Package: PANR

Version: 1.29.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PANR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PANR_1.29.1.tar.gz

StartedAt: 2019-04-09 02:33:18 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:34:25 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 67.0 seconds

RetCode: 0

Status:  OK

CheckDir: PANR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PANR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PANR_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/PANR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PANR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PANR’ version ‘1.29.1’
* 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 ‘PANR’ 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SNR2p,BetaMixture-numeric_Or_integer: no visible global function
  definition for ‘runif’
SNR2p,BetaMixture-numeric_Or_integer: no visible global function
  definition for ‘pbeta’
p2SNR,BetaMixture-numeric_Or_integer: no visible global function
  definition for ‘qbeta’
Undefined global functions or variables:
  pbeta qbeta runif
Consider adding
  importFrom("stats", "pbeta", "qbeta", "runif")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
fitNULL 23.149  0.055  26.508
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/PANR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL PANR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘PANR’ ...
** using staged installation
** R
** data
** inst
** 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 (PANR)

name	user	system	elapsed
BetaMixture-class	0	0	0
PAN-class	0	0	0
SNR2p	0	0	0
assoScore	0.006	0.000	0.005
buildPAN	0.406	0.024	0.429
cosineSim	0.002	0.000	0.002
data-Bakal2007	0.018	0.000	0.017
exportPAN	0.001	0.000	0.000
fitBM	0	0	0
fitNULL	23.149	0.055	26.508
infer	0.209	0.000	0.208
p2SNR	0	0	0
permNULL	0.015	0.000	0.015
pvclustModule	0	0	0
sigModules	0	0	0
summarize	0.031	0.000	0.031
view	0.143	0.004	0.148
viewLegend	0	0	0
viewNestedModules	0	0	0
viewPAN	0	0	0