BioC 3.0: CHECK report for STRINGdb on perceval

Package: STRINGdb

Version: 1.5.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch STRINGdb_1.5.5.tar.gz

StartedAt: 2015-04-10 06:52:17 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 07:10:45 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 1108.1 seconds

RetCode: 0

Status:  OK

CheckDir: STRINGdb.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 --no-multiarch STRINGdb_1.5.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/STRINGdb.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STRINGdb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STRINGdb’ version ‘1.5.5’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘png’ ‘sqldf’ ‘plyr’ ‘igraph’ ‘RCurl’ ‘plotrix’ ‘RColorBrewer’
  ‘gplots’ ‘hash’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘STRINGdb’ can be installed ... [8s/10s] OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘gplots’ ‘hash’ ‘igraph’ ‘methods’ ‘plotrix’ ‘plyr’ ‘png’
  ‘RColorBrewer’ ‘RCurl’ ‘sqldf’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_STRING_species: no visible binding for global variable
  ‘official_name’
postFormSmart: no visible global function definition for ‘curlOptions’
postFormSmart: no visible global function definition for
  ‘getCurlHandle’
postFormSmart: no visible binding for global variable ‘curlEscape’
postFormSmart: no visible global function definition for ‘postForm’
ppi_enrichment: no visible global function definition for ‘V’
ppi_enrichment: no visible global function definition for ‘ecount’
ppi_enrichment: no visible global function definition for
  ‘induced.subgraph’
ppi_enrichment: no visible global function definition for ‘degree’
ppi_enrichment_full: no visible global function definition for ‘V’
ppi_enrichment_full: no visible global function definition for ‘ecount’
ppi_enrichment_full: no visible global function definition for
  ‘induced.subgraph’
ppi_enrichment_full: no visible global function definition for ‘degree’
ppie.getNumEdgesBetween: no visible global function definition for
  ‘neighborhood’
* 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 ... [10m/12m] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
STRINGdb-package 313.313 26.819 442.130
STRINGdb         228.280 23.713 287.016
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [276s/304s]
 [276s/305s] 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/STRINGdb.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
STRINGdb-class	0.002	0.001	0.003
STRINGdb-package	313.313	26.819	442.130
STRINGdb	228.280	23.713	287.016