BioC 3.3: CHECK report for BGmix on linux2.bioconductor.org

Package: BGmix

Version: 1.31.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings BGmix_1.31.0.tar.gz

StartedAt: 2015-10-27 01:58:13 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:59:19 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 65.6 seconds

RetCode: 0

Status:  OK

CheckDir: BGmix.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings BGmix_1.31.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/BGmix.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BGmix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BGmix’ version ‘1.31.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BGmix’ can be installed ... [13s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... 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 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘BGmix/libs/BGmix.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘updates_BGmix.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [39s/39s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
FDRforTailPP 8.247   0.28   8.554
* 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
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/BGmix.Rcheck/00check.log’
for details.

* installing *source* package ‘BGmix’ ...
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking for gcc -std=gnu99 option to accept ISO C99... none needed
checking for cos in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fpic  -g -O2  -DUSING_R -c BGmix_main.cpp -o BGmix_main.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fpic  -g -O2  -DUSING_R -c rundir.cpp -o rundir.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fpic  -g -O2  -DUSING_R -c updates_BGmix.cpp -o updates_BGmix.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o BGmix.so BGmix_main.o rundir.o updates_BGmix.o -lm -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
rm -r ../boostIncl 
installing to /home/biocbuild/bbs-3.3-bioc/meat/BGmix.Rcheck/BGmix/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 (BGmix)

name	user	system	elapsed
BGmix-package	2.967	0.064	3.031
BGmix	4.814	0.044	4.858
EstimatePi0	3.716	0.083	3.801
FDRforTailPP	8.247	0.280	8.554
FDRplotTailPP	2.970	0.072	3.042
TailPP	2.843	0.100	2.947
calcFDR	0.712	0.000	0.715
ccParams	0.799	0.012	0.816
ccPred	0.798	0.004	0.804
ccSummary	0.783	0.012	0.797
ccTrace	1.097	0.012	1.110
histTailPP	3.480	0.088	3.573
plotBasic	0.644	0.004	0.647
plotCompare	0.008	0.000	0.009
plotFDR	0.556	0.004	0.560
plotMixDensity	1.700	0.028	1.729
plotPredChecks	0.687	0.004	0.692
plotTrace	1.115	0.024	1.140