BioC 2.9: CHECK report for flowClust on wilson2

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/flowClust.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowClust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowClust’ version ‘2.12.1’
* 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 ‘flowClust’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Class "Ulist" is defined (with package slot ‘rrcov’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘flowClust’
  Warning: Class "Uvector" is defined (with package slot ‘rrcov’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘flowClust’
  Warning: value of 'results' option should be lowercase
  Warning: value of 'results' option should be lowercase
See ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/flowClust.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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
flowClust: no visible global function definition for ‘mclapply’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  ‘Ulist’ ‘Uvector’
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... 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

WARNING: There were 2 warnings, see
  ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/flowClust.Rcheck/00check.log’
for details

* installing *source* package ‘flowClust’ ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c BoxCox.c -o BoxCox.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Nu.c -o Nu.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c flowClust.c -o flowClust.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c flowClustGaussian.c -o flowClustGaussian.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c ranMVNT.c -o ranMVNT.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o flowClust.so BoxCox.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/flowClust.Rcheck/flowClust/libs
** R
** data
** inst
** preparing package for lazy loading
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning: replacing previous import ‘.__C__character’ when loading ‘methods’
Warning: Class "Ulist" is defined (with package slot ‘rrcov’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘flowClust’
Warning: Class "Uvector" is defined (with package slot ‘rrcov’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘flowClust’
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘flowClust.Rnw’ 
Warning: value of 'results' option should be lowercase
Warning: value of 'results' option should be lowercase
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning message:
replacing previous import ‘.__C__character’ when loading ‘methods’ 

* DONE (flowClust)

name	user	system	elapsed
SimulateMixture	0.012	0.000	0.011
box	0.040	0.004	0.045
flowClust	2.912	0.020	2.937
tmixFilter	2.856	0.016	2.879

Summary

Command output