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BioC 3.5: CHECK report for RCASPAR on tokay2

This page was generated on 2017-08-16 13:21:05 -0400 (Wed, 16 Aug 2017).

Package 1073/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCASPAR 1.22.0
Douaa Mugahid , Lars Kaderali
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/RCASPAR
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: RCASPAR
Version: 1.22.0
Command: rm -rf RCASPAR.buildbin-libdir RCASPAR.Rcheck && mkdir RCASPAR.buildbin-libdir RCASPAR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RCASPAR.buildbin-libdir RCASPAR_1.22.0.tar.gz >RCASPAR.Rcheck\00install.out 2>&1 && cp RCASPAR.Rcheck\00install.out RCASPAR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=RCASPAR.buildbin-libdir --install="check:RCASPAR-install.out" --force-multiarch --no-vignettes --timings RCASPAR_1.22.0.tar.gz
StartedAt: 2017-08-16 02:17:57 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:18:35 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 38.2 seconds
RetCode: 0
Status:  OK  
CheckDir: RCASPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RCASPAR.buildbin-libdir RCASPAR.Rcheck && mkdir RCASPAR.buildbin-libdir RCASPAR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RCASPAR.buildbin-libdir RCASPAR_1.22.0.tar.gz >RCASPAR.Rcheck\00install.out 2>&1 && cp RCASPAR.Rcheck\00install.out RCASPAR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=RCASPAR.buildbin-libdir --install="check:RCASPAR-install.out" --force-multiarch --no-vignettes --timings RCASPAR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/RCASPAR.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 'RCASPAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCASPAR' 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 'RCASPAR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
kmplt: no visible global function definition for 'plot'
kmplt_svrl: no visible global function definition for 'plot'
kmplt_svrl: no visible global function definition for 'lines'
kmplt_svrl: no visible global function definition for 'legend'
logrnk: no visible global function definition for 'pchisq'
pltgamma: no visible global function definition for 'plot'
pltprior: no visible global function definition for 'persp'
survivAURC: no visible global function definition for 'plot'
weights_BLH: no visible global function definition for 'optim'
Undefined global functions or variables:
  legend lines optim pchisq persp plot
Consider adding
  importFrom("graphics", "legend", "lines", "persp", "plot")
  importFrom("stats", "optim", "pchisq")
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
** running examples for arch 'x64' ... OK
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/RCASPAR.Rcheck/00check.log'
for details.


RCASPAR.Rcheck/00install.out:


install for i386

* installing *source* package 'RCASPAR' ...
** 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 'RCASPAR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RCASPAR' as RCASPAR_1.22.0.zip
* DONE (RCASPAR)

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

nameusersystemelapsed
Bergamaschi0.080.000.08
RCASPAR-package1.010.041.06
STpredictor_BLH0.220.030.25
STpredictor_xvBLH3.120.003.12
deriv_weight_estimator_BLH0.000.020.02
deriv_weight_estimator_BLH_noprior000
kmplt000
kmplt_svrl000
logrnk000
pltgamma0.000.020.01
pltprior000
simpson000
survData000
survivAURC0.090.000.10
survivROC0.030.000.03
trapezoid000
weight_estimator_BLH000
weight_estimator_BLH_noprior000
weights_BLH0.000.010.01
weights_xvBLH0.030.000.03

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

nameusersystemelapsed
Bergamaschi0.060.000.06
RCASPAR-package1.140.031.40
STpredictor_BLH0.160.000.16
STpredictor_xvBLH0.570.010.59
deriv_weight_estimator_BLH000
deriv_weight_estimator_BLH_noprior0.000.020.02
kmplt000
kmplt_svrl0.020.000.01
logrnk000
pltgamma000
pltprior000
simpson000
survData000
survivAURC0.100.000.09
survivROC0.030.000.03
trapezoid000
weight_estimator_BLH000
weight_estimator_BLH_noprior0.000.010.02
weights_BLH0.020.000.01
weights_xvBLH0.030.000.03