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This page was generated on 2023-01-02 09:00:33 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 palomino5


To the developers/maintainers of the hopach package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 908/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hopach 2.59.0  (landing page)
Katherine S. Pollard
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/hopach
git_branch: master
git_last_commit: 7682e84
git_last_commit_date: 2022-11-01 10:38:03 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: hopach
Version: 2.59.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hopach.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings hopach_2.59.0.tar.gz
StartedAt: 2022-12-29 00:32:32 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 00:33:30 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 57.6 seconds
RetCode: 0
Status:   OK  
CheckDir: hopach.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hopach.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings hopach_2.59.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/hopach.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'hopach/DESCRIPTION' ... OK
* this is package 'hopach' version '2.59.0'
* 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
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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
* 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 x64 is not available
File 'F:/biocbuild/bbs-3.17-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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'hopach.pdf' from 2173Kb to 334Kb
  consider running tools::compactPDF() on these files
* checking files in 'vignettes' ... OK
* checking examples ... OK
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/hopach.Rcheck/00check.log'
for details.



Installation output

hopach.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL hopach
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'hopach' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rdistances.c -o Rdistances.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hdist.c -o hdist.o
gcc -shared -s -static-libgcc -o hopach.dll tmp.def Rdistances.o hdist.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-hopach/00new/hopach/libs/x64
** 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
** 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
* DONE (hopach)

Tests output


Example timings

hopach.Rcheck/hopach-Ex.timings

nameusersystemelapsed
boot2fuzzy4.360.084.44
bootplot4.000.014.01
bootstrap4.010.144.16
correlationordering0.020.000.01
disscosangle000
distancematrix0.010.000.02
dplot0.050.000.05
hdist-class0.010.000.01
hopach0.250.000.25
hopach.internal000
hopach2tree0.150.020.16
labelstomss0.140.000.14
makeoutput4.090.034.12
prune0.840.030.88