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Package 60/631HostnameOS / ArchBUILDCHECKBUILD BIN
BGmix 1.19.0
Alex Lewin
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BGmix
Last Changed Rev: 70052 / Revision: 72575
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: BGmix
Version: 1.19.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings BGmix_1.19.0.tar.gz
StartedAt: 2013-01-16 00:53:42 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 00:54:58 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 75.6 seconds
RetCode: 0
Status:  OK 
CheckDir: BGmix.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/BGmix.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.19.0’
* 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 ... 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 ‘/loc/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 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
Examples with CPU or elapsed time > 5s
              user system elapsed
FDRforTailPP 9.813  1.148  10.972
BGmix        5.928  0.116   6.052
* 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
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/BGmix.Rcheck/00check.log’
for details.

BGmix.Rcheck/00install.out:

* 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  -DUSING_R -c BGmix_main.cpp -o BGmix_main.o
g++ -I/home/biocbuild/bbs-2.12-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-2.12-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/lib64 -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 /loc/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
   ‘BGmix.Rnw’ 
** testing if installed package can be loaded

* DONE (BGmix)

BGmix.Rcheck/BGmix-Ex.timings:

nameusersystemelapsed
BGmix-package2.6120.0722.691
BGmix5.9280.1166.052
EstimatePi04.1560.3884.546
FDRforTailPP 9.813 1.14810.972
FDRplotTailPP3.6880.4404.131
TailPP3.7440.3364.092
calcFDR0.5760.0160.595
ccParams0.5600.0280.592
ccPred0.6410.0200.672
ccSummary0.6880.0320.718
ccTrace0.7880.0120.802
histTailPP3.5920.3643.966
plotBasic0.6720.0080.684
plotCompare0.0080.0040.014
plotFDR0.6760.0200.695
plotMixDensity2.1000.0522.156
plotPredChecks0.6320.0240.653
plotTrace0.8560.0280.889