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CHECK report for rama on malbec1

This page was generated on 2018-04-12 13:07:06 -0400 (Thu, 12 Apr 2018).

Package 1115/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rama
Version: 1.52.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rama_1.52.0.tar.gz
StartedAt: 2018-04-12 02:08:03 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:08:28 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 25.0 seconds
RetCode: 0
Status:  OK 
CheckDir: rama.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rama_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/rama.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rama/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rama’ version ‘1.52.0’
* checking package namespace information ... OK
* checking package dependencies ... 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 for sufficient/correct file permissions ... OK
* checking whether package ‘rama’ can be installed ... OK
* 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
* 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
File ‘rama/libs/rama.so’:
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Objects: ‘estimation_slice.o’, ‘ex_estimation_slice.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
weight.plot 5.644      0   5.648
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/rama.Rcheck/00check.log’
for details.

Installation output

rama.Rcheck/00install.out

* installing *source* package ‘rama’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-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 -I/home/biocbuild/bbs-3.6-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 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c mean.sd.c -o mean.sd.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c reorder.c -o reorder.o
gcc -I/home/biocbuild/bbs-3.6-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)
          ^
g++ -shared -L/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/rama.Rcheck/rama/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rama)

Tests output

Example timings

rama.Rcheck/rama-Ex.timings

nameusersystemelapsed
arrange.row0.1720.0120.183
est.shift0.4600.0000.459
fit.model0.6320.0040.636
is.row.na0.0000.0000.001
ls.effect0.2120.0040.217
mat.mean0.1040.0000.106
ratio.plot0.4640.0000.462
weight.plot5.6440.0005.648