BGmix 1.20.0
Alex Lewin
| Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/BGmix | | Last Changed Rev: 75263 / Revision: 81334 | | 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 | N O T S U P P O R T E D |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BGmix.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BGmix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BGmix' version '1.20.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'BGmix' can be installed ... [10s/10s] 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 ... NOTE
ccSummary: warning in agrep("genes", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("conds", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("effects", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("mix comps", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("variance", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("mix prior", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("niter", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("nburn", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("nthin", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("seed", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("move", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("fullBayes", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("aa updated", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta updated", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambdas updated", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("tau's", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("t-dist", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("(params)", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("(predictive)", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta_up", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta_down", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambda+ for", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambda- for", summ, max = 0): partial
argument match of 'max' to 'max.distance'
plotFDR: warning in legend(xx, yy, leg = c("FDR=5%", "FDR=10%"), col =
c("red", "blue"), lty = c(1, 1), bg = "white"): partial argument
match of 'leg' to 'legend'
* checking Rd files ... OK
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/BGmix.Rcheck/BGmix/libs/BGmix.so':
Found '__ZSt4cerr', possibly from 'std::cerr' (C++)
Object: 'updates_BGmix.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' ... OK
* checking examples ... [74s/78s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
FDRforTailPP 11.858 1.368 13.375
BGmix 10.096 0.542 12.061
BGmix-package 6.252 0.289 6.778
EstimatePi0 5.854 0.448 6.976
FDRplotTailPP 5.233 0.911 6.800
plotMixDensity 5.632 0.352 6.305
histTailPP 5.213 0.445 5.706
TailPP 5.255 0.393 5.696
* 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/BGmix.Rcheck/00check.log'
for details.
* installing *source* package 'BGmix' ...
checking for gcc... llvm-gcc-4.2 -arch x86_64 -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 llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C99... none needed
checking for cos 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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -mtune=core2 -g -O2 -DUSING_R -c BGmix_main.cpp -o BGmix_main.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -mtune=core2 -g -O2 -DUSING_R -c rundir.cpp -o rundir.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -mtune=core2 -g -O2 -DUSING_R -c updates_BGmix.cpp -o updates_BGmix.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o BGmix.so BGmix_main.o rundir.o updates_BGmix.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
rm -r ../boostIncl
installing to /Users/biocbuild/bbs-2.12-bioc/meat/BGmix.Rcheck/BGmix/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 (BGmix)