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Package 37/294HostnameOS / ArchBUILDCHECKBUILD BIN
BGmix 1.2.0
Alex Lewin
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/BGmix
Last Changed Rev: 34811 / Revision: 38965
Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK  OK  OK 
Package: BGmix
Version: 1.2.0
Command: /home/biocbuild/bbs-2.3-bioc/R/bin/R CMD check --no-vignettes BGmix_1.2.0.tar.gz
StartedAt: 2009-04-18 15:01:29 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 15:02:31 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 62.2 seconds
RetCode: 0
Status: OK
CheckDir: BGmix.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.3-bioc/meat/BGmix.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: UTF-8
* checking for file 'BGmix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BGmix' version '1.2.0'
* 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 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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 ... OK
* creating BGmix-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating BGmix-manual.tex ... OK
* checking BGmix-manual.tex using pdflatex ... OK

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-2.3-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: warning: suggest parentheses around comparison in operand of &
BGmix_main.cpp:178: warning: suggest parentheses around comparison in operand of &
BGmix_main.cpp:179: warning: suggest parentheses around comparison in operand of &
BGmix_main.cpp:546: warning: suggest parentheses around comparison in operand of |
BGmix_main.cpp:621: warning: suggest parentheses around comparison in operand of |
g++ -I/home/biocbuild/bbs-2.3-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-2.3-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: warning: suggest parentheses around comparison in operand of |
updates_BGmix.cpp:200: 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: warning: suggest parentheses around comparison in operand of |
updates_BGmix.cpp:883: warning: suggest parentheses around comparison in operand of |
updates_BGmix.cpp:883: warning: suggest parentheses around comparison in operand of |
updates_BGmix.cpp:893: 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: warning: suggest parentheses around comparison in operand of |
updates_BGmix.cpp:1005: warning: suggest parentheses around comparison in operand of |
updates_BGmix.cpp:1005: warning: suggest parentheses around comparison in operand of |
updates_BGmix.cpp:1015: 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-2.3-bioc/R/lib -lR
rm -r ../boostIncl 
** R
** data
** inst
** preparing package for lazy loading
Loading required package: KernSmooth
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
** help
 >>> Building/Updating help pages for package 'BGmix'
     Formats: text html latex example 
  BGmix-package                     text    html    latex   example
  BGmix                             text    html    latex   example
  EstimatePi0                       text    html    latex   example
  FDRforTailPP                      text    html    latex   example
  FDRplotTailPP                     text    html    latex   example
  TailPP                            text    html    latex   example
  calcFDR                           text    html    latex   example
  ccParams                          text    html    latex   example
  ccPred                            text    html    latex   example
  ccSummary                         text    html    latex   example
  ccTrace                           text    html    latex   example
  histTailPP                        text    html    latex   example
  plotBasic                         text    html    latex   example
  plotCompare                       text    html    latex   example
  plotFDR                           text    html    latex   example
  plotMixDensity                    text    html    latex   example
  plotPredChecks                    text    html    latex   example
  plotTrace                         text    html    latex   example
  readBGX                           text    html    latex
  ss                                text    html    latex
  ybar                              text    html    latex
** building package indices ...
* DONE (BGmix)