BioC 3.2: CHECK report for netbiov on oaxaca

Package: netbiov

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings netbiov_1.4.0.tar.gz

StartedAt: 2016-04-23 02:38:04 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:44:15 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 371.2 seconds

RetCode: 0

Status:  OK

CheckDir: netbiov.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings netbiov_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/netbiov.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netbiov/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netbiov’ version ‘1.4.0’
* 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 ‘netbiov’ can be installed ... [2s/19s] OK
* checking installed package size ... NOTE
  installed size is 18.4Mb
  sub-directories of 1Mb or more:
    doc  17.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* 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’ ... NOTE
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
* checking examples ... [292s/293s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
level.plot           128.655  1.595 130.505
plot.abstract.module  64.575  1.152  65.827
plot.modules          54.881  1.153  56.478
mst.plot              20.167  0.189  20.391
mst.plot.mod          11.552  0.151  11.759
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [19s/20s]
 [20s/20s] 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/netbiov.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
PPI_Athalina	0.025	0.003	0.028
level.plot	128.655	1.595	130.505
mst.plot	20.167	0.189	20.391
mst.plot.mod	11.552	0.151	11.759
plot.NetworkSperical	1.257	0.007	1.286
plot.NetworkSperical.startSet	0.712	0.030	0.744
plot.abstract.module	64.575	1.152	65.827
plot.abstract.nodes	0.393	0.005	0.401
plot.modules	54.881	1.153	56.478
plot.netbiov	2.520	0.022	2.551
plot.spiral.graph	1.056	0.012	1.080
split.mst	1.722	0.017	1.742