* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/BGmix.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.20.0’
* 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 ... [15s/16s] 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 ... NOTE
ccSummary: warning in agrep("genes", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("conds", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("effects", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("mix comps", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("variance", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("mix prior", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("niter", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("nburn", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("nthin", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("seed", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("move", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("fullBayes", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("aa updated", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta updated", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambdas updated", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("tau's", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("t-dist", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("(params)", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("(predictive)", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta_up", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta_down", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambda+ for", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambda- for", summ, max = 0): partial
argument match of 'max' to 'max.distance'
plotFDR: warning in legend(xx, yy, leg = c("FDR=5%", "FDR=10%"), col =
c("red", "blue"), lty = c(1, 1), bg = "white"): partial argument
match of 'leg' to 'legend'
* 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 ... NOTE
File ‘/home/biocbuild/bbs-2.12-bioc/meat/BGmix.Rcheck/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.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [55s/56s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
FDRforTailPP 10.900 1.896 12.814
BGmix 7.268 0.116 7.402
EstimatePi0 4.861 0.640 5.501
* 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
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG -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 ‘&’ [-Wparentheses]
BGmix_main.cpp:178:27: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
BGmix_main.cpp:179:47: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
BGmix_main.cpp:546:48: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
BGmix_main.cpp:621:48: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fpic -g -O2 -Wall -DUSING_R -c rundir.cpp -o rundir.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -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 ‘|’ [-Wparentheses]
updates_BGmix.cpp:200:28: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
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 ‘|’ [-Wparentheses]
updates_BGmix.cpp:883:46: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:883:67: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:893:43: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
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 ‘|’ [-Wparentheses]
updates_BGmix.cpp:1005:46: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:1005:67: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:1015:43: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:986:5: warning: variable ‘ind’ set but not used [-Wunused-but-set-variable]
g++ -shared -L/usr/local/lib -o BGmix.so BGmix_main.o rundir.o updates_BGmix.o -lm -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
rm -r ../boostIncl
installing to /home/biocbuild/bbs-2.12-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)