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CHECK report for RCASPAR on tokay2

This page was generated on 2019-10-16 12:25:12 -0400 (Wed, 16 Oct 2019).

Package 1324/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCASPAR 1.30.0
Douaa Mugahid , Lars Kaderali
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/RCASPAR
Branch: RELEASE_3_9
Last Commit: 23053f2
Last Changed Date: 2019-05-02 11:53:26 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RCASPAR
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCASPAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RCASPAR_1.30.0.tar.gz
StartedAt: 2019-10-16 06:22:49 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:23:30 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 40.9 seconds
RetCode: 0
Status:  OK  
CheckDir: RCASPAR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCASPAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RCASPAR_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RCASPAR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.30.0'
* 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
* 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
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 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-3.9-bioc/meat/RCASPAR.Rcheck/00check.log'
for details.



Installation output

RCASPAR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/RCASPAR_1.30.0.tar.gz && rm -rf RCASPAR.buildbin-libdir && mkdir RCASPAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RCASPAR.buildbin-libdir RCASPAR_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RCASPAR_1.30.0.zip && rm RCASPAR_1.30.0.tar.gz RCASPAR_1.30.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 64605  100 64605    0     0   821k      0 --:--:-- --:--:-- --:--:--  901k

install for i386

* installing *source* package 'RCASPAR' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RCASPAR'
    finding HTML links ... done
    Bergamaschi                             html  
    RCASPAR-package                         html  
    STpredictor_BLH                         html  
    STpredictor_xvBLH                       html  
    deriv_weight_estimator_BLH              html  
    deriv_weight_estimator_BLH_noprior      html  
    kmplt                                   html  
    kmplt_svrl                              html  
    logrnk                                  html  
    pltgamma                                html  
    pltprior                                html  
    simpson                                 html  
    survData                                html  
    survivAURC                              html  
    survivROC                               html  
    trapezoid                               html  
    weight_estimator_BLH                    html  
    weight_estimator_BLH_noprior            html  
    weights_BLH                             html  
    weights_xvBLH                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'RCASPAR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RCASPAR' as RCASPAR_1.30.0.zip
* DONE (RCASPAR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RCASPAR' successfully unpacked and MD5 sums checked

Tests output


Example timings

RCASPAR.Rcheck/examples_i386/RCASPAR-Ex.timings

nameusersystemelapsed
Bergamaschi0.020.000.02
RCASPAR-package0.330.010.34
STpredictor_BLH0.030.000.03
STpredictor_xvBLH2.490.022.50
deriv_weight_estimator_BLH000
deriv_weight_estimator_BLH_noprior0.000.010.01
kmplt000
kmplt_svrl000
logrnk000
pltgamma0.010.000.02
pltprior000
simpson000
survData000
survivAURC0.100.000.09
survivROC0.030.000.03
trapezoid000
weight_estimator_BLH000
weight_estimator_BLH_noprior000
weights_BLH0.010.000.02
weights_xvBLH0.040.000.03

RCASPAR.Rcheck/examples_x64/RCASPAR-Ex.timings

nameusersystemelapsed
Bergamaschi0.000.020.02
RCASPAR-package0.420.010.44
STpredictor_BLH0.030.020.05
STpredictor_xvBLH0.440.020.46
deriv_weight_estimator_BLH0.000.020.01
deriv_weight_estimator_BLH_noprior000
kmplt000
kmplt_svrl000
logrnk000
pltgamma000
pltprior0.010.000.01
simpson000
survData000
survivAURC0.110.000.11
survivROC0.030.000.04
trapezoid000
weight_estimator_BLH000
weight_estimator_BLH_noprior0.020.000.01
weights_BLH0.000.020.02
weights_xvBLH0.030.010.04