BioC 3.2: CHECK report for mmnet on zin1

Package: mmnet

Version: 1.8.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings mmnet_1.8.1.tar.gz

StartedAt: 2016-04-23 03:02:50 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:06:39 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 228.5 seconds

RetCode: 0

Status:  OK

CheckDir: mmnet.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings mmnet_1.8.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/mmnet.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mmnet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mmnet’ version ‘1.8.1’
* 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 ‘mmnet’ can be installed ... [11s/11s] OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc    3.0Mb
* 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
constructMetabolicNetwork: no visible binding for global variable
  ‘RefDbcache’
* 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 ... [110s/110s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
showMetagenomicNet    40.968  0.435  41.483
topologicalAnalyzeNet 23.660  0.076  23.775
constructSSN          19.696  0.040  19.730
estimateAbundance     18.294  0.060  18.340
* 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-3.2-bioc/meat/mmnet.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
RefDbcache	0.044	0.000	0.044
anno	0.730	0.008	0.739
checkMgrastMetagenome	0.008	0.000	0.519
constructMetabolicNetwork	0	0	0
constructSSN	19.696	0.040	19.730
estimateAbundance	18.294	0.060	18.340
generateMgrastWebkey	0	0	0
generateMgrastWebsession	0.000	0.000	0.001
getMgrastAnnotation	0.001	0.000	0.001
listMgrastInbox	0	0	0
listMgrastProject	0	0	0
loadMetabolicData	0	0	0
loginMgrast	0	0	0
saveMetabolicData	0.001	0.000	0.001
showMetagenomicNet	40.968	0.435	41.483
submitMgrastJob	0.001	0.000	0.000
topologicalAnalyzeNet	23.660	0.076	23.775
updateKEGGPathway	0.001	0.000	0.001
uploadMgrast	0.001	0.000	0.000