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BioC 3.3: INSTALL report for rama on zin2

This page was generated on 2016-10-13 12:40:52 -0700 (Thu, 13 Oct 2016).

Package 925/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rama 1.46.0
Raphael Gottardo
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/rama
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rama
Version: 1.46.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD INSTALL rama
StartedAt: 2016-10-12 18:01:02 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 18:01:05 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 3.0 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD INSTALL rama
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.3-bioc/R/library’
* installing *source* package ‘rama’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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)
          ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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;
          ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mean.sd.c -o mean.sd.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c reorder.c -o reorder.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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)
          ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o rama.so estimation_slice.o ex_estimation_slice.o mean.sd.o reorder.o util.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/R/library/rama/libs
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rama)