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Package 265/553HostnameOS / ArchBUILDCHECKBUILD BIN
hopach 2.16.0
Katherine S. Pollard
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/hopach
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: hopach
Version: 2.16.0
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings hopach_2.16.0.tar.gz
StartedAt: 2012-09-24 01:35:57 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 01:37:05 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 68.5 seconds
RetCode: 0
Status:  OK 
CheckDir: hopach.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/hopach.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘2.16.0’
* 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 whether package ‘hopach’ can be installed ... 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 ... NOTE
hopach2tree: warning in matrix(rep(row.labels, 2), nc = 2, dimnames =
  list(NULL, c("label", "medoid"))): partial argument match of 'nc' to
  'ncol'
hopach2tree: warning in matrix(rep(col.labels, 2), nc = 2, dimnames =
  list(NULL, c("label", "medoid"))): partial argument match of 'nc' to
  'ncol'
hopach2tree: warning in matrix(rbind(cdt, c("EWEIGHT", "", "", "",
  array.wts[col.ord]), cbind(paste("GENE", 1:p, "X", sep =
  "")[row.ord], dimnames(data.frame(data))[[1]][row.ord],
  gene.names[row.ord], gene.wts[row.ord], data[row.ord, col.ord])), nr
  = (cdtsize + p + 1), dimnames = list(NULL, NULL)): partial argument
  match of 'nr' to 'nrow'
hopach2tree: warning in matrix(rbind(cdt, c("EWEIGHT", "", "",
  array.wts[col.ord]), cbind(dimnames(data.frame(data))[[1]][row.ord],
  gene.names[row.ord], gene.wts[row.ord], data[row.ord, col.ord])), nr
  = (cdtsize + p + 1), dimnames = list(NULL, NULL)): partial argument
  match of 'nr' to 'nrow'
makeTree: warning in matrix(NA, nc = maxnode, dimnames = list(NULL,
  paste("child", 1:maxnode, sep = ""))): partial argument match of 'nc'
  to 'ncol'
* 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 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/hopach.Rcheck/00check.log’
for details.

hopach.Rcheck/00install.out:

* installing *source* package ‘hopach’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-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-2.10-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/lib64 -o hopach.so Rdistances.o hdist.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/hopach.Rcheck/hopach/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘as.vector’ from package ‘base’ in package ‘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
   ‘hopach.Rnw’ 
** testing if installed package can be loaded

* DONE (hopach)

hopach.Rcheck/hopach-Ex.timings:

nameusersystemelapsed
boot2fuzzy5.4760.0085.488
bootplot4.9840.0044.995
bootstrap5.3730.0005.375
correlationordering0.0640.0000.063
disscosangle0.0040.0000.002
distancematrix0.0080.0000.009
dplot0.10.00.1
hdist-class0.0160.0000.016
hopach0.5520.0000.552
hopach.internal000
hopach2tree0.3280.0000.330
labelstomss0.2880.0000.286
makeoutput5.5680.0005.574
prune2.0600.0082.070