BioC 2.12: CHECK report for hopach on george2

Package: hopach

Version: 2.20.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings hopach_2.20.0.tar.gz

StartedAt: 2013-10-09 02:33:35 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:35:17 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 102.3 seconds

RetCode: 0

Status:  OK

CheckDir: hopach.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/hopach.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘2.20.0’
* 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 ... [6s/6s] 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 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 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 ... [37s/38s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
boot2fuzzy 8.060  0.012   8.110
bootstrap  7.444  0.016   7.734
makeoutput 7.397  0.008   7.860
bootplot   7.213  0.024   7.253
* 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/hopach.Rcheck/00check.log’
for details.

* installing *source* package ‘hopach’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-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-2.12-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-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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
** testing if installed package can be loaded
* DONE (hopach)

name	user	system	elapsed
boot2fuzzy	8.060	0.012	8.110
bootplot	7.213	0.024	7.253
bootstrap	7.444	0.016	7.734
correlationordering	0.088	0.012	0.101
disscosangle	0.016	0.004	0.018
distancematrix	0.044	0.000	0.045
dplot	0.124	0.004	0.128
hdist-class	0.224	0.008	0.231
hopach	0.776	0.012	0.790
hopach.internal	0.012	0.000	0.011
hopach2tree	0.476	0.000	0.504
labelstomss	0.380	0.000	0.399
makeoutput	7.397	0.008	7.860
prune	2.552	0.000	2.552