BioC 2.7: CHECK report for BGmix on liverpool

Package: BGmix

Version: 1.10.0

Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings BGmix_1.10.0.tar.gz

StartedAt: 2011-03-31 05:36:10 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 05:39:17 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 187.2 seconds

RetCode: 0

Status: OK

CheckDir: BGmix.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/BGmix.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BGmix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BGmix' version '1.10.0'
* 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 package directory ... OK
* checking for portable file names ... 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 data for non-ASCII characters ... 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 package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'BGmix' ...
** libs
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I ../boostIncl     -DUSING_R   -O2 -Wall  -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"E:/biocbld/BBS-2˜1.7-B/R/include" -I ../boostIncl     -DUSING_R   -O2 -Wall  -c rundir.cpp -o rundir.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I ../boostIncl     -DUSING_R   -O2 -Wall  -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 -s -static-libgcc -o BGmix.dll tmp.def BGmix_main.o rundir.o updates_BGmix.o -LE:/biocbld/BBS-2˜1.7-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.7-bioc/meat/BGmix.Rcheck/BGmix/libs/i386
** 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 ...
** testing if installed package can be loaded

* DONE (BGmix)

name	user	system	elapsed
BGmix-package	13.44	0.16	13.76
BGmix	31.20	0.09	31.66
EstimatePi0	9.00	0.11	9.20
FDRforTailPP	18.49	0.47	19.34
FDRplotTailPP	8.56	0.30	9.42
TailPP	8.67	0.20	10.07
calcFDR	3.40	0.01	3.55
ccParams	3.40	0.04	3.45
ccPred	3.42	0.00	3.46
ccSummary	3.34	0.06	3.42
ccTrace	4.05	0.00	4.06
histTailPP	8.79	0.17	9.08
plotBasic	3.49	0.05	3.73
plotCompare	0.00	0.00	0.02
plotFDR	3.43	0.01	3.43
plotMixDensity	13.09	0.05	13.22
plotPredChecks	3.38	0.08	3.47
plotTrace	4.12	0.03	4.17

Summary

Command output