BioC 3.4: CHECK report for CINdex on zin1

Package: CINdex

Version: 1.1.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CINdex_1.1.2.tar.gz

StartedAt: 2016-09-20 04:32:01 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:34:23 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 141.6 seconds

RetCode: 0

Status:  OK

CheckDir: CINdex.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CINdex_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/CINdex.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 ‘CINdex/DESCRIPTION’ ... OK
* this is package ‘CINdex’ version ‘1.1.2’
* 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 ‘CINdex’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data  17.7Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
comp.heatmap: no visible binding for global variable ‘dataMatrix’
process.probe.anno: no visible binding for global variable ‘ID’
process.probe.anno: no visible binding for global variable ‘midpoint’
process.reference.genome: no visible binding for global variable
  ‘chrom’
process.reference.genome: no visible binding for global variable ‘name’
process.reference.genome: no visible binding for global variable
  ‘stain’
Undefined global functions or variables:
  ID chrom dataMatrix midpoint name stain
* 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 sizes of PDF files under ‘inst/doc’ ... 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
run.cin.cyto 13.18  0.284  13.476
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘RunTests.R’
 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/CINdex.Rcheck/00check.log’
for details.

* installing *source* package ‘CINdex’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CINdex)

name	user	system	elapsed
comp.heatmap	0.744	0.012	0.775
extract.genes.in.cyto.regions	1.760	0.056	1.817
run.cin.chr	0.280	0.000	0.279
run.cin.cyto	13.180	0.284	13.476
ttest.cyto.cin.heatmap	0.500	0.000	0.503