BioC 3.2: CHECK report for mmnet on perceval

Package: mmnet

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mmnet_1.8.0.tar.gz

StartedAt: 2015-11-10 07:10:39 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 07:16:07 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 328.9 seconds

RetCode: 0

Status:  OK

CheckDir: mmnet.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mmnet_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/mmnet.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.8.0’
* 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 ... [17s/17s] OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  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 ... [149s/152s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
showMetagenomicNet    52.690  1.218  54.275
topologicalAnalyzeNet 33.177  0.391  35.253
constructSSN          27.248  0.144  27.393
estimateAbundance     24.289  0.094  24.386
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/mmnet.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
RefDbcache	0.057	0.004	0.061
anno	1.022	0.042	1.063
checkMgrastMetagenome	0.028	0.002	0.893
constructMetabolicNetwork	0.001	0.000	0.001
constructSSN	27.248	0.144	27.393
estimateAbundance	24.289	0.094	24.386
generateMgrastWebkey	0.000	0.000	0.001
generateMgrastWebsession	0.000	0.000	0.001
getMgrastAnnotation	0.000	0.001	0.001
listMgrastInbox	0.001	0.000	0.001
listMgrastProject	0.001	0.000	0.001
loadMetabolicData	0	0	0
loginMgrast	0	0	0
saveMetabolicData	0.001	0.000	0.000
showMetagenomicNet	52.690	1.218	54.275
submitMgrastJob	0	0	0
topologicalAnalyzeNet	33.177	0.391	35.253
updateKEGGPathway	0.000	0.001	0.001
uploadMgrast	0.001	0.000	0.001