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CHECK report for hopach on tokay1

This page was generated on 2021-05-05 12:12:07 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the hopach package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 845/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hopach 2.50.0  (landing page)
Katherine S. Pollard
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/hopach
Branch: RELEASE_3_12
Last Commit: 22812f7
Last Changed Date: 2020-10-27 10:24:47 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
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: hopach
Version: 2.50.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hopach.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings hopach_2.50.0.tar.gz
StartedAt: 2021-05-05 03:42:21 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 03:45:13 -0400 (Wed, 05 May 2021)
EllapsedTime: 172.0 seconds
RetCode: 0
Status:   OK   
CheckDir: hopach.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:hopach.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings hopach_2.50.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/hopach.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'hopach/DESCRIPTION' ... OK
* this is package 'hopach' version '2.50.0'
* 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 'hopach' 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 ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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/hopach/libs/i386/hopach.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/hopach/libs/x64/hopach.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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
bootstrap  12.11      0   12.28
boot2fuzzy 11.75      0   13.10
bootplot   11.54      0   11.62
makeoutput 10.87      0   10.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
makeoutput 13.01      0   13.33
boot2fuzzy 12.75      0   13.75
bootplot   12.47      0   13.29
bootstrap  12.02      0   12.34
* 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/hopach.Rcheck/00check.log'
for details.



Installation output

hopach.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/hopach_2.50.0.tar.gz && rm -rf hopach.buildbin-libdir && mkdir hopach.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hopach.buildbin-libdir hopach_2.50.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL hopach_2.50.0.zip && rm hopach_2.50.0.tar.gz hopach_2.50.0.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  886k  100  886k    0     0  87.3M      0 --:--:-- --:--:-- --:--:-- 96.1M

install for i386

* installing *source* package 'hopach' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rdistances.c -o Rdistances.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hdist.c -o hdist.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o hopach.dll tmp.def Rdistances.o hdist.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/hopach.buildbin-libdir/00LOCK-hopach/00new/hopach/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function from function 'as.hdist' in package 'hopach'
** help
*** installing help indices
  converting help for package 'hopach'
    finding HTML links ... done
    boot2fuzzy                              html  
    bootplot                                html  
    bootstrap                               html  
    correlationordering                     html  
    disscosangle                            html  
    distancematrix                          html  
    dplot                                   html  
    golub                                   html  
    hdist-class                             html  
    hopach                                  html  
    hopach.internal                         html  
    hopach2tree                             html  
    labelstomss                             html  
    makeoutput                              html  
    prune                                   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 'hopach' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rdistances.c -o Rdistances.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hdist.c -o hdist.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o hopach.dll tmp.def Rdistances.o hdist.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/hopach.buildbin-libdir/hopach/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hopach' as hopach_2.50.0.zip
* DONE (hopach)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'hopach' successfully unpacked and MD5 sums checked

Tests output


Example timings

hopach.Rcheck/examples_i386/hopach-Ex.timings

nameusersystemelapsed
boot2fuzzy11.75 0.0013.10
bootplot11.54 0.0011.62
bootstrap12.11 0.0012.28
correlationordering0.040.000.05
disscosangle000
distancematrix000
dplot0.090.000.09
hdist-class0.030.000.03
hopach0.580.001.56
hopach.internal000
hopach2tree0.310.001.05
labelstomss0.270.000.26
makeoutput10.87 0.0010.92
prune2.130.022.36

hopach.Rcheck/examples_x64/hopach-Ex.timings

nameusersystemelapsed
boot2fuzzy12.75 0.0013.75
bootplot12.47 0.0013.29
bootstrap12.02 0.0012.34
correlationordering0.050.001.05
disscosangle000
distancematrix0.000.010.02
dplot0.090.000.41
hdist-class0.030.000.03
hopach0.600.000.59
hopach.internal000
hopach2tree0.370.000.38
labelstomss0.300.000.29
makeoutput13.01 0.0013.33
prune1.880.031.91