##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rama.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rama_1.68.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/rama.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.68.0’
* 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’
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 quantile
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "image")
  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 ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rama/libs/rama.so’:
  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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/rama.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rama
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘rama’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c estimation_slice.c -o estimation_slice.o
estimation_slice.c:115:25: warning: unused variable 'dens_epsilon_new' [-Wunused-variable]
  double dens_epsilon=0,dens_epsilon_new=0;
                        ^
estimation_slice.c:121:10: warning: unused variable 'SSeps_sd' [-Wunused-variable]
  double SSeps_sd=0.;
         ^
estimation_slice.c:116:10: warning: unused variable 'SSR1' [-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:122:10: warning: unused variable 'SSeps_sd_new' [-Wunused-variable]
  double SSeps_sd_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:114:22: warning: unused variable 'l_epsilon_new' [-Wunused-variable]
  double l_epsilon=0,l_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: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:116:24: warning: unused variable 'SS12' [-Wunused-variable]
  double SSR1=0,SSR2=0,SS12=0;
                       ^
estimation_slice.c:117:10: warning: unused variable 'pi' [-Wunused-variable]
  double pi=3.14;
         ^
12 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ex_estimation_slice.c -o ex_estimation_slice.o
ex_estimation_slice.c:112:10: warning: unused variable 'pi' [-Wunused-variable]
  double pi=3.14;
         ^
ex_estimation_slice.c:143:10: warning: unused variable 'old_b' [-Wunused-variable]
  double old_b=0,width_b=5.;
         ^
ex_estimation_slice.c:144:10: warning: unused variable 'old_a' [-Wunused-variable]
  double old_a=0,width_a=1.;
         ^
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:119:19: warning: unused variable 'dens_t_new' [-Wunused-variable]
  double dens_t=0,dens_t_new=0;
                  ^
ex_estimation_slice.c:137:10: warning: unused variable 'sum_res1' [-Wunused-variable]
  double sum_res1;
         ^
ex_estimation_slice.c:138:10: warning: unused variable 'sum_res2' [-Wunused-variable]
  double sum_res2;
         ^
7 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mean.sd.c -o mean.sd.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c reorder.c -o reorder.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c util.c -o util.o
util.c:574:11: warning: unused variable 'k' [-Wunused-variable]
  int i,j,k;
          ^
util.c:629:13: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
  while(K>0 & (z<log_f_L | z<log_f_R))
        ~~~~^
util.c:629:13: note: place parentheses around the '>' expression to silence this warning
  while(K>0 & (z<log_f_L | z<log_f_R))
            ^
        (  )
util.c:629:13: note: place parentheses around the & expression to evaluate it first
  while(K>0 & (z<log_f_L | z<log_f_R))
            ^
          (                          )
util.c:613:13: warning: unused variable 'v' [-Wunused-variable]
  double u, v, L, R, z, a1;
            ^
util.c:703:13: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
  while(K>0 & (z<log_f_L | z<log_f_R))
        ~~~~^
util.c:703:13: note: place parentheses around the '>' expression to silence this warning
  while(K>0 & (z<log_f_L | z<log_f_R))
            ^
        (  )
util.c:703:13: note: place parentheses around the & expression to evaluate it first
  while(K>0 & (z<log_f_L | z<log_f_R))
            ^
          (                          )
util.c:686:13: warning: unused variable 'v' [-Wunused-variable]
  double u, v, L, R, z, b1;
            ^
util.c:876:13: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
  while(K>0 & (z<log_f_L | z<log_f_R))
        ~~~~^
util.c:876:13: note: place parentheses around the '>' expression to silence this warning
  while(K>0 & (z<log_f_L | z<log_f_R))
            ^
        (  )
util.c:876:13: note: place parentheses around the & expression to evaluate it first
  while(K>0 & (z<log_f_L | z<log_f_R))
            ^
          (                          )
util.c:860:13: warning: unused variable 'v' [-Wunused-variable]
  double u, v, L, R, z, rho_new;
            ^
util.c:1019:13: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
  while(K>0 & (z<log_f_L | z<log_f_R))
        ~~~~^
util.c:1019:13: note: place parentheses around the '>' expression to silence this warning
  while(K>0 & (z<log_f_L | z<log_f_R))
            ^
        (  )
util.c:1019:13: note: place parentheses around the & expression to evaluate it first
  while(K>0 & (z<log_f_L | z<log_f_R))
            ^
          (                          )
util.c:1000:13: warning: unused variable 'v' [-Wunused-variable]
  double u, v, L, R, z, shift_new;
            ^
util.c:1082:13: warning: unused variable 'v' [-Wunused-variable]
  double u, v, L, R, z, shift_new;
            ^
10 warnings generated.
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rama.so estimation_slice.o ex_estimation_slice.o mean.sd.o reorder.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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)