Package: bridge

Version: 1.18.0

Command: rm -rf bridge.buildbin-libdir && mkdir bridge.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bridge.buildbin-libdir bridge_1.18.0.tar.gz >bridge-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=bridge.buildbin-libdir --install="check:bridge-install.out" --force-multiarch --no-vignettes --timings bridge_1.18.0.tar.gz && mv bridge.buildbin-libdir/* bridge.Rcheck/ && rmdir bridge.buildbin-libdir

StartedAt: 2012-03-24 00:40:54 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 00:41:27 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 32.4 seconds

RetCode: 0

Status:  OK

CheckDir: bridge.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/bridge.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bridge/DESCRIPTION' ... OK
* this is package 'bridge' version '1.18.0'
* 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 'bridge' can be installed ... OK
* checking installed package size ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 'D:/biocbld/bbs-2.9-bioc/meat/bridge.buildbin-libdir/bridge/libs/i386/bridge.dll':
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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

install for i386

* installing *source* package 'bridge' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c bridge2.affy.c -o bridge2.affy.o
bridge2.affy.c: In function 'gene_express_2s':
bridge2.affy.c:37:7: warning: unused variable 'count_model' [-Wunused-variable]
bridge2.affy.c:36:7: warning: unused variable 'old_model' [-Wunused-variable]
bridge2.affy.c: In function 'up_date_w2':
bridge2.affy.c:302:3: warning: implicit declaration of function 'dirichlet' [-Wimplicit-function-declaration]
bridge2.affy.c:282:10: warning: unused variable 'w_new' [-Wunused-variable]
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c bridge2.c -o bridge2.o
bridge2.c: In function 'mcmc':
bridge2.c:199:18: warning: unused variable 'width_a' [-Wunused-variable]
bridge2.c:199:10: warning: unused variable 'old_a' [-Wunused-variable]
bridge2.c:198:18: warning: unused variable 'width_b' [-Wunused-variable]
bridge2.c:198:10: warning: unused variable 'old_b' [-Wunused-variable]
bridge2.c:192:10: warning: unused variable 'sum_res2' [-Wunused-variable]
bridge2.c:191:10: warning: unused variable 'sum_res1' [-Wunused-variable]
bridge2.c:177:7: warning: unused variable 'countp' [-Wunused-variable]
bridge2.c:175:7: warning: unused variable 'countb_eps' [-Wunused-variable]
bridge2.c:174:7: warning: unused variable 'counta_eps' [-Wunused-variable]
bridge2.c:173:7: warning: unused variable 'counta' [-Wunused-variable]
bridge2.c:171:7: warning: unused variable 'countrho' [-Wunused-variable]
bridge2.c:166:22: warning: unused variable 'b_eps_new' [-Wunused-variable]
bridge2.c:166:10: warning: unused variable 'a_eps_new' [-Wunused-variable]
bridge2.c:165:17: warning: unused variable 'l_ab_new' [-Wunused-variable]
bridge2.c:165:10: warning: unused variable 'l_ab' [-Wunused-variable]
bridge2.c:164:24: warning: variable 'mean_gamma2' set but not used [-Wunused-but-set-variable]
bridge2.c:164:10: warning: variable 'mean_gamma1' set but not used [-Wunused-but-set-variable]
bridge2.c:163:26: warning: unused variable 'post_prec_eta' [-Wunused-variable]
bridge2.c:163:10: warning: unused variable 'post_mean_eta' [-Wunused-variable]
bridge2.c:162:28: warning: unused variable 'post_prec_delta' [-Wunused-variable]
bridge2.c:162:10: warning: unused variable 'post_mean_delta' [-Wunused-variable]
bridge2.c:161:28: warning: unused variable 'post_prec_alpha' [-Wunused-variable]
bridge2.c:161:10: warning: unused variable 'post_mean_alpha' [-Wunused-variable]
bridge2.c:160:27: warning: unused variable 'post_prec_beta' [-Wunused-variable]
bridge2.c:160:10: warning: unused variable 'post_mean_beta' [-Wunused-variable]
bridge2.c:159:25: warning: unused variable 'post_prec_mu' [-Wunused-variable]
bridge2.c:159:10: warning: unused variable 'post_mean_mu' [-Wunused-variable]
bridge2.c:154:19: warning: unused variable 'dens_t_new' [-Wunused-variable]
bridge2.c:154:10: warning: unused variable 'dens_t' [-Wunused-variable]
bridge2.c:150:21: warning: variable 'SSgammasd' set but not used [-Wunused-but-set-variable]
bridge2.c:150:10: warning: variable 'SSgamma' set but not used [-Wunused-but-set-variable]
bridge2.c:145:10: warning: unused variable 'pi' [-Wunused-variable]
bridge2.c:143:19: warning: unused variable 'dens_rho_new' [-Wunused-variable]
bridge2.c:143:10: warning: unused variable 'dens_rho' [-Wunused-variable]
bridge2.c:142:20: warning: unused variable 'sum_rho_new' [-Wunused-variable]
bridge2.c:142:10: warning: unused variable 'sum_rho' [-Wunused-variable]
bridge2.c:138:10: warning: unused variable 'rho_new' [-Wunused-variable]
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c bridge2_util.c -o bridge2_util.o
bridge2_util.c: In function 'qr_solve':
bridge2_util.c:570:5: warning: implicit declaration of function 'dqrdc2_' [-Wimplicit-function-declaration]
bridge2_util.c:585:5: warning: implicit declaration of function 'dqrcf_' [-Wimplicit-function-declaration]
bridge2_util.c:549:11: warning: unused variable 'vmax' [-Wunused-variable]
bridge2_util.c: In function 'inverse':
bridge2_util.c:608:9: warning: unused variable 'j' [-Wunused-variable]
bridge2_util.c: In function 'product_mat_vec':
bridge2_util.c:655:11: warning: unused variable 'k' [-Wunused-variable]
bridge2_util.c: In function 'slice_sampling_b':
bridge2_util.c:763:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c:771:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c: In function 'slice_sampling_a':
bridge2_util.c:818:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c:826:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c: In function 'slice_sampling_rho':
bridge2_util.c:875:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c:884:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c: In function 'slice_sampling_p':
bridge2_util.c:961:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c:969:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c bridge3.c -o bridge3.o
bridge3.c: In function 'gene_express_3s':
bridge3.c:38:7: warning: unused variable 'count_model' [-Wunused-variable]
bridge3.c:37:7: warning: unused variable 'old_model' [-Wunused-variable]
bridge3.c: In function 'all_gibbs':
bridge3.c:190:7: warning: variable 'old_model' set but not used [-Wunused-but-set-variable]
bridge3.c: In function 'gibbs_mu':
bridge3.c:332:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge3.c: In function 'up_date_w':
bridge3.c:362:10: warning: unused variable 'w_new' [-Wunused-variable]
gcc -shared -s -static-libgcc -o bridge.dll tmp.def bridge2.affy.o bridge2.o bridge2_util.o bridge3.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/bridge.buildbin-libdir/bridge/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'bridge.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'bridge' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bridge2.affy.c -o bridge2.affy.o
bridge2.affy.c: In function 'gene_express_2s':
bridge2.affy.c:37:7: warning: unused variable 'count_model' [-Wunused-variable]
bridge2.affy.c:36:7: warning: unused variable 'old_model' [-Wunused-variable]
bridge2.affy.c: In function 'up_date_w2':
bridge2.affy.c:302:3: warning: implicit declaration of function 'dirichlet' [-Wimplicit-function-declaration]
bridge2.affy.c:282:10: warning: unused variable 'w_new' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bridge2.c -o bridge2.o
bridge2.c: In function 'mcmc':
bridge2.c:199:18: warning: unused variable 'width_a' [-Wunused-variable]
bridge2.c:199:10: warning: unused variable 'old_a' [-Wunused-variable]
bridge2.c:198:18: warning: unused variable 'width_b' [-Wunused-variable]
bridge2.c:198:10: warning: unused variable 'old_b' [-Wunused-variable]
bridge2.c:192:10: warning: unused variable 'sum_res2' [-Wunused-variable]
bridge2.c:191:10: warning: unused variable 'sum_res1' [-Wunused-variable]
bridge2.c:177:7: warning: unused variable 'countp' [-Wunused-variable]
bridge2.c:175:7: warning: unused variable 'countb_eps' [-Wunused-variable]
bridge2.c:174:7: warning: unused variable 'counta_eps' [-Wunused-variable]
bridge2.c:173:7: warning: unused variable 'counta' [-Wunused-variable]
bridge2.c:171:7: warning: unused variable 'countrho' [-Wunused-variable]
bridge2.c:166:22: warning: unused variable 'b_eps_new' [-Wunused-variable]
bridge2.c:166:10: warning: unused variable 'a_eps_new' [-Wunused-variable]
bridge2.c:165:17: warning: unused variable 'l_ab_new' [-Wunused-variable]
bridge2.c:165:10: warning: unused variable 'l_ab' [-Wunused-variable]
bridge2.c:164:24: warning: variable 'mean_gamma2' set but not used [-Wunused-but-set-variable]
bridge2.c:164:10: warning: variable 'mean_gamma1' set but not used [-Wunused-but-set-variable]
bridge2.c:163:26: warning: unused variable 'post_prec_eta' [-Wunused-variable]
bridge2.c:163:10: warning: unused variable 'post_mean_eta' [-Wunused-variable]
bridge2.c:162:28: warning: unused variable 'post_prec_delta' [-Wunused-variable]
bridge2.c:162:10: warning: unused variable 'post_mean_delta' [-Wunused-variable]
bridge2.c:161:28: warning: unused variable 'post_prec_alpha' [-Wunused-variable]
bridge2.c:161:10: warning: unused variable 'post_mean_alpha' [-Wunused-variable]
bridge2.c:160:27: warning: unused variable 'post_prec_beta' [-Wunused-variable]
bridge2.c:160:10: warning: unused variable 'post_mean_beta' [-Wunused-variable]
bridge2.c:159:25: warning: unused variable 'post_prec_mu' [-Wunused-variable]
bridge2.c:159:10: warning: unused variable 'post_mean_mu' [-Wunused-variable]
bridge2.c:154:19: warning: unused variable 'dens_t_new' [-Wunused-variable]
bridge2.c:154:10: warning: unused variable 'dens_t' [-Wunused-variable]
bridge2.c:150:21: warning: variable 'SSgammasd' set but not used [-Wunused-but-set-variable]
bridge2.c:150:10: warning: variable 'SSgamma' set but not used [-Wunused-but-set-variable]
bridge2.c:145:10: warning: unused variable 'pi' [-Wunused-variable]
bridge2.c:143:19: warning: unused variable 'dens_rho_new' [-Wunused-variable]
bridge2.c:143:10: warning: unused variable 'dens_rho' [-Wunused-variable]
bridge2.c:142:20: warning: unused variable 'sum_rho_new' [-Wunused-variable]
bridge2.c:142:10: warning: unused variable 'sum_rho' [-Wunused-variable]
bridge2.c:138:10: warning: unused variable 'rho_new' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bridge2_util.c -o bridge2_util.o
bridge2_util.c: In function 'qr_solve':
bridge2_util.c:570:5: warning: implicit declaration of function 'dqrdc2_' [-Wimplicit-function-declaration]
bridge2_util.c:585:5: warning: implicit declaration of function 'dqrcf_' [-Wimplicit-function-declaration]
bridge2_util.c:549:11: warning: unused variable 'vmax' [-Wunused-variable]
bridge2_util.c: In function 'inverse':
bridge2_util.c:608:9: warning: unused variable 'j' [-Wunused-variable]
bridge2_util.c: In function 'product_mat_vec':
bridge2_util.c:655:11: warning: unused variable 'k' [-Wunused-variable]
bridge2_util.c: In function 'slice_sampling_b':
bridge2_util.c:763:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c:771:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c: In function 'slice_sampling_a':
bridge2_util.c:818:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c:826:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c: In function 'slice_sampling_rho':
bridge2_util.c:875:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c:884:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c: In function 'slice_sampling_p':
bridge2_util.c:961:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge2_util.c:969:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bridge3.c -o bridge3.o
bridge3.c: In function 'gene_express_3s':
bridge3.c:38:7: warning: unused variable 'count_model' [-Wunused-variable]
bridge3.c:37:7: warning: unused variable 'old_model' [-Wunused-variable]
bridge3.c: In function 'all_gibbs':
bridge3.c:190:7: warning: variable 'old_model' set but not used [-Wunused-but-set-variable]
bridge3.c: In function 'gibbs_mu':
bridge3.c:332:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
bridge3.c: In function 'up_date_w':
bridge3.c:362:10: warning: unused variable 'w_new' [-Wunused-variable]
gcc -m64 -shared -s -static-libgcc -o bridge.dll tmp.def bridge2.affy.o bridge2.o bridge2_util.o bridge3.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/bridge.buildbin-libdir/bridge/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bridge' as bridge_1.18.0.zip

* DONE (bridge)