BioC experimental data: CHECK report for hgu2beta7 on perceval

Package: hgu2beta7

Version: 1.2.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch hgu2beta7_1.2.9.tar.gz

StartedAt: 2014-04-04 11:10:29 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 11:11:41 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 72.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: hgu2beta7.Rcheck

Warnings: 3

* using log directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/hgu2beta7.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hgu2beta7/DESCRIPTION’ ... OK
* this is package ‘hgu2beta7’ version ‘1.2.9’
* 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/2s] 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 ... OK
* 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 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 ... OK
* 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 ... [12s/13s] OK
* checking PDF version of manual ... OK

WARNING: There were 3 warnings.
NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.469	0.030	0.498
hgu2beta7CHR	0.290	0.012	0.302
hgu2beta7CHRLENGTHS	0.055	0.000	0.056
hgu2beta7CHRLOC	0.464	0.009	0.472
hgu2beta7ENZYME	0.306	0.007	0.313
hgu2beta7ENZYME2PROBE	0.057	0.001	0.058
hgu2beta7GENENAME	0.377	0.010	0.386
hgu2beta7GO	2.404	0.077	2.481
hgu2beta7GO2ALLPROBES	0.817	0.033	0.850
hgu2beta7GO2PROBE	0.090	0.014	0.103
hgu2beta7GRIF	0.158	0.022	0.180
hgu2beta7LOCUSID	0.152	0.007	0.159
hgu2beta7MAP	0.162	0.008	0.170
hgu2beta7OMIM	0.194	0.008	0.202
hgu2beta7ORGANISM	0.002	0.002	0.004
hgu2beta7PATH	0.161	0.008	0.169
hgu2beta7PATH2PROBE	0.022	0.004	0.026
hgu2beta7PMID	0.353	0.017	0.370
hgu2beta7PMID2PROBE	1.803	0.024	1.828
hgu2beta7REFSEQ	0.372	0.018	0.390
hgu2beta7SUMFUNC	0.374	0.024	0.437
hgu2beta7SYMBOL	0.708	0.011	0.737
hgu2beta7UNIGENE	0.285	0.012	0.296