Back to Multiple platform build/check report for BioC 3.14
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-22 12:04:17 -0400 (Fri, 22 Oct 2021).

CHECK results for AlphaBeta on riesling1

To the developers/maintainers of the AlphaBeta package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AlphaBeta.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 43/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaBeta 1.7.1  (landing page)
Yadollah Shahryary Dizaji
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/AlphaBeta
git_branch: master
git_last_commit: c1297f8
git_last_commit_date: 2021-07-28 06:45:00 -0400 (Wed, 28 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AlphaBeta
Version: 1.7.1
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AlphaBeta.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AlphaBeta_1.7.1.tar.gz
StartedAt: 2021-10-21 23:53:32 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-22 00:03:34 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 602.4 seconds
RetCode: 0
Status:   OK  
CheckDir: AlphaBeta.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AlphaBeta.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AlphaBeta_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/AlphaBeta.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.7.1'
* 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  58.20   0.00   58.25
ABselectUU 55.22   0.00   55.22
ABselectMM 45.47   0.00   45.47
ABneutral  40.14   0.01   40.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
BOOTmodel  60.53   0.00   60.53
ABselectUU 55.92   0.00   55.92
ABselectMM 46.76   0.00   46.78
ABneutral  36.72   0.01   36.73
* 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:/biocbuild/bbs-3.14-bioc/meat/AlphaBeta.Rcheck/00check.log'
for details.



Installation output

AlphaBeta.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/AlphaBeta_1.7.1.tar.gz && rm -rf AlphaBeta.buildbin-libdir && mkdir AlphaBeta.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AlphaBeta.buildbin-libdir AlphaBeta_1.7.1.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL AlphaBeta_1.7.1.zip && rm AlphaBeta_1.7.1.tar.gz AlphaBeta_1.7.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2530k  100 2530k    0     0  4289k      0 --:--:-- --:--:-- --:--:-- 4282k

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_1.7.1.zip
* DONE (AlphaBeta)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'AlphaBeta' successfully unpacked and MD5 sums checked

Tests output


Example timings

AlphaBeta.Rcheck/examples_i386/AlphaBeta-Ex.timings

nameusersystemelapsed
ABneutral40.14 0.0140.16
ABneutralSOMA3.540.003.53
ABnull0.010.000.02
ABplot0.170.030.20
ABselectMM45.47 0.0045.47
ABselectMMSOMA3.110.003.11
ABselectUU55.22 0.0055.22
ABselectUUSOMA3.860.003.86
BOOTmodel58.20 0.0058.25
FtestRSS000
buildPedigree0.490.022.92
dMatrix0.070.000.08
plotPedigree0.070.000.06
rc.meth.lvl0.310.002.81

AlphaBeta.Rcheck/examples_x64/AlphaBeta-Ex.timings

nameusersystemelapsed
ABneutral36.72 0.0136.73
ABneutralSOMA3.620.003.63
ABnull000
ABplot0.170.040.20
ABselectMM46.76 0.0046.78
ABselectMMSOMA2.80.02.8
ABselectUU55.92 0.0055.92
ABselectUUSOMA3.960.003.95
BOOTmodel60.53 0.0060.53
FtestRSS000
buildPedigree0.500.012.94
dMatrix0.070.000.08
plotPedigree0.070.000.06
rc.meth.lvl0.360.022.63