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Package 184/251HostnameOS / ArchBUILDCHECKBUILD BIN
rama 1.12.0
Raphael Gottardo
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rama
Last Changed Rev: 29127 / Revision: 29143
Last Changed Date: 2007-12-10 08:46:24 -0800 (Mon, 10 Dec 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  OK  OK 
Package: rama
Version: 1.12.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check rama_1.12.0.tar.gz
StartedAt: 2007-12-11 08:03:13 -0800 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 08:10:14 -0800 (Tue, 11 Dec 2007)
EllapsedTime: 420.9 seconds
RetCode: 0
Status: OK
CheckDir: rama.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/rama.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-09 r43632)
* checking for file 'rama/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rama' version '1.12.0'
* 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
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './rama.tex' ...
LaTeX Warning: Citation `bib:lindley72' on page 1 undefined on input line 45.
LaTeX Warning: Citation `bib:besag_higdon99' on page 1 undefined on input line 
LaTeX Warning: Citation `bib:lewin03' on page 1 undefined on input line 47.
LaTeX Warning: Citation `bib:kerr00' on page 1 undefined on input line 48.
LaTeX Warning: Citation `bib:gottardo2003b' on page 1 undefined on input line 4
LaTeX Warning: Citation `bib:gelfand90' on page 1 undefined on input line 52.
LaTeX Warning: Citation `bib:brooks98' on page 1 undefined on input line 52.
LaTeX Warning: Citation `bib:radford03' on page 1 undefined on input line 54.
LaTeX Warning: Citation `bib:wout03' on page 2 undefined on input line 120.
LaTeX Warning: Citation `bib:tukey57' on page 3 undefined on input line 146.
LaTeX Warning: Citation `bib:box_cox64' on page 3 undefined on input line 148.
LaTeX Warning: Citation `bib:kerr00' on page 6 undefined on input line 223.
LaTeX Warning: Citation `bib:cui02' on page 6 undefined on input line 223.
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './rama.tex' ...
LaTeX Warning: Citation `bib:lindley72' on page 1 undefined on input line 45.
LaTeX Warning: Citation `bib:besag_higdon99' on page 1 undefined on input line 
LaTeX Warning: Citation `bib:lewin03' on page 1 undefined on input line 47.
LaTeX Warning: Citation `bib:kerr00' on page 1 undefined on input line 48.
LaTeX Warning: Citation `bib:gottardo2003b' on page 1 undefined on input line 4
LaTeX Warning: Citation `bib:gelfand90' on page 1 undefined on input line 52.
LaTeX Warning: Citation `bib:brooks98' on page 1 undefined on input line 52.
LaTeX Warning: Citation `bib:radford03' on page 1 undefined on input line 54.
LaTeX Warning: Citation `bib:wout03' on page 2 undefined on input line 120.
LaTeX Warning: Citation `bib:tukey57' on page 3 undefined on input line 146.
LaTeX Warning: Citation `bib:box_cox64' on page 3 undefined on input line 148.
LaTeX Warning: Citation `bib:kerr00' on page 6 undefined on input line 223.
LaTeX Warning: Citation `bib:cui02' on page 6 undefined on input line 223.
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './rama.tex' ...
* creating rama-manual.tex ... OK
* checking rama-manual.tex ... OK

rama.Rcheck/00install.out:

/loc/home/biocbuild/bbs-2.2-bioc/meat/rama.Rcheck
* Installing *source* package 'rama' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-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:122: warning: unused variable ‘SSeps_sd_new’
estimation_slice.c:121: warning: unused variable ‘SSeps_sd’
estimation_slice.c:117: warning: unused variable ‘pi’
estimation_slice.c:116: warning: unused variable ‘SS12’
estimation_slice.c:116: warning: unused variable ‘SSR2’
estimation_slice.c:116: warning: unused variable ‘SSR1’
estimation_slice.c:115: warning: unused variable ‘dens_epsilon_new’
estimation_slice.c:115: warning: unused variable ‘dens_epsilon’
estimation_slice.c:114: warning: unused variable ‘l_epsilon_new’
estimation_slice.c:114: warning: unused variable ‘l_epsilon’
estimation_slice.c:113: warning: unused variable ‘lambda_eps2_new’
estimation_slice.c:113: warning: unused variable ‘lambda_eps1_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/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-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:144: warning: unused variable ‘old_a’
ex_estimation_slice.c:143: warning: unused variable ‘old_b’
ex_estimation_slice.c:138: warning: unused variable ‘sum_res2’
ex_estimation_slice.c:137: warning: unused variable ‘sum_res1’
ex_estimation_slice.c:119: warning: unused variable ‘dens_t_new’
ex_estimation_slice.c:119: warning: unused variable ‘dens_t’
ex_estimation_slice.c:112: warning: unused variable ‘pi’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c mean.sd.c -o mean.sd.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c reorder.c -o reorder.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c util.c -o util.o
util.c: In function ‘product_mat_vec’:
util.c:574: warning: unused variable ‘k’
util.c: In function ‘slice_sampling_a’:
util.c:629: warning: suggest parentheses around comparison in operand of |
util.c:629: warning: suggest parentheses around comparison in operand of &
util.c:636: warning: suggest parentheses around comparison in operand of &
util.c:643: warning: suggest parentheses around comparison in operand of &
util.c:613: warning: unused variable ‘v’
util.c: In function ‘slice_sampling_b’:
util.c:703: warning: suggest parentheses around comparison in operand of |
util.c:703: warning: suggest parentheses around comparison in operand of &
util.c:710: warning: suggest parentheses around comparison in operand of &
util.c:717: warning: suggest parentheses around comparison in operand of &
util.c:686: warning: unused variable ‘v’
util.c: In function ‘slice_sampling_b2’:
util.c:767: warning: suggest parentheses around comparison in operand of &
util.c:775: warning: suggest parentheses around comparison in operand of &
util.c: In function ‘slice_sampling_a2’:
util.c:822: warning: suggest parentheses around comparison in operand of &
util.c:830: warning: suggest parentheses around comparison in operand of &
util.c: In function ‘slice_sampling_rho’:
util.c:876: warning: suggest parentheses around comparison in operand of |
util.c:876: warning: suggest parentheses around comparison in operand of &
util.c:883: warning: suggest parentheses around comparison in operand of &
util.c:890: warning: suggest parentheses around comparison in operand of &
util.c:860: warning: unused variable ‘v’
util.c: In function ‘slice_sampling_rho2’:
util.c:935: warning: suggest parentheses around comparison in operand of &
util.c:944: warning: suggest parentheses around comparison in operand of &
util.c: In function ‘slice_sampling_shift’:
util.c:1019: warning: suggest parentheses around comparison in operand of |
util.c:1019: warning: suggest parentheses around comparison in operand of &
util.c:1026: warning: suggest parentheses around comparison in operand of &
util.c:1033: warning: suggest parentheses around comparison in operand of &
util.c:1000: warning: unused variable ‘v’
util.c: In function ‘slice_sampling_shift2’:
util.c:1100: warning: suggest parentheses around comparison in operand of &
util.c:1108: warning: suggest parentheses around comparison in operand of &
util.c:1082: warning: unused variable ‘v’
util.c: In function ‘slice_sampling_p’:
util.c:1248: warning: suggest parentheses around comparison in operand of &
util.c:1256: 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/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** inst
** help
Note: ignoring empty \keyword entries
Note: removing empty section \details
 >>> 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)