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CHECK report for rama on malbec2

This page was generated on 2019-04-09 11:23:04 -0400 (Tue, 09 Apr 2019).

Package 1281/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rama 1.57.0
Raphael Gottardo
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/rama
Branch: master
Last Commit: a1a1fbb
Last Changed Date: 2018-10-30 11:54:26 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: rama
Version: 1.57.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rama.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rama_1.57.0.tar.gz
StartedAt: 2019-04-09 02:59:45 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:00:15 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 30.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: rama.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rama.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rama_1.57.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rama.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.57.0’
* 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 ... 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 ‘/home/biocbuild/bbs-3.9-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
* 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 is not available
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/rama/libs/rama.so’:
  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 ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
weight.plot 5.275      0   5.298
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/rama.Rcheck/00check.log’
for details.

Installation output

rama.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL rama
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘rama’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-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-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c reorder.c -o reorder.o
gcc -I"/home/biocbuild/bbs-3.9-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 -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-rama/00new/rama/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rama)

Tests output

Example timings

rama.Rcheck/rama-Ex.timings

nameusersystemelapsed
arrange.row0.1390.0030.148
est.shift0.3940.0000.395
fit.model0.3980.0000.399
is.row.na0.0000.0000.001
ls.effect0.1860.0040.194
mat.mean0.1720.0000.172
ratio.plot0.4370.0000.438
weight.plot5.2750.0005.298