bridge 1.17.0
Raphael Gottardo
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bridge | | Last Changed Rev: 54802 / Revision: 56603 | | Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/bridge.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bridge/DESCRIPTION’ ... OK
* this is package ‘bridge’ version ‘1.17.0’
* 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 installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... 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 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 examples ... 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
* installing *source* package ‘bridge’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -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:37:7: warning: unused variable ‘count_model’
bridge2.affy.c:36:7: warning: unused variable ‘old_model’
bridge2.affy.c: In function ‘up_date_w2’:
bridge2.affy.c:302:3: warning: implicit declaration of function ‘dirichlet’
bridge2.affy.c:282:10: warning: unused variable ‘w_new’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c bridge2.c -o bridge2.o
bridge2.c: In function ‘mcmc’:
bridge2.c:199:18: warning: unused variable ‘width_a’
bridge2.c:199:10: warning: unused variable ‘old_a’
bridge2.c:198:18: warning: unused variable ‘width_b’
bridge2.c:198:10: warning: unused variable ‘old_b’
bridge2.c:192:10: warning: unused variable ‘sum_res2’
bridge2.c:191:10: warning: unused variable ‘sum_res1’
bridge2.c:177:7: warning: unused variable ‘countp’
bridge2.c:175:7: warning: unused variable ‘countb_eps’
bridge2.c:174:7: warning: unused variable ‘counta_eps’
bridge2.c:173:7: warning: unused variable ‘counta’
bridge2.c:171:7: warning: unused variable ‘countrho’
bridge2.c:166:22: warning: unused variable ‘b_eps_new’
bridge2.c:166:10: warning: unused variable ‘a_eps_new’
bridge2.c:165:17: warning: unused variable ‘l_ab_new’
bridge2.c:165:10: warning: unused variable ‘l_ab’
bridge2.c:163:26: warning: unused variable ‘post_prec_eta’
bridge2.c:163:10: warning: unused variable ‘post_mean_eta’
bridge2.c:162:28: warning: unused variable ‘post_prec_delta’
bridge2.c:162:10: warning: unused variable ‘post_mean_delta’
bridge2.c:161:28: warning: unused variable ‘post_prec_alpha’
bridge2.c:161:10: warning: unused variable ‘post_mean_alpha’
bridge2.c:160:27: warning: unused variable ‘post_prec_beta’
bridge2.c:160:10: warning: unused variable ‘post_mean_beta’
bridge2.c:159:25: warning: unused variable ‘post_prec_mu’
bridge2.c:159:10: warning: unused variable ‘post_mean_mu’
bridge2.c:154:19: warning: unused variable ‘dens_t_new’
bridge2.c:154:10: warning: unused variable ‘dens_t’
bridge2.c:145:10: warning: unused variable ‘pi’
bridge2.c:143:19: warning: unused variable ‘dens_rho_new’
bridge2.c:143:10: warning: unused variable ‘dens_rho’
bridge2.c:142:20: warning: unused variable ‘sum_rho_new’
bridge2.c:142:10: warning: unused variable ‘sum_rho’
bridge2.c:138:10: warning: unused variable ‘rho_new’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -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:570:5: warning: implicit declaration of function ‘dqrdc2_’
bridge2_util.c:585:5: warning: implicit declaration of function ‘dqrcf_’
bridge2_util.c:549:11: warning: unused variable ‘vmax’
bridge2_util.c: In function ‘inverse’:
bridge2_util.c:608:9: warning: unused variable ‘j’
bridge2_util.c: In function ‘product_mat_vec’:
bridge2_util.c:655:11: warning: unused variable ‘k’
bridge2_util.c: In function ‘slice_sampling_b’:
bridge2_util.c:763:3: warning: suggest parentheses around comparison in operand of ‘&’
bridge2_util.c:771:3: warning: suggest parentheses around comparison in operand of ‘&’
bridge2_util.c: In function ‘slice_sampling_a’:
bridge2_util.c:818:3: warning: suggest parentheses around comparison in operand of ‘&’
bridge2_util.c:826:3: warning: suggest parentheses around comparison in operand of ‘&’
bridge2_util.c: In function ‘slice_sampling_rho’:
bridge2_util.c:875:3: warning: suggest parentheses around comparison in operand of ‘&’
bridge2_util.c:884:3: warning: suggest parentheses around comparison in operand of ‘&’
bridge2_util.c: In function ‘slice_sampling_p’:
bridge2_util.c:961:3: warning: suggest parentheses around comparison in operand of ‘&’
bridge2_util.c:969:3: warning: suggest parentheses around comparison in operand of ‘&’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c bridge3.c -o bridge3.o
bridge3.c: In function ‘gene_express_3s’:
bridge3.c:38:7: warning: unused variable ‘count_model’
bridge3.c:37:7: warning: unused variable ‘old_model’
bridge3.c: In function ‘gibbs_mu’:
bridge3.c:332:3: warning: suggest parentheses around comparison in operand of ‘&’
bridge3.c: In function ‘up_date_w’:
bridge3.c:362:10: warning: unused variable ‘w_new’
gcc -std=gnu99 -shared -L/usr/local/lib64 -o bridge.so bridge2.affy.o bridge2.o bridge2_util.o bridge3.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/bridge.Rcheck/bridge/libs
** 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
* DONE (bridge)