Package: BGmix

Version: 1.13.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings BGmix_1.13.0.tar.gz

StartedAt: 2011-05-09 11:38:07 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 11:39:41 -0700 (Mon, 09 May 2011)

EllapsedTime: 93.4 seconds

RetCode: 0

Status:  OK

CheckDir: BGmix.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/BGmix.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-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 ‘1.13.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘BGmix’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* 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-2.9-bioc/R/include -I ../boostIncl -I/usr/local/include    -fpic  -g -O2 -Wall -DUSING_R -c BGmix_main.cpp -o BGmix_main.o
BGmix_main.cpp: In function ‘void BGmix(int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double*, double*, double*, int*, int&, double*, int*, char**, char**, char**, char**, char**)’:
BGmix_main.cpp:165:31: warning: suggest parentheses around comparison in operand of ‘&’
BGmix_main.cpp:178:27: warning: suggest parentheses around comparison in operand of ‘&’
BGmix_main.cpp:179:47: warning: suggest parentheses around comparison in operand of ‘&’
BGmix_main.cpp:546:48: warning: suggest parentheses around comparison in operand of ‘|’
BGmix_main.cpp:621:48: warning: suggest parentheses around comparison in operand of ‘|’
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I ../boostIncl -I/usr/local/include    -fpic  -g -O2 -Wall -DUSING_R -c rundir.cpp -o rundir.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I ../boostIncl -I/usr/local/include    -fpic  -g -O2 -Wall -DUSING_R -c updates_BGmix.cpp -o updates_BGmix.o
updates_BGmix.cpp: In function ‘void update_z_beta1_joint2(int*, double**, int*, int&, int&, double*, double&, double&, double**, double**, double**, int*, double**, double**, int&, int&, int&, int*, int&, int&, int&, Random&)’:
updates_BGmix.cpp:192:29: warning: suggest parentheses around comparison in operand of ‘|’
updates_BGmix.cpp:200:28: warning: suggest parentheses around comparison in operand of ‘|’
updates_BGmix.cpp: In function ‘void predict(double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double*, double**, double*, double**, double**, double**, double**, double*, double*, int*, double**, double**, int*, double*, double&, double&, double&, double&, double&, int&, int&, int&, int&, int&, int*, int&, Random&)’:
updates_BGmix.cpp:870:41: warning: suggest parentheses around comparison in operand of ‘|’
updates_BGmix.cpp:883:46: warning: suggest parentheses around comparison in operand of ‘|’
updates_BGmix.cpp:883:67: warning: suggest parentheses around comparison in operand of ‘|’
updates_BGmix.cpp:893:43: warning: suggest parentheses around comparison in operand of ‘|’
updates_BGmix.cpp: In function ‘void predict_t(double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double*, double*, double*, int*, double**, double**, int*, double*, double&, double&, double&, double&, double&, int&, int&, int&, int&, int&, int*, int&, Random&)’:
updates_BGmix.cpp:992:41: warning: suggest parentheses around comparison in operand of ‘|’
updates_BGmix.cpp:1005:46: warning: suggest parentheses around comparison in operand of ‘|’
updates_BGmix.cpp:1005:67: warning: suggest parentheses around comparison in operand of ‘|’
updates_BGmix.cpp:1015:43: warning: suggest parentheses around comparison in operand of ‘|’
g++ -shared -L/usr/local/lib64 -o BGmix.so BGmix_main.o rundir.o updates_BGmix.o -lm -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
rm -r ../boostIncl 
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/BGmix.Rcheck/BGmix/libs
** R
** data
** inst
** preparing package for lazy loading
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘BGmix.Rnw’ 
** testing if installed package can be loaded

* DONE (BGmix)

name	user	system	elapsed
BGmix-package	2.372	0.084	2.463
BGmix	5.924	0.124	6.052
EstimatePi0	4.028	0.396	4.431
FDRforTailPP	9.205	1.168	10.465
FDRplotTailPP	3.624	0.480	4.218
TailPP	3.600	0.456	4.056
calcFDR	0.656	0.028	0.685
ccParams	0.664	0.016	0.678
ccPred	0.672	0.012	0.684
ccSummary	0.652	0.020	0.676
ccTrace	0.821	0.036	0.875
histTailPP	3.628	0.480	4.224
plotBasic	0.684	0.012	0.698
plotCompare	0.004	0.000	0.003
plotFDR	0.676	0.016	0.693
plotMixDensity	1.996	0.096	2.094
plotPredChecks	0.676	0.008	0.681
plotTrace	0.904	0.012	0.921