rama 1.47.0
Raphael Gottardo
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rama | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | [ OK ] | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / 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 http://zin1/BBS/3.4/bioc/src/contrib/rama_1.47.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=rama.buildbin-libdir --merge-multiarch rama_1.47.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL rama_1.47.0.zip && rm rama_1.47.0.tar.gz rama_1.47.0.zip
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install for i386
* installing *source* package 'rama' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c mean.sd.c -o mean.sd.o
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c reorder.c -o reorder.o
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -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/gcc -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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/rama.buildbin-libdir/rama/libs/i386
** R
** data
** 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 'rama' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c mean.sd.c -o mean.sd.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c reorder.c -o reorder.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -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/gcc -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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/rama.buildbin-libdir/rama/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rama' as rama_1.47.0.zip
* DONE (rama)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'rama' successfully unpacked and MD5 sums checked