Package: OCplus

Version: 1.58.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OCplus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OCplus_1.58.0.tar.gz

StartedAt: 2019-10-16 05:09:54 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:11:55 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 120.4 seconds

RetCode: 0

Status:  OK

CheckDir: OCplus.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OCplus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OCplus_1.58.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/OCplus.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OCplus/DESCRIPTION’ ... OK
* this is package ‘OCplus’ version ‘1.58.0’
* 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 ‘OCplus’ can be installed ... 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 ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.FDR.result plot.fdr1d.result plot.fdr2d.result
  summary.fdr.result
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
samplesize 9.949  0.862  10.813
tMixture   5.334  0.659   5.994
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/OCplus.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL OCplus
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘OCplus’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (OCplus)

name	user	system	elapsed
EOC	0.769	0.303	1.072
FDR	0.004	0.001	0.005
MAsim.smyth	0.418	0.112	0.530
OCshow	2.050	0.551	2.600
TOC	0.488	0.066	0.556
average.fdr	1.311	0.496	1.811
fdr1d	0.851	0.223	1.075
fdr2d	0.942	0.242	1.184
plot.FDR.result	0.126	0.070	0.198
plot.fdr1d.result	0.594	0.187	0.783
plot.fdr2d.result	0.870	0.285	1.155
samplesize	9.949	0.862	10.813
smooth1d	0.063	0.016	0.089
summary.fdr.result	0.728	0.244	0.973
tMixture	5.334	0.659	5.994