Package: bridge

Version: 1.10.0

Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check bridge_1.10.0.tar.gz

RetCode: 0

Time: 81.8 seconds

Status: OK

CheckDir: bridge.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.1-bioc/meat/bridge.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'bridge/DESCRIPTION' ... OK
* this is package 'bridge' version '1.10.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'bridge' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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 use of $BLAS_LIBS ... OK
* creating bridge-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating bridge-manual.tex ... OK
* checking bridge-manual.tex ... OK

installing R.css in E:/biocbld/bbs-2.1-bioc/meat/bridge.Rcheck


---------- Making package bridge ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making bridge2.affy.d from bridge2.affy.c
making bridge2.d from bridge2.c
making bridge2_util.d from bridge2_util.c
making bridge3.d from bridge3.c
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c bridge2.affy.c -o bridge2.affy.o
bridge2.affy.c: In function 'gene_express_2s':
bridge2.affy.c:37: warning: unused variable 'count_model'
bridge2.affy.c:36: warning: unused variable 'old_model'
bridge2.affy.c: In function 'up_date_w2':
bridge2.affy.c:300: warning: implicit declaration of function 'dirichlet'
bridge2.affy.c:280: warning: unused variable 'w_new'
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c bridge2.c -o bridge2.o
bridge2.c: In function 'mcmc':
bridge2.c:199: warning: unused variable 'width_a'
bridge2.c:199: warning: unused variable 'old_a'
bridge2.c:198: warning: unused variable 'width_b'
bridge2.c:198: warning: unused variable 'old_b'
bridge2.c:192: warning: unused variable 'sum_res2'
bridge2.c:191: warning: unused variable 'sum_res1'
bridge2.c:177: warning: unused variable 'countp'
bridge2.c:175: warning: unused variable 'countb_eps'
bridge2.c:174: warning: unused variable 'counta_eps'
bridge2.c:173: warning: unused variable 'counta'
bridge2.c:171: warning: unused variable 'countrho'
bridge2.c:166: warning: unused variable 'b_eps_new'
bridge2.c:166: warning: unused variable 'a_eps_new'
bridge2.c:165: warning: unused variable 'l_ab_new'
bridge2.c:165: warning: unused variable 'l_ab'
bridge2.c:163: warning: unused variable 'post_prec_eta'
bridge2.c:163: warning: unused variable 'post_mean_eta'
bridge2.c:162: warning: unused variable 'post_prec_delta'
bridge2.c:162: warning: unused variable 'post_mean_delta'
bridge2.c:161: warning: unused variable 'post_prec_alpha'
bridge2.c:161: warning: unused variable 'post_mean_alpha'
bridge2.c:160: warning: unused variable 'post_prec_beta'
bridge2.c:160: warning: unused variable 'post_mean_beta'
bridge2.c:159: warning: unused variable 'post_prec_mu'
bridge2.c:159: warning: unused variable 'post_mean_mu'
bridge2.c:154: warning: unused variable 'dens_t_new'
bridge2.c:154: warning: unused variable 'dens_t'
bridge2.c:145: warning: unused variable 'pi'
bridge2.c:143: warning: unused variable 'dens_rho_new'
bridge2.c:143: warning: unused variable 'dens_rho'
bridge2.c:142: warning: unused variable 'sum_rho_new'
bridge2.c:142: warning: unused variable 'sum_rho'
bridge2.c:138: warning: unused variable 'rho_new'
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c bridge2_util.c -o bridge2_util.o
bridge2_util.c: In function 'qr_solve':
bridge2_util.c:570: warning: implicit declaration of function 'dqrdc2_'
bridge2_util.c:585: warning: implicit declaration of function 'dqrcf_'
bridge2_util.c:549: warning: unused variable 'vmax'
bridge2_util.c: In function 'inverse':
bridge2_util.c:608: warning: unused variable 'j'
bridge2_util.c: In function 'product_mat_vec':
bridge2_util.c:655: warning: unused variable 'k'
bridge2_util.c: In function 'slice_sampling_b':
bridge2_util.c:763: warning: suggest parentheses around comparison in operand of &
bridge2_util.c:771: warning: suggest parentheses around comparison in operand of &
bridge2_util.c: In function 'slice_sampling_a':
bridge2_util.c:818: warning: suggest parentheses around comparison in operand of &
bridge2_util.c:826: warning: suggest parentheses around comparison in operand of &
bridge2_util.c: In function 'slice_sampling_rho':
bridge2_util.c:875: warning: suggest parentheses around comparison in operand of &
bridge2_util.c:884: warning: suggest parentheses around comparison in operand of &
bridge2_util.c: In function 'slice_sampling_p':
bridge2_util.c:961: warning: suggest parentheses around comparison in operand of &
bridge2_util.c:969: warning: suggest parentheses around comparison in operand of &
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c bridge3.c -o bridge3.o
bridge3.c: In function 'gene_express_3s':
bridge3.c:39: warning: unused variable 'count_model'
bridge3.c:38: warning: unused variable 'old_model'
bridge3.c: In function 'gibbs_mu':
bridge3.c:335: warning: suggest parentheses around comparison in operand of &
bridge3.c: In function 'up_date_w':
bridge3.c:365: warning: unused variable 'w_new'
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.1-bioc/R/include  -i bridge_res.rc -o bridge_res.o
gcc-sjlj  -std=gnu99  -shared -s  -o bridge.dll bridge.def bridge2.affy.o bridge2.o bridge2_util.o bridge3.o bridge_res.o  -Le:/biocbld/bbs-2.1-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'bridge'
     Formats: text html latex example chm 
  bridge.2samples                   text    html    latex   example chm
  bridge.3samples                   text    html    latex   example chm
  hiv                               text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.1-bioc\meat\bridge.Rcheck\00_pkg_src\bridge\chm\bridge.chm


Compile time: 0 minutes, 0 seconds
4	Topics
8	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.1-bioc\meat\bridge.Rcheck\00_pkg_src\bridge\chm\bridge.chm, 23,639 bytes
Compression decreased file by 1,819 bytes.
  adding MD5 sums

* DONE (bridge)