Package: rama

Version: 1.10.0

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check rama_1.10.0.tar.gz

RetCode: 0

Time: 75.8 seconds

Status: OK

CheckDir: rama.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/rama.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'rama/DESCRIPTION' ... OK
* this is package 'rama' version '1.10.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'rama' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... 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 ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating rama-Ex.R ... OK
* checking examples ... OK
* creating rama-manual.tex ... OK
* checking rama-manual.tex ... OK

* Installing *source* package 'rama' ...
** libs
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -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:113: warning: unused variable `lambda_eps1_new'
estimation_slice.c:113: warning: unused variable `lambda_eps2_new'
estimation_slice.c:114: warning: unused variable `l_epsilon'
estimation_slice.c:114: warning: unused variable `l_epsilon_new'
estimation_slice.c:115: warning: unused variable `dens_epsilon'
estimation_slice.c:115: warning: unused variable `dens_epsilon_new'
estimation_slice.c:116: warning: unused variable `SSR1'
estimation_slice.c:116: warning: unused variable `SSR2'
estimation_slice.c:116: warning: unused variable `SS12'
estimation_slice.c:117: warning: unused variable `pi'
estimation_slice.c:121: warning: unused variable `SSeps_sd'
estimation_slice.c:122: warning: unused variable `SSeps_sd_new'
estimation_slice.c: In function `slice_sampling_lambda_eps':
estimation_slice.c:484: warning: suggest parentheses around comparison in operand of &
estimation_slice.c:493: warning: suggest parentheses around comparison in operand of &
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -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:112: warning: unused variable `pi'
ex_estimation_slice.c:119: warning: unused variable `dens_t'
ex_estimation_slice.c:119: warning: unused variable `dens_t_new'
ex_estimation_slice.c:137: warning: unused variable `sum_res1'
ex_estimation_slice.c:138: warning: unused variable `sum_res2'
ex_estimation_slice.c:143: warning: unused variable `old_b'
ex_estimation_slice.c:144: warning: unused variable `old_a'
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c mean.sd.c -o mean.sd.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c reorder.c -o reorder.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c util.c -o util.o
util.c: In function `qr_solve':
util.c:570: warning: implicit declaration of function `dqrdc2_'
util.c:585: warning: implicit declaration of function `dqrcf_'
util.c:549: warning: unused variable `vmax'
util.c: In function `inverse':
util.c:608: warning: unused variable `j'
util.c: In function `product_mat_vec':
util.c:655: warning: unused variable `k'
util.c: In function `slice_sampling_a':
util.c:752: warning: suggest parentheses around comparison in operand of |
util.c:752: warning: suggest parentheses around comparison in operand of &
util.c:759: warning: suggest parentheses around comparison in operand of &
util.c:766: warning: suggest parentheses around comparison in operand of &
util.c:736: warning: unused variable `v'
util.c: In function `slice_sampling_b':
util.c:826: warning: suggest parentheses around comparison in operand of |
util.c:826: warning: suggest parentheses around comparison in operand of &
util.c:833: warning: suggest parentheses around comparison in operand of &
util.c:840: warning: suggest parentheses around comparison in operand of &
util.c:809: warning: unused variable `v'
util.c: In function `slice_sampling_b2':
util.c:890: warning: suggest parentheses around comparison in operand of &
util.c:898: warning: suggest parentheses around comparison in operand of &
util.c: In function `slice_sampling_a2':
util.c:945: warning: suggest parentheses around comparison in operand of &
util.c:953: warning: suggest parentheses around comparison in operand of &
util.c: In function `slice_sampling_rho':
util.c:999: warning: suggest parentheses around comparison in operand of |
util.c:999: warning: suggest parentheses around comparison in operand of &
util.c:1006: warning: suggest parentheses around comparison in operand of &
util.c:1013: warning: suggest parentheses around comparison in operand of &
util.c:983: warning: unused variable `v'
util.c: In function `slice_sampling_rho2':
util.c:1058: warning: suggest parentheses around comparison in operand of &
util.c:1067: warning: suggest parentheses around comparison in operand of &
util.c: In function `slice_sampling_shift':
util.c:1142: warning: suggest parentheses around comparison in operand of |
util.c:1142: warning: suggest parentheses around comparison in operand of &
util.c:1149: warning: suggest parentheses around comparison in operand of &
util.c:1156: warning: suggest parentheses around comparison in operand of &
util.c:1123: warning: unused variable `v'
util.c: In function `slice_sampling_shift2':
util.c:1223: warning: suggest parentheses around comparison in operand of &
util.c:1231: warning: suggest parentheses around comparison in operand of &
util.c:1205: warning: unused variable `v'
util.c: In function `slice_sampling_p':
util.c:1371: warning: suggest parentheses around comparison in operand of &
util.c:1379: warning: suggest parentheses around comparison in operand of &
gcc -std=gnu99 -shared -L/usr/local/lib -o rama.so estimation_slice.o ex_estimation_slice.o mean.sd.o reorder.o util.o   -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** inst
** help
Note: unmatched right brace in 'arrange.row' on or after line 23
Note: unmatched right brace in 'arrange.row' on or after line 27
Note: unmatched right brace in 'est.shift' on or after line 76
Note: unmatched right brace in 'fit.model' on or after line 95
Note: unmatched right brace in 'ls.effect' on or after line 43
Note: unmatched right brace in 'ratio.plot' on or after line 20
Note: unmatched right brace in 'ratio.plot' on or after line 24
Note: unmatched right brace in 'weight.plot' on or after line 26
Note: unmatched right brace in 'weight.plot' on or after line 30
 >>> Building/Updating help pages for package 'rama'
     Formats: text html latex example 
  arrange.row                       text    html    latex   example
  est.shift                         text    html    latex   example
  fit.model                         text    html    latex   example
  hiv                               text    html    latex
  is.row.na                         text    html    latex   example
  ls.effect                         text    html    latex   example
  mat.mean                          text    html    latex   example
  ratio.plot                        text    html    latex   example
  weight.plot                       text    html    latex   example
** building package indices ...
* DONE (rama)