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Package 88/671HostnameOS / ArchBUILDCHECKBUILD BIN
bridge 1.24.0
Raphael Gottardo
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/bridge
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: bridge
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch bridge_1.24.0.tar.gz
StartedAt: 2013-05-01 03:08:43 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 03:09:07 -0700 (Wed, 01 May 2013)
EllapsedTime: 23.8 seconds
RetCode: 0
Status:  OK 
CheckDir: bridge.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/bridge.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'bridge/DESCRIPTION' ... OK
* this is package 'bridge' version '1.24.0'
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'bridge' can be installed ... [2s/3s] 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
File 'bridge/R/zzz.R':
  .onLoad calls:
    require("rama", quietly = TRUE)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
* 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/bridge.Rcheck/bridge/libs/bridge.so':
  Found '_printf', possibly from 'printf' (C)
    Objects: 'bridge2.affy.o', 'bridge2.o', 'bridge3.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' ... NOTE
The following files should probably not be installed:
  'chicago.bst', 'chicago.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [1s/1s] 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 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/bridge.Rcheck/00check.log'
for details.

bridge.Rcheck/00install.out:

* installing *source* package 'bridge' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c bridge2.affy.c -o bridge2.affy.o
bridge2.affy.c:36:7: warning: unused variable 'old_model' [-Wunused-variable]
  int old_model;
      ^
bridge2.affy.c:37:7: warning: unused variable 'count_model' [-Wunused-variable]
  int count_model=0;
      ^
bridge2.affy.c:302:3: warning: implicit declaration of function 'dirichlet' is invalid in C99 [-Wimplicit-function-declaration]
  dirichlet(gamma, 2, w);
  ^
bridge2.affy.c:282:10: warning: unused variable 'w_new' [-Wunused-variable]
  double w_new[2];
         ^
bridge2.affy.c:367:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
      nu_new=nu_choice[(int)(runif(0.,1.)*(nb_nu))];  
            ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c bridge2.c -o bridge2.o
bridge2.c:143:19: warning: unused variable 'dens_rho_new' [-Wunused-variable]
  double dens_rho,dens_rho_new;
                  ^
bridge2.c:160:27: warning: unused variable 'post_prec_beta' [-Wunused-variable]
  double post_mean_beta=0,post_prec_beta=0;
                          ^
bridge2.c:199:10: warning: unused variable 'old_a' [-Wunused-variable]
  double old_a=0,width_a=5;
         ^
bridge2.c:161:10: warning: unused variable 'post_mean_alpha' [-Wunused-variable]
  double post_mean_alpha=0,post_prec_alpha=0;
         ^
bridge2.c:198:18: warning: unused variable 'width_b' [-Wunused-variable]
  double old_b=0,width_b=5;
                 ^
bridge2.c:162:10: warning: unused variable 'post_mean_delta' [-Wunused-variable]
  double post_mean_delta=0,post_prec_delta=0;
         ^
bridge2.c:145:10: warning: unused variable 'pi' [-Wunused-variable]
  double pi=3.14;
         ^
bridge2.c:161:28: warning: unused variable 'post_prec_alpha' [-Wunused-variable]
  double post_mean_alpha=0,post_prec_alpha=0;
                           ^
bridge2.c:162:28: warning: unused variable 'post_prec_delta' [-Wunused-variable]
  double post_mean_delta=0,post_prec_delta=0;
                           ^
bridge2.c:199:18: warning: unused variable 'width_a' [-Wunused-variable]
  double old_a=0,width_a=5;
                 ^
bridge2.c:163:26: warning: unused variable 'post_prec_eta' [-Wunused-variable]
  double post_mean_eta=0,post_prec_eta=0;
                         ^
bridge2.c:163:10: warning: unused variable 'post_mean_eta' [-Wunused-variable]
  double post_mean_eta=0,post_prec_eta=0;
         ^
bridge2.c:165:17: warning: unused variable 'l_ab_new' [-Wunused-variable]
  double l_ab=0,l_ab_new=0;
                ^
bridge2.c:165:10: warning: unused variable 'l_ab' [-Wunused-variable]
  double l_ab=0,l_ab_new=0;
         ^
bridge2.c:166:22: warning: unused variable 'b_eps_new' [-Wunused-variable]
  double a_eps_new=0,b_eps_new=0;
                     ^
bridge2.c:166:10: warning: unused variable 'a_eps_new' [-Wunused-variable]
  double a_eps_new=0,b_eps_new=0;
         ^
bridge2.c:138:10: warning: unused variable 'rho_new' [-Wunused-variable]
  double rho_new;
         ^
bridge2.c:191:10: warning: unused variable 'sum_res1' [-Wunused-variable]
  double sum_res1;
         ^
bridge2.c:171:7: warning: unused variable 'countrho' [-Wunused-variable]
  int countrho=0;
      ^
bridge2.c:154:19: warning: unused variable 'dens_t_new' [-Wunused-variable]
  double dens_t=0,dens_t_new=0;
                  ^
bridge2.c:175:7: warning: unused variable 'countb_eps' [-Wunused-variable]
  int countb_eps=0;
      ^
bridge2.c:173:7: warning: unused variable 'counta' [-Wunused-variable]
  int counta=0;
      ^
bridge2.c:154:10: warning: unused variable 'dens_t' [-Wunused-variable]
  double dens_t=0,dens_t_new=0;
         ^
bridge2.c:174:7: warning: unused variable 'counta_eps' [-Wunused-variable]
  int counta_eps=0;
      ^
bridge2.c:142:10: warning: unused variable 'sum_rho' [-Wunused-variable]
  double sum_rho=0,sum_rho_new=0;
         ^
bridge2.c:192:10: warning: unused variable 'sum_res2' [-Wunused-variable]
  double sum_res2;
         ^
bridge2.c:159:10: warning: unused variable 'post_mean_mu' [-Wunused-variable]
  double post_mean_mu=0,post_prec_mu=0;
         ^
bridge2.c:198:10: warning: unused variable 'old_b' [-Wunused-variable]
  double old_b=0,width_b=5;
         ^
bridge2.c:142:20: warning: unused variable 'sum_rho_new' [-Wunused-variable]
  double sum_rho=0,sum_rho_new=0;
                   ^
bridge2.c:160:10: warning: unused variable 'post_mean_beta' [-Wunused-variable]
  double post_mean_beta=0,post_prec_beta=0;
         ^
bridge2.c:143:10: warning: unused variable 'dens_rho' [-Wunused-variable]
  double dens_rho,dens_rho_new;
         ^
bridge2.c:159:25: warning: unused variable 'post_prec_mu' [-Wunused-variable]
  double post_mean_mu=0,post_prec_mu=0;
                        ^
bridge2.c:177:7: warning: unused variable 'countp' [-Wunused-variable]
  int countp=0;
      ^
33 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c bridge2_util.c -o bridge2_util.o
bridge2_util.c:570:14: warning: implicit declaration of function 'dqrdc2_' is invalid in C99 [-Wimplicit-function-declaration]
    F77_CALL(dqrdc2)(xt, &n, &n, &p, &tol, &rank,qraux, pivot, work);
             ^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:82:22: note: expanded from macro 'F77_CALL'
# define F77_CALL(x)    x ## _
                        ^
<scratch space>:29:1: note: expanded from macro 'dqrdc2'
dqrdc2_
^
bridge2_util.c:585:14: warning: implicit declaration of function 'dqrcf_' is invalid in C99 [-Wimplicit-function-declaration]
    F77_CALL(dqrcf)(xt, &n, &rank, qraux,yt, &n, coeft, &info);
             ^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:82:22: note: expanded from macro 'F77_CALL'
# define F77_CALL(x)    x ## _
                        ^
<scratch space>:29:10: note: expanded from macro 'dqrcf'
dqrdc2_<U+0000><U+000A>dqrcf_
                       ^
bridge2_util.c:549:11: warning: unused variable 'vmax' [-Wunused-variable]
    char *vmax;
          ^
bridge2_util.c:608:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
bridge2_util.c:655:11: warning: unused variable 'k' [-Wunused-variable]
  int i,j,k;
          ^
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c bridge3.c -o bridge3.o
bridge3.c:38:7: warning: unused variable 'count_model' [-Wunused-variable]
  int count_model=0;
      ^
bridge3.c:37:7: warning: unused variable 'old_model' [-Wunused-variable]
  int old_model;
      ^
bridge3.c:332:25: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
  else if((w_star[3]<u) & u<w_star[4])
                        ^˜˜˜˜˜˜˜˜˜˜˜˜
bridge3.c:332:25: note: place parentheses around the '<' expression to silence this warning
  else if((w_star[3]<u) & u<w_star[4])
                        ^
                          (          )
bridge3.c:332:25: note: place parentheses around the & expression to evaluate it first
  else if((w_star[3]<u) & u<w_star[4])
                        ^
          (                )
bridge3.c:362:10: warning: unused variable 'w_new' [-Wunused-variable]
  double w_new[5];
         ^
bridge3.c:489:12: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    nu_new=nu_choice[(int)(runif(0.,1.)*(nb_nu))];  
          ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
5 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o bridge.so bridge2.affy.o bridge2.o bridge2_util.o bridge3.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/bridge.Rcheck/bridge/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 (bridge)

bridge.Rcheck/bridge-Ex.timings:

nameusersystemelapsed
bridge.2samples0.4230.0070.447
bridge.3samples0.0200.0010.022