BioC experimental data: CHECK report for hgu2beta7 on morelia

Package: hgu2beta7

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hgu2beta7_1.11.0.tar.gz

StartedAt: 2015-11-25 10:43:26 -0800 (Wed, 25 Nov 2015)

EndedAt: 2015-11-25 10:44:20 -0800 (Wed, 25 Nov 2015)

EllapsedTime: 54.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: hgu2beta7.Rcheck

Warnings: 3

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hgu2beta7_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/hgu2beta7.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hgu2beta7/DESCRIPTION’ ... OK
* this is package ‘hgu2beta7’ version ‘1.11.0’
* 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 ‘hgu2beta7’ can be installed ... [1s/11s] OK
* checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory ‘data’ contains no data sets.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
hgu2beta7: no visible binding for global variable ‘hgu2beta7QC’
Undefined global functions or variables:
  hgu2beta7QC
* 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 ... WARNING
'library' or 'require' call not declared from: ‘annotate’
* checking contents of ‘data’ directory ... WARNING
Files not of a type allowed in a ‘data’ directory:
  ‘Rdata.rdb’ ‘Rdata.rds’ ‘Rdata.rdx’
Please use e.g. ‘inst/extdata’ for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [3s/5s] OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/hgu2beta7.Rcheck/00check.log’
for details.

* installing *source* package ‘hgu2beta7’ ...
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (hgu2beta7)

name	user	system	elapsed
hgu2beta7ACCNUM	0.196	0.012	0.208
hgu2beta7CHR	0.102	0.002	0.103
hgu2beta7CHRLENGTHS	0.001	0.000	0.001
hgu2beta7CHRLOC	0.065	0.003	0.068
hgu2beta7ENZYME	0.056	0.003	0.059
hgu2beta7ENZYME2PROBE	0.003	0.000	0.003
hgu2beta7GENENAME	0.125	0.003	0.129
hgu2beta7GO	0.563	0.033	0.604
hgu2beta7GO2ALLPROBES	0.224	0.009	0.234
hgu2beta7GO2PROBE	0.041	0.003	0.045
hgu2beta7GRIF	0.070	0.003	0.074
hgu2beta7LOCUSID	0.050	0.003	0.054
hgu2beta7MAP	0.056	0.003	0.059
hgu2beta7OMIM	0.038	0.003	0.041
hgu2beta7ORGANISM	0.001	0.000	0.001
hgu2beta7PATH	0.190	0.007	0.197
hgu2beta7PATH2PROBE	0.003	0.001	0.003
hgu2beta7PMID	0.105	0.007	0.113
hgu2beta7PMID2PROBE	0.577	0.015	0.595
hgu2beta7REFSEQ	0.137	0.005	0.173
hgu2beta7SUMFUNC	0.132	0.007	0.144
hgu2beta7SYMBOL	0.137	0.002	0.140
hgu2beta7UNIGENE	0.073	0.003	0.125