bgx 1.22.0
Ernest Turro
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/bgx | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/bgx.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bgx/DESCRIPTION’ ... OK
* this is package ‘bgx’ version ‘1.22.0’
* 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 whether package ‘bgx’ can be installed ... OK
* checking installed package size ... 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 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: analysis.bgx.Rd:48-49: Dropping empty section \examples
prepare_Rd: mcmc.bgx.Rd:48-49: Dropping empty section \examples
prepare_Rd: readOutput.bgx.Rd:23-24: Dropping empty section \examples
prepare_Rd: saveAffinityPlot.bgx.Rd:18-19: Dropping empty section \details
prepare_Rd: saveAffinityPlot.bgx.Rd:20-21: Dropping empty section \value
prepare_Rd: saveAffinityPlot.bgx.Rd:26-27: Dropping empty section \examples
prepare_Rd: setupVars.bgx.Rd:21-22: Dropping empty section \details
prepare_Rd: setupVars.bgx.Rd:43-44: Dropping empty section \examples
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/bgx.Rcheck/bgx/libs/bgx.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Objects: ‘bgx.o’, ‘bgx_frontend.o’, ‘sokal.o’
Found ‘exit’, possibly from ‘exit’ (C)
Objects: ‘bgx.o’, ‘bgx_frontend.o’
Compiled code should not call functions 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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
bgx 37.05 0.368 38.144
* 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 2 notes.
See
‘/loc/home/biocbuild/bbs-2.11-bioc/meat/bgx.Rcheck/00check.log’
for details.
* installing *source* package ‘bgx’ ...
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking for C compiler vendor... gnu
checking whether C compiler accepts -ffast-math... yes
checking whether C compiler accepts -O3... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc architecture flag...
checking for x86 cpuid 0 output... a:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 6f6:6020800:4e3bd:bfebfbff
checking whether C compiler accepts -march=pentiumpro... no
checking whether C compiler accepts -mcpu=pentiumpro... no
checking whether C compiler accepts -mpentiumpro... no
checking for gcc architecture flag... unknown
checking for gcc -std=gnu99 option to accept ISO C99... none needed
checking for main in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fpic -g -O2 -Wall -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fpic -g -O2 -Wall -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fpic -g -O2 -Wall -g -O2 -ffast-math -O3 -c qnorm.c -o qnorm.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fpic -g -O2 -Wall -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fpic -g -O2 -Wall -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
g++ -shared -L/usr/local/lib64 -o bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
rm -r ../boostIncl
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/bgx.Rcheck/bgx/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘bgx.Rnw’
** testing if installed package can be loaded
* DONE (bgx)