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CHECK report for QuaternaryProd on tokay1

This page was generated on 2021-02-22 12:40:05 -0500 (Mon, 22 Feb 2021).

To the developers/maintainers of the QuaternaryProd package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1437/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuaternaryProd 1.24.0
Carl Tony Fakhry
Snapshot Date: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 2021)
URL: https://git.bioconductor.org/packages/QuaternaryProd
Branch: RELEASE_3_12
Last Commit: b94d3a2
Last Changed Date: 2020-10-27 11:10:17 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: QuaternaryProd
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QuaternaryProd.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings QuaternaryProd_1.24.0.tar.gz
StartedAt: 2021-02-22 06:02:28 -0500 (Mon, 22 Feb 2021)
EndedAt: 2021-02-22 06:04:21 -0500 (Mon, 22 Feb 2021)
EllapsedTime: 112.1 seconds
RetCode: 0
Status:   OK   
CheckDir: QuaternaryProd.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:QuaternaryProd.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings QuaternaryProd_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/QuaternaryProd.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 'QuaternaryProd/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'QuaternaryProd' version '1.24.0'
* 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 'QuaternaryProd' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 17.7Mb
  sub-directories of 1Mb or more:
    extdata  15.3Mb
    libs      2.2Mb
* 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/QuaternaryProd/libs/i386/QuaternaryProd.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/QuaternaryProd/libs/x64/QuaternaryProd.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
RunCRE_HSAStringDB 27.56   0.49   28.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
RunCRE_HSAStringDB 20.89   0.07   20.96
* 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/QuaternaryProd.Rcheck/00check.log'
for details.



Installation output

QuaternaryProd.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/QuaternaryProd_1.24.0.tar.gz && rm -rf QuaternaryProd.buildbin-libdir && mkdir QuaternaryProd.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=QuaternaryProd.buildbin-libdir QuaternaryProd_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL QuaternaryProd_1.24.0.zip && rm QuaternaryProd_1.24.0.tar.gz QuaternaryProd_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
 52 10.7M   52 5824k    0     0  65.3M      0 --:--:-- --:--:-- --:--:-- 67.7M
100 10.7M  100 10.7M    0     0  63.8M      0 --:--:-- --:--:-- --:--:-- 64.8M

install for i386

* installing *source* package 'QuaternaryProd' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c QuaternaryProd.cpp -o QuaternaryProd.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c QuaternaryProdUtils.cpp -o QuaternaryProdUtils.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o QuaternaryProd.dll tmp.def QuaternaryProd.o QuaternaryProdUtils.o RcppExports.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/QuaternaryProd.buildbin-libdir/00LOCK-QuaternaryProd/00new/QuaternaryProd/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'QuaternaryProd'
    finding HTML links ... done
    QP_Pmf                                  html  
    QP_Probability                          html  
    QP_Pvalue                               html  
    QP_SigPvalue                            html  
    QP_Support                              html  
    QuaternaryProd-package                  html  
    RunCRE_HSAStringDB                      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 'QuaternaryProd' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c QuaternaryProd.cpp -o QuaternaryProd.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c QuaternaryProdUtils.cpp -o QuaternaryProdUtils.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o QuaternaryProd.dll tmp.def QuaternaryProd.o QuaternaryProdUtils.o RcppExports.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/QuaternaryProd.buildbin-libdir/QuaternaryProd/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QuaternaryProd' as QuaternaryProd_1.24.0.zip
* DONE (QuaternaryProd)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'QuaternaryProd' successfully unpacked and MD5 sums checked

Tests output


Example timings

QuaternaryProd.Rcheck/examples_i386/QuaternaryProd-Ex.timings

nameusersystemelapsed
QP_Pmf0.580.000.58
QP_Probability0.020.000.01
QP_Pvalue0.030.000.03
QP_SigPvalue0.050.000.04
QP_Support0.020.000.02
RunCRE_HSAStringDB27.56 0.4928.16

QuaternaryProd.Rcheck/examples_x64/QuaternaryProd-Ex.timings

nameusersystemelapsed
QP_Pmf0.420.000.46
QP_Probability000
QP_Pvalue0.030.000.03
QP_SigPvalue0.030.000.03
QP_Support000
RunCRE_HSAStringDB20.89 0.0720.96