rama 1.33.0
Raphael Gottardo
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rama | | Last Changed Rev: 74164 / Revision: 74774 | | Last Changed Date: 2013-03-11 11:14:51 -0700 (Mon, 11 Mar 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 Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/rama.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'rama/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rama' version '1.33.0'
* 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 ... [5s/5s] 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/i386/rama.so':
Found '_printf', possibly from 'printf' (C)
Objects: 'estimation_slice.o', 'ex_estimation_slice.o'
Found '_puts', possibly from 'printf' (C), 'puts' (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 sizes of PDF files under 'inst/doc' ... OK
* 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 ... [12s/12s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
weight.plot 6.473 0.063 6.545
* 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.
* installing *source* package 'rama' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -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 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -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 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c mean.sd.c -o mean.sd.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c reorder.c -o reorder.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -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 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'rama.Rnw'
** testing if installed package can be loaded
* DONE (rama)