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CHECK 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:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rama.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rama_1.56.0.tar.gz
StartedAt: 2019-04-13 04:50:55 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:52:35 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 100.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: rama.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rama.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rama_1.56.0.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/rama.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rama/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rama' version '1.56.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'rama' can be installed ... WARNING
Found the following significant warnings:
  estimation_slice.c:484:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  estimation_slice.c:493:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:629:17: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  util.c:629:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:636:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:643:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:703:17: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  util.c:703:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:710:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:717:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:767:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:775:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:822:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:830:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:876:17: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  util.c:876:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:883:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:890:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:935:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:944:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:1019:17: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  util.c:1019:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:1026:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:1033:8: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:1100:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:1108:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:1248:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  util.c:1256:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/rama.Rcheck/00install.out' for details.
* 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
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fit.model: no visible global function definition for 'median'
fit.model: no visible global function definition for 'mad'
fit.model: no visible global function definition for 'quantile'
ratio.plot: no visible global function definition for 'plot'
weight.plot: no visible global function definition for 'image'
weight.plot: no visible global function definition for 'grey'
Undefined global functions or variables:
  grey image mad median plot quantile
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "image", "plot")
  importFrom("stats", "mad", "median", "quantile")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: is.row.na.Rd:40: Dropping empty section \keyword
prepare_Rd: ls.effect.Rd:38-39: Dropping empty section \details
* 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:/Users/biocbuild/bbs-3.8-bioc/R/library/rama/libs/i386/rama.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
weight.plot 6.94      0    6.94
** running examples for arch 'x64' ... 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/rama.Rcheck/00check.log'
for details.

Installation output

rama.Rcheck/00install.out

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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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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
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

Tests output

Example timings

rama.Rcheck/examples_i386/rama-Ex.timings

nameusersystemelapsed
arrange.row0.110.000.11
est.shift0.400.000.41
fit.model0.410.020.42
is.row.na000
ls.effect0.160.010.17
mat.mean0.150.000.16
ratio.plot0.380.000.37
weight.plot6.940.006.94

rama.Rcheck/examples_x64/rama-Ex.timings

nameusersystemelapsed
arrange.row0.070.020.09
est.shift0.380.010.39
fit.model0.320.000.31
is.row.na000
ls.effect0.180.000.19
mat.mean0.160.000.15
ratio.plot0.360.000.36
weight.plot4.780.024.83