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INSTALL report for rama on tokay1

This page was generated on 2019-04-13 11:19:23 -0400 (Sat, 13 Apr 2019).

Package 1244/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rama 1.56.0
Raphael Gottardo
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/rama
Branch: RELEASE_3_8
Last Commit: a611930
Last Changed Date: 2018-10-30 11:41:41 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rama
Version: 1.56.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/rama_1.56.0.tar.gz && rm -rf rama.buildbin-libdir && mkdir rama.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rama.buildbin-libdir rama_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL rama_1.56.0.zip && rm rama_1.56.0.tar.gz rama_1.56.0.zip
StartedAt: 2019-04-12 18:38:01 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 18:38:29 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 27.5 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/rama_1.56.0.tar.gz && rm -rf rama.buildbin-libdir && mkdir rama.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rama.buildbin-libdir rama_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL rama_1.56.0.zip && rm rama_1.56.0.tar.gz rama_1.56.0.zip
###
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100  321k  100  321k    0     0  4452k      0 --:--:-- --:--:-- --:--:-- 4666k

install for i386

* installing *source* package 'rama' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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/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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/rama.buildbin-libdir/rama/libs/i386
** R
** data
** byte-compile and prepare 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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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/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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/rama.buildbin-libdir/rama/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rama' as rama_1.56.0.zip
* DONE (rama)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'rama' successfully unpacked and MD5 sums checked
In R CMD INSTALL