BioC 2.12: CHECK report for deepSNV on george2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/deepSNV.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deepSNV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘deepSNV’ version ‘1.5.0’
* 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 ‘deepSNV’ can be installed ... [29s/32s] 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 ... 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 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [66s/68s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
RCC                        18.725  0.184  20.178
estimateDirichlet-methods  13.085  0.040  13.963
estimateDispersion-methods 11.681  0.040  11.723
* 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

* installing *source* package ‘deepSNV’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for off_t... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
Found /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usretc//Rsamtools.mk .
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function ‘int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*)’:
bam2R.cpp:85:6: warning: unused variable ‘c’ [-Wunused-variable]
g++ -shared -L/usr/local/lib -o deepSNV.so bam2R.o /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
Found /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usretc//Rsamtools.mk .
installing to /home/biocbuild/bbs-2.12-bioc/meat/deepSNV.Rcheck/deepSNV/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘deepSNV.Rnw’ 
** testing if installed package can be loaded
* DONE (deepSNV)

name	user	system	elapsed
Extract-methods	0.044	0.016	0.061
RCC	18.725	0.184	20.178
RF	0.016	0.004	0.021
bam2R	0.032	0.000	0.044
consensusSequence-methods	0.056	0.000	0.074
control-methods	0.016	0.004	0.021
coordinates-methods	0.020	0.000	0.024
deepSNV-class	0.384	0.024	0.576
deepSNV-methods	0.208	0.000	0.214
deepSNV-package	0.232	0.000	0.234
estimateDirichlet-methods	13.085	0.040	13.963
estimateDispersion-methods	11.681	0.040	11.723
manhattanPlot	0.192	0.008	0.200
normalize-methods	2.728	0.020	2.748
p.combine	0.188	0.016	0.206
p.val-methods	0.020	0.000	0.019
phiX	3.564	0.020	3.585
plot.deepSNV	0.264	0.012	0.275
repeatMask-methods	1.973	0.000	1.980
show-commadeepSNV-method	0.208	0.000	0.212
summary-methods	0.216	0.000	0.259
test-methods	0.012	0.000	0.019
trueSNVs	0.052	0.000	0.060

Summary

Command output