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CHECK report for ASGSCA on tokay1

This page was generated on 2020-11-24 11:57:30 -0500 (Tue, 24 Nov 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ASGSCA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 92/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASGSCA 1.24.0
Hela Romdhani
Snapshot Date: 2020-11-23 14:42:42 -0500 (Mon, 23 Nov 2020)
URL: https://git.bioconductor.org/packages/ASGSCA
Branch: RELEASE_3_12
Last Commit: 7f9f2f0
Last Changed Date: 2020-10-27 10:59:45 -0500 (Tue, 27 Oct 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: ASGSCA
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASGSCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ASGSCA_1.24.0.tar.gz
StartedAt: 2020-11-24 00:26:32 -0500 (Tue, 24 Nov 2020)
EndedAt: 2020-11-24 00:34:35 -0500 (Tue, 24 Nov 2020)
EllapsedTime: 483.3 seconds
RetCode: 0
Status:  OK  
CheckDir: ASGSCA.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:ASGSCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ASGSCA_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ASGSCA.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ASGSCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ASGSCA' version '1.24.0'
* 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 'ASGSCA' 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 ... 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
GSCAestim: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
GSCA           101.50   0.02  101.51
ASGSCA-package  94.21   0.06   94.28
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
GSCA           116.51   0.01  116.98
ASGSCA-package 113.92   0.06  114.36
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/ASGSCA.Rcheck/00check.log'
for details.



Installation output

ASGSCA.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/ASGSCA_1.24.0.tar.gz && rm -rf ASGSCA.buildbin-libdir && mkdir ASGSCA.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASGSCA.buildbin-libdir ASGSCA_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ASGSCA_1.24.0.zip && rm ASGSCA_1.24.0.tar.gz ASGSCA_1.24.0.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  612k  100  612k    0     0  16.1M      0 --:--:-- --:--:-- --:--:-- 18.1M

install for i386

* installing *source* package 'ASGSCA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ASGSCA'
    finding HTML links ... done
    ASGSCA-package                          html  
    B0                                      html  
    GSCA                                    html  
    GSCAestim                               html  
    GenPhen                                 html  
    QCAHS                                   html  
    ResQCAHS                                html  
    W0                                      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 'ASGSCA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ASGSCA' as ASGSCA_1.24.0.zip
* DONE (ASGSCA)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ASGSCA' successfully unpacked and MD5 sums checked

Tests output


Example timings

ASGSCA.Rcheck/examples_i386/ASGSCA-Ex.timings

nameusersystemelapsed
ASGSCA-package94.21 0.0694.28
GSCA101.50 0.02101.51
GSCAestim0.000.010.02

ASGSCA.Rcheck/examples_x64/ASGSCA-Ex.timings

nameusersystemelapsed
ASGSCA-package113.92 0.06114.36
GSCA116.51 0.01116.98
GSCAestim0.000.020.02