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CHECK report for AlphaBeta on tokay1

This page was generated on 2020-08-13 11:45:49 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE AlphaBeta PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 43/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaBeta 1.3.3
Yadollah Shahryary Dizaji
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/AlphaBeta
Branch: master
Last Commit: 3497a14
Last Changed Date: 2020-06-06 09:46:58 -0400 (Sat, 06 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AlphaBeta
Version: 1.3.3
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AlphaBeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AlphaBeta_1.3.3.tar.gz
StartedAt: 2020-08-13 05:58:05 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 06:18:14 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 1209.2 seconds
RetCode: 0
Status:  OK  
CheckDir: AlphaBeta.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AlphaBeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AlphaBeta_1.3.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/AlphaBeta.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AlphaBeta/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AlphaBeta' version '1.3.3'
* package encoding: UTF-8
* 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 'AlphaBeta' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
ABplot: no visible binding for global variable 'delta.t'
ABplot: no visible binding for global variable 'div.obs'
BOOTmodel : LSE_intercept: no visible binding for global variable 'sel'
BOOTmodel: no visible binding for global variable 'sel'
BOOTmodel: multiple local function definitions for 'divergence' with
  different formal arguments
plotPedigree: no visible binding for global variable 'meth'
plotPedigree: no visible binding for global variable 'V1'
plotPedigree: no visible binding for global variable 'V2'
Undefined global functions or variables:
  V1 V2 delta.t div.obs meth sel
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
BOOTmodel      122.22   0.00  122.24
ABselectMM     121.93   0.00  122.18
ABselectUU     113.83   0.00  113.83
ABneutral       88.33   0.00   96.44
ABneutralSOMA    9.23   0.01    9.26
ABselectUUSOMA   8.72   0.01    8.73
ABselectMMSOMA   5.75   0.02    5.76
buildPedigree    0.83   0.05    5.57
rc.meth.lvl      0.50   0.01    5.56
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
ABselectUU     164.59   0.00  165.09
BOOTmodel      159.89   0.01  160.16
ABselectMM     122.88   0.00  123.06
ABneutral      110.89   0.02  111.24
ABselectUUSOMA  12.08   0.02   12.61
ABneutralSOMA   12.04   0.01   12.08
ABselectMMSOMA   7.66   0.01    7.67
buildPedigree    1.04   0.03    6.08
rc.meth.lvl      0.71   0.02    5.84
* 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-3.12-bioc/meat/AlphaBeta.Rcheck/00check.log'
for details.



Installation output

AlphaBeta.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/AlphaBeta_1.3.3.tar.gz && rm -rf AlphaBeta.buildbin-libdir && mkdir AlphaBeta.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AlphaBeta.buildbin-libdir AlphaBeta_1.3.3.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL AlphaBeta_1.3.3.zip && rm AlphaBeta_1.3.3.tar.gz AlphaBeta_1.3.3.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 2532k  100 2532k    0     0  15.4M      0 --:--:-- --:--:-- --:--:-- 15.8M

install for i386

* installing *source* package 'AlphaBeta' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AlphaBeta'
    finding HTML links ... done
    ABneutral                               html  
    ABneutralSOMA                           html  
    ABnull                                  html  
    ABplot                                  html  
    ABselectMM                              html  
    ABselectMMSOMA                          html  
    ABselectUU                              html  
    ABselectUUSOMA                          html  
    BOOTmodel                               html  
    FtestRSS                                html  
    buildPedigree                           html  
    dMatrix                                 html  
    plotPedigree                            html  
    rc.meth.lvl                             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 'AlphaBeta' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AlphaBeta' as AlphaBeta_1.3.3.zip
* DONE (AlphaBeta)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'AlphaBeta' successfully unpacked and MD5 sums checked

Tests output


Example timings

AlphaBeta.Rcheck/examples_i386/AlphaBeta-Ex.timings

nameusersystemelapsed
ABneutral88.33 0.0096.44
ABneutralSOMA9.230.019.26
ABnull0.030.000.03
ABplot0.440.000.44
ABselectMM121.93 0.00122.18
ABselectMMSOMA5.750.025.76
ABselectUU113.83 0.00113.83
ABselectUUSOMA8.720.018.73
BOOTmodel122.22 0.00122.24
FtestRSS0.010.000.01
buildPedigree0.830.055.57
dMatrix0.130.000.12
plotPedigree0.080.000.08
rc.meth.lvl0.500.015.56

AlphaBeta.Rcheck/examples_x64/AlphaBeta-Ex.timings

nameusersystemelapsed
ABneutral110.89 0.02111.24
ABneutralSOMA12.04 0.0112.08
ABnull0.020.020.03
ABplot0.460.000.47
ABselectMM122.88 0.00123.06
ABselectMMSOMA7.660.017.67
ABselectUU164.59 0.00165.09
ABselectUUSOMA12.08 0.0212.61
BOOTmodel159.89 0.01160.16
FtestRSS0.010.000.01
buildPedigree1.040.036.08
dMatrix0.210.000.22
plotPedigree0.140.000.14
rc.meth.lvl0.710.025.84