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BioC 3.0: CHECK report for mmnet on oaxaca

This page was generated on 2015-04-10 10:08:21 -0700 (Fri, 10 Apr 2015).

Package 568/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mmnet 1.4.0
Yang Cao , Fei Li
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/mmnet
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: mmnet
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch mmnet_1.4.0.tar.gz
StartedAt: 2015-04-10 01:28:46 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:39:05 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 619.2 seconds
RetCode: 0
Status:  OK 
CheckDir: mmnet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch mmnet_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/mmnet.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.0’
* 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 ‘mmnet’ can be installed ... [23s/24s] OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  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 ... [234s/307s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
topologicalAnalyzeNet 62.150  0.392  72.025
estimateAbundance     58.721  0.280  87.650
constructSSN          55.675  0.342  76.167
showMetagenomicNet    42.232  0.496  52.731
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/mmnet.Rcheck/00check.log’
for details.

mmnet.Rcheck/00install.out:

* installing *source* package ‘mmnet’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “file” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “pipe” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “textConnection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “file” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “pipe” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “textConnection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
* DONE (mmnet)

mmnet.Rcheck/mmnet-Ex.timings:

nameusersystemelapsed
RefDbcache0.0540.0030.064
anno1.3760.0361.584
checkMgrastMetagenome0.4790.0021.677
constructMetabolicNetwork0.0010.0000.000
constructSSN55.675 0.34276.167
estimateAbundance58.721 0.28087.650
generateMgrastWebkey0.0000.0000.001
generateMgrastWebsession0.0010.0000.001
getMgrastAnnotation0.0010.0010.000
listMgrastInbox0.0010.0000.001
listMgrastProject0.0010.0000.001
loadMetabolicData0.0010.0000.000
loginMgrast0.0010.0000.001
saveMetabolicData0.0010.0000.001
showMetagenomicNet42.232 0.49652.731
submitMgrastJob0.0010.0010.001
topologicalAnalyzeNet62.150 0.39272.025
updateKEGGPathway0.0010.0000.000
uploadMgrast0.0010.0000.000