BioC 3.0: CHECK report for SPEM on zin1

Package: SPEM

Version: 1.6.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SPEM_1.6.0.tar.gz

StartedAt: 2015-04-10 04:35:31 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:36:46 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 74.6 seconds

RetCode: 0

Status:  OK

CheckDir: SPEM.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SPEM_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/SPEM.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPEM’ version ‘1.6.0’
* 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 ‘SPEM’ can be installed ... [2s/2s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘Rsolnp’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
opt_parameter: no visible global function definition for ‘solnp’
SPEM,ExpressionSet: no visible global function definition for ‘exprs’
SPEM,ExpressionSet: no visible global function definition for ‘pData’
row_optimize,ExpressionSet: no visible global function definition for
  ‘exprs’
s_diff,ExpressionSet: no visible global function definition for ‘exprs’
s_diff,ExpressionSet: no visible global function definition for ‘pData’
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [44s/47s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
row_optimize 42.662   0.04  45.015
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/SPEM.Rcheck/00check.log’
for details.

* installing *source* package ‘SPEM’ ...
** 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 (SPEM)

name	user	system	elapsed
SPEM	0.372	0.000	0.373
row_optimize	42.662	0.040	45.015
s_diff	0.208	0.000	0.207
sos	0.004	0.000	0.001