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BioC 3.2: CHECK report for netbiov on zin1

This page was generated on 2015-08-24 10:50:01 -0700 (Mon, 24 Aug 2015).

Package 680/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netbiov 1.3.1
Shailesh tripathi
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/netbiov
Last Changed Rev: 106583 / Revision: 107696
Last Changed Date: 2015-07-20 10:05:43 -0700 (Mon, 20 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: netbiov
Version: 1.3.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings netbiov_1.3.1.tar.gz
StartedAt: 2015-08-24 02:08:25 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 02:13:06 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 280.7 seconds
RetCode: 0
Status:  OK 
CheckDir: netbiov.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings netbiov_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/netbiov.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.3.1’
* 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 ... [1s/1s] OK
* checking installed package size ... NOTE
  installed size is 18.6Mb
  sub-directories of 1Mb or more:
    doc  17.8Mb
* 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 ... [238s/239s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
level.plot           99.210  0.323  99.691
plot.abstract.module 55.453  0.052  55.811
plot.modules         44.480  0.024  44.522
mst.plot             22.266  0.052  22.362
mst.plot.mod          9.485  0.028   9.577
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [16s/16s]
 [16s/16s] 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-3.2-bioc/meat/netbiov.Rcheck/00check.log’
for details.


netbiov.Rcheck/00install.out:

* 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)

netbiov.Rcheck/netbiov-Ex.timings:

nameusersystemelapsed
PPI_Athalina0.0190.0000.019
level.plot99.210 0.32399.691
mst.plot22.266 0.05222.362
mst.plot.mod9.4850.0289.577
plot.NetworkSperical0.9140.0000.913
plot.NetworkSperical.startSet0.5720.0160.588
plot.abstract.module55.453 0.05255.811
plot.abstract.nodes0.5110.0120.528
plot.modules44.480 0.02444.522
plot.netbiov1.8560.0081.870
plot.spiral.graph0.5860.0040.591
split.mst1.6550.0041.657