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BioC 3.5: CHECK report for PANR on tokay2

This page was generated on 2017-08-16 13:21:17 -0400 (Wed, 16 Aug 2017).

Package 943/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PANR 1.22.0
Xin Wang
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/PANR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PANR
Version: 1.22.0
Command: rm -rf PANR.buildbin-libdir PANR.Rcheck && mkdir PANR.buildbin-libdir PANR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PANR.buildbin-libdir PANR_1.22.0.tar.gz >PANR.Rcheck\00install.out 2>&1 && cp PANR.Rcheck\00install.out PANR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=PANR.buildbin-libdir --install="check:PANR-install.out" --force-multiarch --no-vignettes --timings PANR_1.22.0.tar.gz
StartedAt: 2017-08-16 01:47:09 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:49:02 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 112.7 seconds
RetCode: 0
Status:  OK  
CheckDir: PANR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PANR.buildbin-libdir PANR.Rcheck && mkdir PANR.buildbin-libdir PANR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PANR.buildbin-libdir PANR_1.22.0.tar.gz >PANR.Rcheck\00install.out 2>&1 && cp PANR.Rcheck\00install.out PANR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=PANR.buildbin-libdir --install="check:PANR-install.out" --force-multiarch --no-vignettes --timings PANR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/PANR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.22.0'
* 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
** checking loading without being on the library search path ... 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 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
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 27.67   0.08   27.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
fitNULL 26.37   0.16   26.54
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/PANR.Rcheck/00check.log'
for details.


PANR.Rcheck/00install.out:


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_1.22.0.zip
* DONE (PANR)

PANR.Rcheck/examples_i386/PANR-Ex.timings:

nameusersystemelapsed
BetaMixture-class000
PAN-class000
SNR2p000
assoScore0.010.000.02
buildPAN0.640.000.64
cosineSim000
data-Bakal20070.020.010.03
exportPAN000
fitBM000
fitNULL27.67 0.0827.75
infer0.270.000.27
p2SNR000
permNULL0.000.020.02
pvclustModule000
sigModules000
summarize0.070.000.06
view0.210.010.24
viewLegend000
viewNestedModules000
viewPAN000

PANR.Rcheck/examples_x64/PANR-Ex.timings:

nameusersystemelapsed
BetaMixture-class000
PAN-class000
SNR2p000
assoScore0.020.000.01
buildPAN0.860.030.89
cosineSim000
data-Bakal20070.000.030.04
exportPAN000
fitBM000
fitNULL26.37 0.1626.54
infer0.600.020.61
p2SNR000
permNULL0.010.010.03
pvclustModule0.000.000.03
sigModules000
summarize0.060.000.06
view0.420.020.44
viewLegend000
viewNestedModules000
viewPAN000