BioC 2.13: CHECK report for cn.farms on zin1

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/cn.farms.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 ‘cn.farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.farms’ version ‘1.10.0’
* 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 ‘cn.farms’ can be installed ... [14s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘snow’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘ff’ ‘methods’ ‘snow’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 R/sysdata.rda ... 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 files in ‘vignettes’ ... OK
* checking examples ... [21s/21s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/cn.farms.Rcheck/00check.log’
for details.

* installing *source* package ‘cn.farms’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c laplace.cpp -o laplace.o
laplace.cpp: In function ‘SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
laplace.cpp:442:6: warning: unused variable ‘method’ [-Wunused-variable]
laplace.cpp: In function ‘void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)’:
laplace.cpp:368:57: warning: ‘I1right’ may be used uninitialized in this function [-Wuninitialized]
laplace.cpp:367:53: warning: ‘I1left’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sparse_farms.c -o sparse_farms.o
g++ -shared -L/usr/local/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/cn.farms.Rcheck/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.farms)

name	user	system	elapsed
combineData	1.220	0.036	1.304
createAnnotation	0.004	0.000	0.003
distributionDistance	0.296	0.008	0.306
dnaCopySf	0.120	0.004	0.122
fragLengCorr	2.940	0.004	2.948
mlSummarization	4.052	0.064	4.134
normalizeAverage	0.000	0.000	0.004
normalizeCels	0.004	0.000	0.003
normalizeNpData	0.004	0.000	0.002
plotDendrogram	0.124	0.000	0.123
plotDensity	0.672	0.024	0.699
plotEvalIc	0.552	0.004	0.556
plotRegions	0.141	0.008	0.152
plotSmoothScatter	0.480	0.004	0.488
plotViolines	0.136	0.004	0.139
slSummarization	3.416	0.012	3.432
sparseFarmsC	0.000	0.000	0.003
summarizeFarmsExact	0.012	0.000	0.010
summarizeFarmsExact2	0.004	0.004	0.009
summarizeFarmsExact3	0.008	0.004	0.010
summarizeFarmsGaussian	0.004	0.000	0.005
summarizeFarmsMethods	0.004	0.000	0.004
summarizeFarmsVariational	0.008	0.000	0.007
summarizeWindowBps	0.012	0.000	0.010
summarizeWindowMethods	0.004	0.000	0.005
summarizeWindowStd	0.008	0.000	0.006

BioC 2.13: CHECK report for cn.farms on zin1

Summary

Command output