rama 1.52.0
Raphael Gottardo
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/rama |
| Branch: RELEASE_3_6 |
| Last Commit: 4c52f41 |
| Last Changed Date: 2017-10-30 12:39:01 -0400 (Mon, 30 Oct 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf rama.buildbin-libdir && mkdir rama.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/rama_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=rama.buildbin-libdir --merge-multiarch rama_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL rama_1.52.0.zip && rm rama_1.52.0.tar.gz rama_1.52.0.zip
###
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install for i386
* installing *source* package 'rama' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c estimation_slice.c -o estimation_slice.o
estimation_slice.c: In function 'mcmc_shift':
estimation_slice.c:122:10: warning: unused variable 'SSeps_sd_new' [-Wunused-variable]
double SSeps_sd_new=0.;
^
estimation_slice.c:121:10: warning: unused variable 'SSeps_sd' [-Wunused-variable]
double SSeps_sd=0.;
^
estimation_slice.c:117:10: warning: unused variable 'pi' [-Wunused-variable]
double pi=3.14;
^
estimation_slice.c:116:24: warning: unused variable 'SS12' [-Wunused-variable]
double SSR1=0,SSR2=0,SS12=0;
^
estimation_slice.c:116:17: warning: unused variable 'SSR2' [-Wunused-variable]
double SSR1=0,SSR2=0,SS12=0;
^
estimation_slice.c:116:10: warning: unused variable 'SSR1' [-Wunused-variable]
double SSR1=0,SSR2=0,SS12=0;
^
estimation_slice.c:115:25: warning: unused variable 'dens_epsilon_new' [-Wunused-variable]
double dens_epsilon=0,dens_epsilon_new=0;
^
estimation_slice.c:115:10: warning: unused variable 'dens_epsilon' [-Wunused-variable]
double dens_epsilon=0,dens_epsilon_new=0;
^
estimation_slice.c:114:22: warning: unused variable 'l_epsilon_new' [-Wunused-variable]
double l_epsilon=0,l_epsilon_new=0;
^
estimation_slice.c:114:10: warning: unused variable 'l_epsilon' [-Wunused-variable]
double l_epsilon=0,l_epsilon_new=0;
^
estimation_slice.c:113:27: warning: unused variable 'lambda_eps2_new' [-Wunused-variable]
double lambda_eps1_new, lambda_eps2_new;
^
estimation_slice.c:113:10: warning: unused variable 'lambda_eps1_new' [-Wunused-variable]
double lambda_eps1_new, lambda_eps2_new;
^
estimation_slice.c: In function 'slice_sampling_lambda_eps':
estimation_slice.c:484:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(J>0 & z<log_f_L)
^
estimation_slice.c:493:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & z<log_f_R)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c ex_estimation_slice.c -o ex_estimation_slice.o
ex_estimation_slice.c: In function 'mcmc':
ex_estimation_slice.c:144:10: warning: unused variable 'old_a' [-Wunused-variable]
double old_a=0,width_a=1.;
^
ex_estimation_slice.c:143:10: warning: unused variable 'old_b' [-Wunused-variable]
double old_b=0,width_b=5.;
^
ex_estimation_slice.c:138:10: warning: unused variable 'sum_res2' [-Wunused-variable]
double sum_res2;
^
ex_estimation_slice.c:137:10: warning: unused variable 'sum_res1' [-Wunused-variable]
double sum_res1;
^
ex_estimation_slice.c:119:19: warning: unused variable 'dens_t_new' [-Wunused-variable]
double dens_t=0,dens_t_new=0;
^
ex_estimation_slice.c:119:10: warning: unused variable 'dens_t' [-Wunused-variable]
double dens_t=0,dens_t_new=0;
^
ex_estimation_slice.c:112:10: warning: unused variable 'pi' [-Wunused-variable]
double pi=3.14;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c mean.sd.c -o mean.sd.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c reorder.c -o reorder.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c util.c -o util.o
util.c: In function 'product_mat_vec':
util.c:574:11: warning: unused variable 'k' [-Wunused-variable]
int i,j,k;
^
util.c: In function 'slice_sampling_a':
util.c:629:17: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:629:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:636:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_L & mL<L)
^
util.c:643:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_R & mR>R)
^
util.c:613:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, a1;
^
util.c: In function 'slice_sampling_b':
util.c:703:17: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:703:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:710:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_L & mL<L)
^
util.c:717:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_R & mR>R)
^
util.c:686:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, b1;
^
util.c: In function 'slice_sampling_b2':
util.c:767:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(J>0 & z<log_f_L)
^
util.c:775:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & z<log_f_R)
^
util.c: In function 'slice_sampling_a2':
util.c:822:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(J>0 & z<log_f_L)
^
util.c:830:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & z<log_f_R)
^
util.c: In function 'slice_sampling_rho':
util.c:876:17: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:876:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:883:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_L & mL<L)
^
util.c:890:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_R & mR>R)
^
util.c:860:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, rho_new;
^
util.c: In function 'slice_sampling_rho2':
util.c:935:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(J>0 & z<log_f_L)
^
util.c:944:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & z<log_f_R)
^
util.c: In function 'slice_sampling_shift':
util.c:1019:17: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:1019:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:1026:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_L & mL<L)
^
util.c:1033:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_R & mR>R)
^
util.c:1000:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, shift_new;
^
util.c: In function 'slice_sampling_shift2':
util.c:1100:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(J>0 & z<log_f_L)
^
util.c:1108:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & z<log_f_R)
^
util.c:1082:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, shift_new;
^
util.c: In function 'slice_sampling_p':
util.c:1248:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(J>0 & z<log_f_L)
^
util.c:1256:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & z<log_f_R)
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o rama.dll tmp.def estimation_slice.o ex_estimation_slice.o mean.sd.o reorder.o util.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/rama.buildbin-libdir/rama/libs/i386
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'rama'
finding HTML links ... done
arrange.row html
est.shift html
fit.model html
hiv html
is.row.na html
ls.effect html
mat.mean html
ratio.plot html
weight.plot html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'rama' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c estimation_slice.c -o estimation_slice.o
estimation_slice.c: In function 'mcmc_shift':
estimation_slice.c:122:10: warning: unused variable 'SSeps_sd_new' [-Wunused-variable]
double SSeps_sd_new=0.;
^
estimation_slice.c:121:10: warning: unused variable 'SSeps_sd' [-Wunused-variable]
double SSeps_sd=0.;
^
estimation_slice.c:117:10: warning: unused variable 'pi' [-Wunused-variable]
double pi=3.14;
^
estimation_slice.c:116:24: warning: unused variable 'SS12' [-Wunused-variable]
double SSR1=0,SSR2=0,SS12=0;
^
estimation_slice.c:116:17: warning: unused variable 'SSR2' [-Wunused-variable]
double SSR1=0,SSR2=0,SS12=0;
^
estimation_slice.c:116:10: warning: unused variable 'SSR1' [-Wunused-variable]
double SSR1=0,SSR2=0,SS12=0;
^
estimation_slice.c:115:25: warning: unused variable 'dens_epsilon_new' [-Wunused-variable]
double dens_epsilon=0,dens_epsilon_new=0;
^
estimation_slice.c:115:10: warning: unused variable 'dens_epsilon' [-Wunused-variable]
double dens_epsilon=0,dens_epsilon_new=0;
^
estimation_slice.c:114:22: warning: unused variable 'l_epsilon_new' [-Wunused-variable]
double l_epsilon=0,l_epsilon_new=0;
^
estimation_slice.c:114:10: warning: unused variable 'l_epsilon' [-Wunused-variable]
double l_epsilon=0,l_epsilon_new=0;
^
estimation_slice.c:113:27: warning: unused variable 'lambda_eps2_new' [-Wunused-variable]
double lambda_eps1_new, lambda_eps2_new;
^
estimation_slice.c:113:10: warning: unused variable 'lambda_eps1_new' [-Wunused-variable]
double lambda_eps1_new, lambda_eps2_new;
^
estimation_slice.c: In function 'slice_sampling_lambda_eps':
estimation_slice.c:484:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(J>0 & z<log_f_L)
^
estimation_slice.c:493:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & z<log_f_R)
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c ex_estimation_slice.c -o ex_estimation_slice.o
ex_estimation_slice.c: In function 'mcmc':
ex_estimation_slice.c:144:10: warning: unused variable 'old_a' [-Wunused-variable]
double old_a=0,width_a=1.;
^
ex_estimation_slice.c:143:10: warning: unused variable 'old_b' [-Wunused-variable]
double old_b=0,width_b=5.;
^
ex_estimation_slice.c:138:10: warning: unused variable 'sum_res2' [-Wunused-variable]
double sum_res2;
^
ex_estimation_slice.c:137:10: warning: unused variable 'sum_res1' [-Wunused-variable]
double sum_res1;
^
ex_estimation_slice.c:119:19: warning: unused variable 'dens_t_new' [-Wunused-variable]
double dens_t=0,dens_t_new=0;
^
ex_estimation_slice.c:119:10: warning: unused variable 'dens_t' [-Wunused-variable]
double dens_t=0,dens_t_new=0;
^
ex_estimation_slice.c:112:10: warning: unused variable 'pi' [-Wunused-variable]
double pi=3.14;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c mean.sd.c -o mean.sd.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c reorder.c -o reorder.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c util.c -o util.o
util.c: In function 'product_mat_vec':
util.c:574:11: warning: unused variable 'k' [-Wunused-variable]
int i,j,k;
^
util.c: In function 'slice_sampling_a':
util.c:629:17: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:629:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:636:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_L & mL<L)
^
util.c:643:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_R & mR>R)
^
util.c:613:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, a1;
^
util.c: In function 'slice_sampling_b':
util.c:703:17: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:703:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:710:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_L & mL<L)
^
util.c:717:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_R & mR>R)
^
util.c:686:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, b1;
^
util.c: In function 'slice_sampling_b2':
util.c:767:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(J>0 & z<log_f_L)
^
util.c:775:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & z<log_f_R)
^
util.c: In function 'slice_sampling_a2':
util.c:822:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(J>0 & z<log_f_L)
^
util.c:830:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & z<log_f_R)
^
util.c: In function 'slice_sampling_rho':
util.c:876:17: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:876:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:883:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_L & mL<L)
^
util.c:890:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_R & mR>R)
^
util.c:860:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, rho_new;
^
util.c: In function 'slice_sampling_rho2':
util.c:935:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(J>0 & z<log_f_L)
^
util.c:944:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & z<log_f_R)
^
util.c: In function 'slice_sampling_shift':
util.c:1019:17: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:1019:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
^
util.c:1026:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_L & mL<L)
^
util.c:1033:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(z>log_f_R & mR>R)
^
util.c:1000:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, shift_new;
^
util.c: In function 'slice_sampling_shift2':
util.c:1100:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(J>0 & z<log_f_L)
^
util.c:1108:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & z<log_f_R)
^
util.c:1082:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, shift_new;
^
util.c: In function 'slice_sampling_p':
util.c:1248:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(J>0 & z<log_f_L)
^
util.c:1256:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(K>0 & z<log_f_R)
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o rama.dll tmp.def estimation_slice.o ex_estimation_slice.o mean.sd.o reorder.o util.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/rama.buildbin-libdir/rama/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rama' as rama_1.52.0.zip
* DONE (rama)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'rama' successfully unpacked and MD5 sums checked
In R CMD INSTALL