BioC 3.1: CHECK report for EBarrays on zin2

Package: EBarrays

Version: 2.32.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings EBarrays_2.32.0.tar.gz

StartedAt: 2015-10-09 00:45:25 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:46:38 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 72.9 seconds

RetCode: 0

Status:  OK

CheckDir: EBarrays.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings EBarrays_2.32.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/EBarrays.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBarrays/DESCRIPTION’ ... OK
* this is package ‘EBarrays’ version ‘2.32.0’
* 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 ‘EBarrays’ can be installed ... [2s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘lattice’ ‘methods’
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' call to ‘lattice’ which was already attached by Depends.
  Please remove these calls from your code.
* 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 ... NOTE
prepare_Rd: crit.fun.Rd:51: Dropping empty section \keyword
prepare_Rd: ebplots.Rd:116-117: Dropping empty section \examples
* 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 ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/9s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
crit.fun 5.792  0.033   7.776
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [13s/17s]
 [13s/18s] OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/EBarrays.Rcheck/00check.log’
for details.

* installing *source* package ‘EBarrays’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ebarrays.c -o ebarrays.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o EBarrays.so ebarrays.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/EBarrays.Rcheck/EBarrays/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EBarrays)

name	user	system	elapsed
crit.fun	5.792	0.033	7.776
ebarraysFamily-class	0.005	0.000	0.005
emfit	0.232	0.008	0.249
gould	0.003	0.004	0.008
postprob	0.238	0.000	0.310
utilities	0.002	0.000	0.002