Skip to content

Instantly share code, notes, and snippets.

@dtenenba
Created July 29, 2014 04:00
Show Gist options
  • Save dtenenba/e3b9beaf02e4d4f772f8 to your computer and use it in GitHub Desktop.
Save dtenenba/e3b9beaf02e4d4f772f8 to your computer and use it in GitHub Desktop.
$ R CMD BiocCheck KEGGREST_1.1.1.tar.gz
* This is BiocCheck, version 1.1.7.
* BiocCheck is a work in progress. Output and severity of issues may
change.
* Installing package...
* This is a software package, checking vignette directories...
* # of chunks: 23, # of eval=FALSE: 1 (4%)
* Checking version number...
* Checking biocViews...
* RECOMMENDED: Use valid biocViews. Invalid ones: ConnectTools
* Checking build system compatibility...
* Checking unit tests...
* Checking native routine registration...
* Checking for deprecated package usage...
* Parsing R code in R directory, examples, vignettes...
* Checking for T...
Found T in R/utilities.R (line 66, column 53)
* RECOMMENDED: Use TRUE instead of T (found in 1 files)
* Checking for F...
* Checking for browser()...
* Checking for <<-...
* Checking for library/require of KEGGREST...
* Checking DESCRIPTION/NAMESPACE consistency...
* RECOMMENDED: Import methods in NAMESPACE as well as DESCRIPTION.
* Checking function lengths.............
* The longest function is 79 lines long
* The longest 5 functions are:
* .flatFileParser() (R/parsers.R, line 112): 79 lines
* _anonymous_.238() (R/parsers.R, line 238): 39 lines
* keggGet() (R/KEGGREST.R, line 38): 30 lines
* .get_parser_REFERENCE() (R/parsers.R, line 40): 23 lines
* color.pathway.by.objects() (R/KEGGREST.R, line 120): 21 lines
* Checking exported objects have runnable examples...
* Checking package NEWS...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* CONSIDER: Shortening lines; 7 lines (0%) are > 80 characters
long.
* CONSIDER: Indenting lines with a multiple of 4 spaces; 95 lines
(7%) are not.
See http://bioconductor.org/developers/how-to/coding-style/
* Checking for canned comments in man pages...
* CONSIDER: Removing generated comments from man pages keggList.Rd
* Checking for bioc-devel mailing list subscription...
* Maintainer email is ok.
Summary:
REQUIRED count: 0
RECOMMENDED count: 3
CONSIDERATION count: 3
For detailed information about these checks, see the BiocCheck
vignette, available at
http://www.bioconductor.org/packages/3.0/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#Interpreting_BiocCheck_output
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment