BioC 3.0: CHECK report for RTCA on perceval

Package: RTCA

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RTCA_1.18.0.tar.gz

StartedAt: 2015-04-10 06:02:16 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 06:03:22 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 66.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RTCA.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RTCA_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/RTCA.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTCA’ version ‘1.18.0’
* 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 ‘RTCA’ can be installed ... [4s/7s] 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
'library' or 'require' call to ‘RColorBrewer’ 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 ... NOTE
parseRTCA: warning in read.table(file, skip = skipnum, sep = "\t", head
  = TRUE, dec = dec, ...): partial argument match of 'head' to 'header'
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘essentials.R’ [4s/4s]
 [5s/5s] 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/RTCA.Rcheck/00check.log’
for details.

* installing *source* package ‘RTCA’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘time’ from package ‘stats’ in package ‘RTCA’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘RTCA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RTCA)

name	user	system	elapsed
RTCA-class	0.364	0.004	0.369
RTCAtimeline-class	0.003	0.000	0.003
alphaNames	0.007	0.001	0.008
combineRTCA	0.295	0.008	0.304
controlView	0.381	0.011	0.394
derivativeTransform	0.243	0.005	0.248
factor2numeric	0.003	0.001	0.003
interpolationTransform	0.753	0.021	0.775
nearestTimeIndex	0.249	0.005	0.255
parseRTCA	0.886	0.008	0.893
plateView	0.515	0.004	0.520
plotGridEffect	0.537	0.004	0.545
ratioTransform	0.331	0.004	0.335
rgrTransform	0.626	0.019	0.646
sliceRTCA	0.247	0.003	0.251
smoothTransform	0.433	0.003	0.437
spectramaxImport	0.024	0.006	0.031