BioC 3.3: CHECK report for STRINGdb on linux2.bioconductor.org

Package: STRINGdb

Version: 1.11.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings STRINGdb_1.11.0.tar.gz

StartedAt: 2015-10-27 08:26:58 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:38:30 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 692.4 seconds

RetCode: 0

Status:  OK

CheckDir: STRINGdb.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings STRINGdb_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/STRINGdb.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ‘1.11.0’
* 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 ... [3s/3s] OK
* checking installed package size ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.3Mb
* 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:
  ‘RColorBrewer’ ‘RCurl’ ‘gplots’ ‘hash’ ‘igraph’ ‘methods’ ‘plotrix’
  ‘plyr’ ‘png’ ‘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’
Undefined global functions or variables:
  V curlEscape curlOptions degree ecount getCurlHandle induced.subgraph
  neighborhood official_name postForm
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [376s/467s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
STRINGdb-package 197.950  2.653 256.212
STRINGdb         169.549  4.161 208.536
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [177s/194s]
 [178s/194s] 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-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	0.000	0.002
STRINGdb-package	197.950	2.653	256.212
STRINGdb	169.549	4.161	208.536