bridge 1.10.0
Raphael Gottardo
| Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/bridge | | Last Changed Rev: 42684 / Revision: 43539 | | Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009) |
| 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 (10.5.8) / i386 | OK | [ OK ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.5-bioc/meat/bridge.Rcheck'
* using R version 2.10.0 Patched (2009-10-27 r50222)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 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 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* installing *source* package ‘bridge’ ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -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:302: warning: implicit declaration of function ‘dirichlet’
bridge2.affy.c:282: warning: unused variable ‘w_new’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c bridge3.c -o bridge3.o
bridge3.c: In function ‘gene_express_3s’:
bridge3.c:38: warning: unused variable ‘count_model’
bridge3.c:37: warning: unused variable ‘old_model’
bridge3.c: In function ‘gibbs_mu’:
bridge3.c:332: warning: suggest parentheses around comparison in operand of &
bridge3.c: In function ‘up_date_w’:
bridge3.c:362: warning: unused variable ‘w_new’
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c bridge2.affy.c -o bridge2.affy.o
bridge2.affy.c: In function ‘up_date_w2’:
bridge2.affy.c:302: warning: implicit declaration of function ‘dirichlet’
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c bridge2.c -o bridge2.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -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_’
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c bridge3.c -o bridge3.o
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -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:302: warning: implicit declaration of function ‘dirichlet’
bridge2.affy.c:282: warning: unused variable ‘w_new’
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c bridge3.c -o bridge3.o
bridge3.c: In function ‘gene_express_3s’:
bridge3.c:38: warning: unused variable ‘count_model’
bridge3.c:37: warning: unused variable ‘old_model’
bridge3.c: In function ‘gibbs_mu’:
bridge3.c:332: warning: suggest parentheses around comparison in operand of &
bridge3.c: In function ‘up_date_w’:
bridge3.c:362: warning: unused variable ‘w_new’
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
* DONE (bridge)