BioC 2.14: CHECK report for iBMQ on zin2

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings iBMQ_1.4.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/iBMQ.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iBMQ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iBMQ’ version ‘1.4.2’
* 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 ‘iBMQ’ can be installed ... [5s/6s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘ggplot2’
  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 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 compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* 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 ... [8s/8s] 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 were 2 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/iBMQ.Rcheck/00check.log’
for details.

* installing *source* package ‘iBMQ’ ...
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
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 omp.h usability... yes
checking omp.h presence... yes
checking for omp.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c ARS.c -o ARS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c RngStream.c -o RngStream.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c iBMQ_common.c -o iBMQ_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c main_parallel_sparse.c -o main_parallel_sparse.o
main_parallel_sparse.c: In function ‘iBMQ_main’:
main_parallel_sparse.c:289:9: warning: ‘Cfile’ may be used uninitialized in this function [-Wuninitialized]
main_parallel_sparse.c:288:9: warning: ‘Sig2file’ may be used uninitialized in this function [-Wuninitialized]
main_parallel_sparse.c:287:9: warning: ‘Mufile’ may be used uninitialized in this function [-Wuninitialized]
main_parallel_sparse.c:285:9: warning: ‘Bfile’ may be used uninitialized in this function [-Wuninitialized]
main_parallel_sparse.c:284:9: warning: ‘Afile’ may be used uninitialized in this function [-Wuninitialized]
main_parallel_sparse.c:286:9: warning: ‘Pfile’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c main_parallel_sparse_constC.c -o main_parallel_sparse_constC.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c norm_gamma_generation.c -o norm_gamma_generation.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c sparse.c -o sparse.o
gcc -std=gnu99 -shared -L/usr/local/lib -o iBMQ.so ARS.o RngStream.o iBMQ_common.o main_parallel_sparse.o main_parallel_sparse_constC.o norm_gamma_generation.o sparse.o -lgsl -lgslcblas -lm -lgomp -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/iBMQ.Rcheck/iBMQ/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iBMQ)

name	user	system	elapsed
PPA.liver	0.220	0.008	0.227
calculateThreshold	0.600	0.012	0.615
eqtlClassifier	4.920	0.024	4.991
eqtlFinder	0.436	0.004	0.439
eqtlMcmc	0.056	0.000	0.056
gene	0.044	0.000	0.042
genepos	0.004	0.000	0.003
genotype.liver	0.004	0.004	0.007
hotspotFinder	0.436	0.012	0.449
map.liver	0.004	0.000	0.002
phenotype.liver	0.048	0.000	0.049
probe.liver	0.012	0.000	0.010
snp	0.012	0.000	0.012
snppos	0.004	0.000	0.004

BioC 2.14: CHECK report for iBMQ on zin2

Summary

Command output