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BioC 3.4: CHECK report for RCASPAR on moscato1

This page was generated on 2016-09-21 03:43:28 -0700 (Wed, 21 Sep 2016).

Package 982/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCASPAR 1.19.0
Douaa Mugahid , Lars Kaderali
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCASPAR
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  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RCASPAR
Version: 1.19.0
Command: rm -rf RCASPAR.buildbin-libdir RCASPAR.Rcheck && mkdir RCASPAR.buildbin-libdir RCASPAR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RCASPAR.buildbin-libdir RCASPAR_1.19.0.tar.gz >RCASPAR.Rcheck\00install.out 2>&1 && cp RCASPAR.Rcheck\00install.out RCASPAR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RCASPAR.buildbin-libdir --install="check:RCASPAR-install.out" --force-multiarch --no-vignettes --timings RCASPAR_1.19.0.tar.gz
StartedAt: 2016-09-20 14:56:15 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 14:57:14 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 58.2 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RCASPAR.buildbin-libdir RCASPAR_1.19.0.tar.gz >RCASPAR.Rcheck\00install.out 2>&1 && cp RCASPAR.Rcheck\00install.out RCASPAR-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RCASPAR.buildbin-libdir --install="check:RCASPAR-install.out" --force-multiarch --no-vignettes --timings RCASPAR_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/RCASPAR.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 'RCASPAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCASPAR' 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 '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
Examples with CPU or elapsed time > 5s
                  user system elapsed
STpredictor_xvBLH 7.05   0.03    7.18
** 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
  'D:/biocbld/bbs-3.4-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_1.19.0.zip
* DONE (RCASPAR)

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

nameusersystemelapsed
Bergamaschi0.030.000.04
RCASPAR-package0.610.000.64
STpredictor_BLH0.090.010.10
STpredictor_xvBLH7.050.037.18
deriv_weight_estimator_BLH0.020.000.02
deriv_weight_estimator_BLH_noprior000
kmplt0.010.000.01
kmplt_svrl000
logrnk0.020.000.02
pltgamma000
pltprior000
simpson000
survData000
survivAURC0.150.000.14
survivROC0.030.001.03
trapezoid000
weight_estimator_BLH000
weight_estimator_BLH_noprior0.010.000.02
weights_BLH0.020.000.02
weights_xvBLH0.090.020.10

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

nameusersystemelapsed
Bergamaschi0.020.010.03
RCASPAR-package0.740.020.82
STpredictor_BLH0.180.000.18
STpredictor_xvBLH0.960.010.98
deriv_weight_estimator_BLH0.020.000.01
deriv_weight_estimator_BLH_noprior000
kmplt000
kmplt_svrl0.010.000.02
logrnk000
pltgamma0.020.000.02
pltprior000
simpson000
survData000
survivAURC0.190.000.18
survivROC0.040.000.05
trapezoid000
weight_estimator_BLH000
weight_estimator_BLH_noprior000
weights_BLH0.010.000.01
weights_xvBLH0.080.000.08