Package: BGmix

Version: 1.16.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings BGmix_1.16.0.tar.gz

StartedAt: 2012-03-31 23:49:04 -0700 (Sat, 31 Mar 2012)

EndedAt: 2012-03-31 23:50:03 -0700 (Sat, 31 Mar 2012)

EllapsedTime: 59.6 seconds

RetCode: 0

Status:  OK

CheckDir: BGmix.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/BGmix.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-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 '1.16.0'
* 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 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 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 '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/BGmix.Rcheck/BGmix/libs/BGmix.so':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'updates_BGmix.o'

Compiled code should not call functions 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 ... 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

NOTE: There were 2 notes.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-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/hpages/test-puck5/bbs-2.10-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/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fpic  -g -O2  -DUSING_R -c rundir.cpp -o rundir.o
g++ -I/home/hpages/test-puck5/bbs-2.10-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/usr/local/lib -o BGmix.so BGmix_main.o rundir.o updates_BGmix.o -lm -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
rm -r ../boostIncl 
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/BGmix.Rcheck/BGmix/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'BGmix.Rnw' 
** testing if installed package can be loaded

* DONE (BGmix)

name	user	system	elapsed
BGmix-package	2.184	0.036	2.230
BGmix	5.268	0.020	5.303
EstimatePi0	3.004	0.196	3.220
FDRforTailPP	7.161	0.492	7.672
FDRplotTailPP	2.820	0.196	3.032
TailPP	2.844	0.188	3.047
calcFDR	0.668	0.016	0.697
ccParams	0.680	0.008	0.701
ccPred	0.640	0.008	0.659
ccSummary	0.568	0.004	0.579
ccTrace	0.784	0.012	0.805
histTailPP	2.920	0.220	3.157
plotBasic	0.676	0.016	0.703
plotCompare	0.012	0.000	0.010
plotFDR	0.660	0.016	0.691
plotMixDensity	2.253	0.020	2.467
plotPredChecks	0.684	0.008	0.715
plotTrace	0.892	0.012	0.917