BioC 3.0: CHECK report for hypergraph on zin1

Package: hypergraph

Version: 1.38.1

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings hypergraph_1.38.1.tar.gz

StartedAt: 2015-04-10 01:07:39 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:08:03 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 24.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: hypergraph.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings hypergraph_1.38.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/hypergraph.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hypergraph/DESCRIPTION’ ... OK
* this is package ‘hypergraph’ version ‘1.38.1’
* 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 ‘hypergraph’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package 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
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘hypergraph/R/AllClasses.R’:
  .onLoad calls:
    require("methods", quietly = TRUE)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
* checking Rd files ... NOTE
prepare_Rd: kCores.Rd:29: Dropping empty section \seealso
prepare_Rd: vCover.Rd:32: Dropping empty section \seealso
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  inst/unitTests/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] OK
* checking PDF version of manual ... OK
* DONE

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/hypergraph.Rcheck/00check.log’
for details.

* installing *source* package ‘hypergraph’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘head’ from package ‘utils’ in package ‘hypergraph’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘hypergraph’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hypergraph)

name	user	system	elapsed
DirectedHyperedge-class	0.000	0.000	0.001
Hyperedge-class	0.000	0.000	0.001
Hypergraph-class	0.004	0.000	0.002
kCores	0.012	0.000	0.012
l2hel	0.000	0.000	0.001
vCover	0.008	0.000	0.009