BioC 3.3: CHECK report for PANR on moscato2

Package: PANR

Version: 1.18.0

Command: rm -rf PANR.buildbin-libdir PANR.Rcheck && mkdir PANR.buildbin-libdir PANR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PANR.buildbin-libdir PANR_1.18.0.tar.gz >PANR.Rcheck\00install.out 2>&1 && cp PANR.Rcheck\00install.out PANR-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=PANR.buildbin-libdir --install="check:PANR-install.out" --force-multiarch --no-vignettes --timings PANR_1.18.0.tar.gz

StartedAt: 2016-10-13 07:06:03 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:08:54 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 171.5 seconds

RetCode: 0

Status:  OK

CheckDir: PANR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf PANR.buildbin-libdir PANR.Rcheck && mkdir PANR.buildbin-libdir PANR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PANR.buildbin-libdir PANR_1.18.0.tar.gz >PANR.Rcheck\00install.out 2>&1 && cp PANR.Rcheck\00install.out PANR-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=PANR.buildbin-libdir --install="check:PANR-install.out" --force-multiarch --no-vignettes --timings PANR_1.18.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/PANR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PANR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PANR' 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
fitNULL 37.55   0.16   40.58
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
fitNULL 36.98   0.08   41.21
* 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
  'E:/biocbld/bbs-3.3-bioc/meat/PANR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'PANR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'PANR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PANR' as PANR_1.18.0.zip
* DONE (PANR)

name	user	system	elapsed
BetaMixture-class	0	0	0
PAN-class	0	0	0
SNR2p	0	0	0
assoScore	0.01	0.00	0.01
buildPAN	0.97	0.02	0.98
cosineSim	0	0	0
data-Bakal2007	0.01	0.01	0.04
exportPAN	0	0	0
fitBM	0	0	0
fitNULL	37.55	0.16	40.58
infer	0.50	0.01	0.51
p2SNR	0	0	0
permNULL	0.01	0.02	0.03
pvclustModule	0	0	0
sigModules	0	0	0
summarize	0.03	0.00	0.03
view	0.33	0.02	0.35
viewLegend	0	0	0
viewNestedModules	0	0	0
viewPAN	0	0	0

name	user	system	elapsed
BetaMixture-class	0	0	0
PAN-class	0.02	0.00	0.01
SNR2p	0	0	0
assoScore	0.01	0.00	0.02
buildPAN	1.39	0.03	1.62
cosineSim	0	0	0
data-Bakal2007	0.05	0.01	0.30
exportPAN	0.00	0.00	0.04
fitBM	0.00	0.00	0.02
fitNULL	36.98	0.08	41.21
infer	0.46	0.02	0.47
p2SNR	0	0	0
permNULL	0.01	0.00	0.02
pvclustModule	0	0	0
sigModules	0.02	0.00	0.01
summarize	0.01	0.00	0.02
view	0.27	0.00	0.26
viewLegend	0	0	0
viewNestedModules	0	0	0
viewPAN	0	0	0