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July 29, 2014 04:00
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$ 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 |
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