bridge 1.34.0
Raphael Gottardo
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/bridge | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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###
### Running command:
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### rm -rf bridge.buildbin-libdir bridge.Rcheck && mkdir bridge.buildbin-libdir bridge.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bridge.buildbin-libdir bridge_1.34.0.tar.gz >bridge.Rcheck\00install.out 2>&1 && cp bridge.Rcheck\00install.out bridge-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=bridge.buildbin-libdir --install="check:bridge-install.out" --force-multiarch --no-vignettes --timings bridge_1.34.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/bridge.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bridge/DESCRIPTION' ... OK
* this is package 'bridge' version '1.34.0'
* 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 whether package 'bridge' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'rama' which was already attached by Depends.
Please remove these calls from your code.
Package in Depends field not imported from: 'rama'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/biocbld/bbs-3.2-bioc/meat/bridge.buildbin-libdir/bridge/libs/i386/bridge.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/biocbld/bbs-3.2-bioc/meat/bridge.buildbin-libdir/bridge/libs/x64/bridge.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [0s] OK
** running examples for arch 'x64' ... [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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'C:/biocbld/bbs-3.2-bioc/meat/bridge.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'bridge' ...
** libs
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/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 -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/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 -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/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 -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/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 -m32 -shared -s -static-libgcc -o bridge.dll tmp.def bridge2.affy.o bridge2.o bridge2_util.o bridge3.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LC:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/bridge.buildbin-libdir/bridge/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'bridge' ...
** libs
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/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"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/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"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/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"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/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/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LC:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/bridge.buildbin-libdir/bridge/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bridge' as bridge_1.34.0.zip
* DONE (bridge)