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Package 517/671HostnameOS / ArchBUILDCHECKBUILD BIN
rama 1.34.0
Raphael Gottardo
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/rama
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: rama
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rama_1.34.0.tar.gz
StartedAt: 2013-05-01 09:51:36 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 09:52:24 -0700 (Wed, 01 May 2013)
EllapsedTime: 47.9 seconds
RetCode: 0
Status:  OK 
CheckDir: rama.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/rama.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'rama/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rama' version '1.34.0'
* 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 ... [3s/4s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... OK
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/rama.Rcheck/rama/libs/rama.so':
  Found '_printf', possibly from 'printf' (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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'chicago.bst', 'chicago.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [17s/18s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
weight.plot 10.312  0.088  10.523
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/rama.Rcheck/00check.log'
for details.

rama.Rcheck/00install.out:

* installing *source* package 'rama' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c estimation_slice.c -o estimation_slice.o
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;
         ^
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:121:10: warning: unused variable 'SSeps_sd' [-Wunused-variable]
  double SSeps_sd=0.;
         ^
estimation_slice.c:122:10: warning: unused variable 'SSeps_sd_new' [-Wunused-variable]
  double SSeps_sd_new=0.;
         ^
12 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ex_estimation_slice.c -o ex_estimation_slice.o
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;
         ^
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:119:19: 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;
         ^
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mean.sd.c -o mean.sd.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c reorder.c -o reorder.o
reorder.c:15:4: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        x=data[i][0];
         ˜^˜˜˜˜˜˜˜˜˜
reorder.c:16:4: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        y=data[i][1];
         ˜^˜˜˜˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -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:1002:9: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  int K=p;
      ˜ ^
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;
            ^
11 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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 /Users/biocbuild/bbs-2.12-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)

rama.Rcheck/rama-Ex.timings:

nameusersystemelapsed
arrange.row0.8100.1110.924
est.shift1.0090.0931.113
fit.model0.8840.0790.972
is.row.na0.0120.0040.375
ls.effect1.5060.0861.616
mat.mean0.4970.0790.588
ratio.plot0.9050.0810.997
weight.plot10.312 0.08810.523