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CHECK report for hopach on tokay2

This page was generated on 2020-10-17 11:56:50 -0400 (Sat, 17 Oct 2020).

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 830/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hopach 2.48.0
Katherine S. Pollard
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/hopach
Branch: RELEASE_3_11
Last Commit: f197761
Last Changed Date: 2020-04-27 14:10:24 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hopach
Version: 2.48.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hopach.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings hopach_2.48.0.tar.gz
StartedAt: 2020-10-17 05:00:17 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:07:05 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 407.5 seconds
RetCode: 0
Status:  OK  
CheckDir: hopach.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hopach.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings hopach_2.48.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/hopach.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 'hopach/DESCRIPTION' ... OK
* this is package 'hopach' version '2.48.0'
* 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-3.11-bioc/R/library/hopach/libs/i386/hopach.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-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
bootplot   7.56      0    7.57
bootstrap  7.12      0    7.13
boot2fuzzy 6.56      0    6.71
makeoutput 6.14      0   10.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
bootstrap  9.71   0.00    9.72
makeoutput 8.02   0.00    8.01
boot2fuzzy 7.59   0.02   12.47
bootplot   6.83   0.00    7.86
* 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-3.11-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 https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/hopach_2.48.0.tar.gz && rm -rf hopach.buildbin-libdir && mkdir hopach.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hopach.buildbin-libdir hopach_2.48.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL hopach_2.48.0.zip && rm hopach_2.48.0.tar.gz hopach_2.48.0.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  885k  100  885k    0     0  11.2M      0 --:--:-- --:--:-- --:--:-- 12.3M

install for i386

* installing *source* package 'hopach' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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-3~1.11-/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-3~1.11-/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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/hopach.buildbin-libdir/hopach/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hopach' as hopach_2.48.0.zip
* DONE (hopach)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'hopach' successfully unpacked and MD5 sums checked

Tests output


Example timings

hopach.Rcheck/examples_i386/hopach-Ex.timings

nameusersystemelapsed
boot2fuzzy6.560.006.71
bootplot7.560.007.57
bootstrap7.120.007.13
correlationordering0.020.000.01
disscosangle000
distancematrix000
dplot0.050.000.05
hdist-class0.010.000.01
hopach0.290.000.28
hopach.internal000
hopach2tree0.170.000.17
labelstomss0.150.000.16
makeoutput 6.14 0.0010.59
prune1.60.01.6

hopach.Rcheck/examples_x64/hopach-Ex.timings

nameusersystemelapsed
boot2fuzzy 7.59 0.0212.47
bootplot6.830.007.86
bootstrap9.710.009.72
correlationordering0.050.000.04
disscosangle000
distancematrix000
dplot0.130.000.12
hdist-class0.010.000.02
hopach0.610.000.61
hopach.internal000
hopach2tree0.380.000.38
labelstomss0.320.000.33
makeoutput8.020.008.01
prune1.730.001.74