hopach 2.20.0
Katherine S. Pollard
| Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/hopach | | Last Changed Rev: 75263 / Revision: 81334 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/hopach.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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/7s] OK
* checking installed package size ... NOTE
installed size is 5.0Mb
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 sizes of PDF files under 'inst/doc' ... NOTE
'qpdf' made some significant size reductions:
compacted 'bootplot.pdf' from 391Kb to 34Kb
compacted 'dplot.pdf' from 1609Kb to 160Kb
compacted 'hopach.pdf' from 2146Kb to 343Kb
consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... OK
* checking examples ... [45s/47s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
boot2fuzzy 9.611 0.066 9.951
makeoutput 9.252 0.053 9.796
bootstrap 9.188 0.067 9.534
bootplot 8.699 0.069 8.943
* 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 3 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/hopach.Rcheck/00check.log'
for details.
* installing *source* package 'hopach' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c Rdistances.c -o Rdistances.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c hdist.c -o hdist.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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-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)