds

RetCode: 0

Status:  OK

CheckDir: erma.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 erma_0.4.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/erma.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 ‘erma/DESCRIPTION’ ... OK
* this is package ‘erma’ version ‘0.4.2’
* 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 ‘erma’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 199.6Mb
  sub-directories of 1Mb or more:
    bed_tabix  161.3Mb
    data        37.1Mb
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
geneTxRange: no visible global function definition for ‘select’
geneTxRange: no visible global function definition for ‘IRanges’
genemodel: no visible global function definition for ‘IRanges’
genemodelOLD: no visible binding for global variable ‘exonsBy’
map2range: no visible global function definition for ‘IRanges’
mapmeta: no visible global function definition for ‘read.csv’
stateProf: no visible global function definition for ‘keys’
stateProfOLD: no visible global function definition for ‘keys’
stateProfOLD : server: possible error in stateProfile(ermaset,
  input$sym, ctsize = 12, width = input$scope): unused argument (width
  = input$scope)
stateProfile: no visible binding for global variable ‘i’
stateProfile: no visible global function definition for ‘genome’
stateProfile: no visible global function definition for ‘seqlevels<-’
stateProfile: no visible global function definition for ‘seqlevels’
stateProfile : <anonymous>: no visible global function definition for
  ‘IRanges’
stateProfile: no visible global function definition for ‘data’
stateProfile: no visible binding for global variable ‘short_celltype’
stateProfile: no visible binding for global variable ‘states_25’
stateProfile: no visible binding for global variable ‘name’
subsetByRanges : <anonymous>: no visible global function definition for
  ‘genome’
subsetByRanges : <anonymous>: no visible global function definition for
  ‘seqlevels<-’
subsetByRanges : <anonymous>: no visible global function definition for
  ‘seqlevels’
Undefined global functions or variables:
  IRanges data exonsBy genome i keys name read.csv select seqlevels
  seqlevels<- short_celltype states_25
Consider adding
  importFrom("utils", "data", "read.csv")
to your NAMESPACE file.
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
erma-package 6.098    0.3   6.629
* 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
  ‘/home/biocbuild/bbs-3.3-bioc/meat/erma.Rcheck/00check.log’
for details.

* installing *source* package ‘erma’ ...
** 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 (erma)

name	user	system	elapsed
ErmaSet-class	0.182	0.012	0.194
erma-package	6.098	0.300	6.629
genemodel	1.219	0.016	1.506
mapmeta	0.079	0.004	0.083
stateProfile	2.050	0.011	2.110
states_25	0.003	0.001	0.002