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BioC 3.5: CHECK report for hopach on veracruz2

This page was generated on 2017-10-18 14:27:36 -0400 (Wed, 18 Oct 2017).

Package 634/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hopach 2.36.0
Katherine S. Pollard
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/hopach
Branch: RELEASE_3_5
Last Commit: 6fd5ebf
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: hopach
Version: 2.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hopach_2.36.0.tar.gz
StartedAt: 2017-10-18 04:50:43 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 04:52:02 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 78.9 seconds
RetCode: 0
Status:  OK 
CheckDir: hopach.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hopach_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/hopach.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hopach/DESCRIPTION’ ... OK
* this is package ‘hopach’ version ‘2.36.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘hopach.pdf’ from 2146Kb to 342Kb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
boot2fuzzy 9.929  0.060  10.249
bootplot   9.251  0.048   9.592
bootstrap  9.085  0.050   9.410
makeoutput 8.994  0.047   9.289
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/hopach.Rcheck/00check.log’
for details.


hopach.Rcheck/00install.out:

* installing *source* package ‘hopach’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rdistances.c -o Rdistances.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hdist.c -o hdist.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o hopach.so Rdistances.o hdist.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/hopach.Rcheck/hopach/libs
** R
** data
** inst
** preparing 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
* DONE (hopach)

hopach.Rcheck/hopach-Ex.timings:

nameusersystemelapsed
boot2fuzzy 9.929 0.06010.249
bootplot9.2510.0489.592
bootstrap9.0850.0509.410
correlationordering0.0310.0010.036
disscosangle0.0020.0000.003
distancematrix0.0080.0010.009
dplot0.0950.0010.101
hdist-class0.0330.0020.035
hopach0.4420.0030.456
hopach.internal0.0000.0000.001
hopach2tree0.2530.0030.262
labelstomss0.2000.0000.206
makeoutput8.9940.0479.289
prune1.4720.0111.528