BioC 2.12: CHECK report for cn.mops on george2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/cn.mops.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 ‘cn.mops/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.mops’ version ‘1.6.7’
* 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.mops’ can be installed ... [24s/27s] OK
* checking installed package size ... OK
* 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
referencecn.mops: no visible binding for global variable ‘input’
* 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 ... [58s/63s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
cn.mops      22.310  0.200  24.158
exomecn.mops  7.532  0.036   7.912
* 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 was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/cn.mops.Rcheck/00check.log’
for details.

* installing *source* package ‘cn.mops’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_cnmops.c -o R_init_cnmops.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c cnmops.cpp -o cnmops.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c segment.cpp -o segment.o
segment.cpp: In function ‘SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
segment.cpp:60:20: warning: variable ‘globalSd’ set but not used [-Wunused-but-set-variable]
segment.cpp:61:9: warning: variable ‘oldStatistic’ set but not used [-Wunused-but-set-variable]
segment.cpp:62:31: warning: variable ‘maxStatistic’ set but not used [-Wunused-but-set-variable]
segment.cpp:63:40: warning: variable ‘maxIdx’ set but not used [-Wunused-but-set-variable]
segment.cpp:65:9: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
g++ -shared -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/cn.mops.Rcheck/cn.mops/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘cn.mops’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.mops)

name	user	system	elapsed
CNVDetectionResult	0.356	0.008	0.399
calcIntegerCopyNumbers	1.304	0.020	1.505
cn.mops	22.310	0.200	24.158
cnvr	0.468	0.004	0.493
cnvs	0.436	0.000	0.437
exomecn.mops	7.532	0.036	7.912
getReadCountsFromBAM	0.376	0.000	0.423
getSegmentReadCountsFromBAM	0.12	0.00	0.14
gr	0.480	0.004	0.543
haplocn.mops	2.300	0.004	2.748
individualCall	0.508	0.004	0.618
iniCall	0.452	0.004	0.459
integerCopyNumber	0.456	0.000	0.498
localAssessments	0.544	0.000	0.579
makeRobustCNVR	0.833	0.004	0.842
normalizeChromosomes	0.904	0.008	0.914
normalizeGenome	1.304	0.000	1.304
normalizedData	0.492	0.008	0.503
params	0.476	0.008	0.485
posteriorProbs	0.476	0.008	0.601
referencecn.mops	2.336	0.012	2.450
sampleNames	0.396	0.004	0.403
segment	0.060	0.000	0.058
segmentation	0.512	0.008	0.536
segplot	2.268	0.004	2.283

BioC 2.12: CHECK report for cn.mops on george2

Summary

Command output