BioC 2.13: CHECK report for KEGGprofile on zin1

Package: KEGGprofile

Version: 1.4.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings KEGGprofile_1.4.0.tar.gz

StartedAt: 2014-04-05 02:06:44 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:08:18 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 94.0 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGprofile.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/KEGGprofile.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGprofile/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGprofile’ version ‘1.4.0’
* 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 ‘KEGGprofile’ can be installed ... [8s/8s] 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 ... NOTE
‘library’ or ‘require’ calls to packages already attached by Depends:
  ‘KEGG.db’ ‘TeachingDemos’ ‘XML’ ‘png’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘KEGG.db’ ‘TeachingDemos’ ‘XML’ ‘png’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
parse_XMLfile: warning in xmlTreeParse(paste(database_dir, "/", specis,
  pathway_id, ".xml", sep = ""), useInternal = TRUE): partial argument
  match of 'useInternal' to 'useInternalNodes'
plot_profile: no visible binding for global variable ‘x’
plot_profile: no visible binding for global variable ‘y’
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘KEGGprofile.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [16s/18s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_pathway 7.204  0.072   7.372
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/KEGGprofile.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
col_by_value	0.032	0.004	0.036
download_KEGGfile	0.012	0.000	1.317
find_enriched_pathway	3.692	0.012	3.736
parse_XMLfile	0.120	0.000	0.121
plot_pathway	7.204	0.072	7.372
plot_profile	1.285	0.020	1.307