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BioC 2.13: CHECK report for hopach on zin1

This page was generated on 2014-04-05 09:47:07 -0700 (Sat, 05 Apr 2014).

Package 348/750HostnameOS / ArchBUILDCHECKBUILD BIN
hopach 2.22.0
Katherine S. Pollard
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/hopach
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: hopach
Version: 2.22.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings hopach_2.22.0.tar.gz
StartedAt: 2014-04-05 01:51:38 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:52:59 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 81.4 seconds
RetCode: 0
Status:  OK 
CheckDir: hopach.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/hopach.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hopach/DESCRIPTION’ ... OK
* this is package ‘hopach’ version ‘2.22.0’
* 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 ... [3s/3s] OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘cluster’ ‘methods’
A package should be listed in only one of these fields.
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘hopach.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [48s/48s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
bootplot   10.721  0.388  11.189
boot2fuzzy 10.976  0.120  11.116
makeoutput 10.808  0.004  10.866
bootstrap  10.541  0.000  10.559
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/hopach.Rcheck/00check.log’
for details.

hopach.Rcheck/00install.out:

* installing *source* package ‘hopach’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rdistances.c -o Rdistances.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c hdist.c -o hdist.o
gcc -std=gnu99 -shared -L/usr/local/lib -o hopach.so Rdistances.o hdist.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/hopach.Rcheck/hopach/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::image’ when loading ‘hopach’
Creating a generic function from function ‘as.hdist’ in package ‘hopach’
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘hopach’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graphics::image’ when loading ‘hopach’
* DONE (hopach)

hopach.Rcheck/hopach-Ex.timings:

nameusersystemelapsed
boot2fuzzy10.976 0.12011.116
bootplot10.721 0.38811.189
bootstrap10.541 0.00010.559
correlationordering0.0520.0000.052
disscosangle0.0040.0000.004
distancematrix0.0120.0000.014
dplot0.0840.0000.083
hdist-class0.0160.0040.020
hopach0.5880.0000.592
hopach.internal0.0000.0000.001
hopach2tree0.3040.0000.433
labelstomss0.2800.0000.281
makeoutput10.808 0.00410.866
prune1.8680.0001.882