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This page was generated on 2022-04-13 12:06:42 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for hopach on tokay2


To the developers/maintainers of the hopach package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hopach.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 882/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hopach 2.54.0  (landing page)
Katherine S. Pollard
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/hopach
git_branch: RELEASE_3_14
git_last_commit: 783c88d
git_last_commit_date: 2021-10-26 11:47:22 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: hopach
Version: 2.54.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hopach.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings hopach_2.54.0.tar.gz
StartedAt: 2022-04-12 21:11:38 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 21:13:57 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 138.8 seconds
RetCode: 0
Status:   OK  
CheckDir: hopach.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hopach.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings hopach_2.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/hopach.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.54.0'
* 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-3.14-bioc/R/library/hopach/libs/i386/hopach.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-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
makeoutput 7.92   0.00    8.17
boot2fuzzy 7.83   0.02    8.34
bootplot   7.71   0.00    7.70
bootstrap  6.80   0.00    6.80
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
boot2fuzzy 7.10      0    7.09
bootstrap  6.98      0    6.98
makeoutput 6.53      0    6.54
bootplot   6.47      0    6.47
* 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-3.14-bioc/meat/hopach.Rcheck/00check.log'
for details.



Installation output

hopach.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/hopach_2.54.0.tar.gz && rm -rf hopach.buildbin-libdir && mkdir hopach.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hopach.buildbin-libdir hopach_2.54.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL hopach_2.54.0.zip && rm hopach_2.54.0.tar.gz hopach_2.54.0.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
 79  883k   79  698k    0     0   749k      0  0:00:01 --:--:--  0:00:01  749k
100  883k  100  883k    0     0   646k      0  0:00:01  0:00:01 --:--:--  647k

install for i386

* installing *source* package 'hopach' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/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-3~1.14-/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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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-3~1.14-/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-3~1.14-/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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/hopach.buildbin-libdir/hopach/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hopach' as hopach_2.54.0.zip
* DONE (hopach)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'hopach' successfully unpacked and MD5 sums checked

Tests output


Example timings

hopach.Rcheck/examples_i386/hopach-Ex.timings

nameusersystemelapsed
boot2fuzzy7.830.028.34
bootplot7.710.007.70
bootstrap6.80.06.8
correlationordering0.010.000.02
disscosangle000
distancematrix000
dplot0.050.000.05
hdist-class0.010.000.02
hopach0.280.000.28
hopach.internal000
hopach2tree0.190.000.18
labelstomss0.160.000.16
makeoutput7.920.008.17
prune1.30.01.3

hopach.Rcheck/examples_x64/hopach-Ex.timings

nameusersystemelapsed
boot2fuzzy7.100.007.09
bootplot6.470.006.47
bootstrap6.980.006.98
correlationordering0.030.000.03
disscosangle000
distancematrix000
dplot0.060.000.07
hdist-class000
hopach0.330.000.32
hopach.internal000
hopach2tree0.210.000.21
labelstomss0.170.000.17
makeoutput6.530.006.54
prune1.640.011.66