BioC 3.5: CHECK report for LOBSTAHS on oaxaca

Package: LOBSTAHS

Version: 1.1.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LOBSTAHS_1.1.4.tar.gz

StartedAt: 2017-03-04 04:58:45 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 05:02:03 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 197.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: LOBSTAHS.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LOBSTAHS_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/LOBSTAHS.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LOBSTAHS/DESCRIPTION’ ... OK
* this is package ‘LOBSTAHS’ version ‘1.1.4’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘LOBSTAHS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... 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 ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                         old_size new_size compress
  default.LOBdbase.RData    1.5Mb    482Kb       xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
loadLOBdbase 15.554  0.114  15.672
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/LOBSTAHS.Rcheck/00check.log’
for details.

* installing *source* package ‘LOBSTAHS’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LOBSTAHS)

name	user	system	elapsed
LOBSet-class	0.002	0.000	0.001
LOBSet	0.001	0.000	0.002
LOBdbase-class	0.002	0.000	0.001
LOBdbase	0.002	0.000	0.003
doLOBscreen	2.303	0.096	2.456
exportDBtoCSV	1.136	0.037	1.174
extractLOBdbasedata	0.293	0.016	0.308
generateLOBdbase	0	0	0
getLOBpeaklist	0.052	0.001	0.052
loadLOBdbase	15.554	0.114	15.672