BioC 3.2: CHECK report for stepNorm on perceval

Package: stepNorm

Version: 1.41.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings stepNorm_1.41.0.tar.gz

StartedAt: 2015-08-24 05:35:52 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 05:38:08 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 135.3 seconds

RetCode: 0

Status:  OK

CheckDir: stepNorm.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings stepNorm_1.41.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/stepNorm.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘stepNorm/DESCRIPTION’ ... OK
* this is package ‘stepNorm’ version ‘1.41.0’
* 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 ‘stepNorm’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘marray’ ‘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 loading without being on the library search path ... 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 ... NOTE
loess2Dfit: warning in loess.control(trace.hat = "approximate",
  iteration = 5, surface = "direct"): partial argument match of
  'iteration' to 'iterations'
loessfit: warning in loess.control(trace.hat = "approximate", iteration
  = 5, surface = "direct"): partial argument match of 'iteration' to
  'iterations'
* 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 examples ... [99s/100s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
stepWithinNorm 41.759  0.228  42.186
fitWithin      37.821  0.102  37.959
fit2DWithin    16.699  0.108  16.818
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/stepNorm.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
calcAIC	0.311	0.027	0.338
calcBIC	0.188	0.010	0.199
fit2DWithin	16.699	0.108	16.818
fitWithin	37.821	0.102	37.959
maCompPlate2	0.025	0.002	0.027
makeStepList	0.06	0.01	0.07
marrayFitClass	0.122	0.029	0.151
seqWithinNorm	0.456	0.022	0.479
stepWithinNorm	41.759	0.228	42.186
withinNorm	0.059	0.009	0.067