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BioC 3.4: CHECK report for PANR on moscato1

This page was generated on 2016-09-21 03:43:50 -0700 (Wed, 21 Sep 2016).

Package 863/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PANR 1.19.0
Xin Wang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PANR
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PANR
Version: 1.19.0
Command: rm -rf PANR.buildbin-libdir PANR.Rcheck && mkdir PANR.buildbin-libdir PANR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PANR.buildbin-libdir PANR_1.19.0.tar.gz >PANR.Rcheck\00install.out 2>&1 && cp PANR.Rcheck\00install.out PANR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=PANR.buildbin-libdir --install="check:PANR-install.out" --force-multiarch --no-vignettes --timings PANR_1.19.0.tar.gz
StartedAt: 2016-09-20 13:32:49 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 13:35:06 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 136.3 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PANR.buildbin-libdir PANR_1.19.0.tar.gz >PANR.Rcheck\00install.out 2>&1 && cp PANR.Rcheck\00install.out PANR-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=PANR.buildbin-libdir --install="check:PANR-install.out" --force-multiarch --no-vignettes --timings PANR_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-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 '1.19.0'
* 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 36.04   0.04    36.4
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
fitNULL 33.72   0.05    35.4
* 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
  'D:/biocbld/bbs-3.4-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_1.19.0.zip
* DONE (PANR)

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

nameusersystemelapsed
BetaMixture-class0.020.000.02
PAN-class000
SNR2p000
assoScore0.010.000.02
buildPAN0.640.020.65
cosineSim000
data-Bakal20070.030.000.03
exportPAN000
fitBM000
fitNULL36.04 0.0436.40
infer0.640.000.64
p2SNR000
permNULL0.030.000.03
pvclustModule000
sigModules000
summarize0.030.000.03
view0.360.000.37
viewLegend0.010.000.02
viewNestedModules000
viewPAN000

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

nameusersystemelapsed
BetaMixture-class000
PAN-class000
SNR2p000
assoScore0.010.000.02
buildPAN0.960.061.01
cosineSim000
data-Bakal20070.010.010.04
exportPAN000
fitBM000
fitNULL33.72 0.0535.40
infer0.440.000.43
p2SNR000
permNULL0.020.000.02
pvclustModule000
sigModules000
summarize0.030.000.03
view0.220.020.24
viewLegend000
viewNestedModules000
viewPAN000