MIMOSA 1.0.0
Greg Finak
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/MIMOSA | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings MIMOSA_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/MIMOSA.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MIMOSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MIMOSA’ version ‘1.0.0’
* 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:
.travis.yml
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 ‘MIMOSA’ can be installed ... [25s/26s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘ggplot2’ ‘reshape’ ‘plyr’ ‘Biobase’ ‘MASS’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking 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 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/22s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MIMOSA-accessors 6.556 0.008 6.573
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘test-all.R’ [6s/6s]
[6s/6s] OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-2.14-bioc/meat/MIMOSA.Rcheck/00check.log’
for details.
* installing *source* package ‘MIMOSA’ ...
** libs
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppArmadillo/include" `/home/biocbuild/bbs-2.14-bioc/R/bin/Rscript -e "RcppArmadillo:::CxxFlags()"` -fpic -g -O2 -Wall -c BetaMix.cpp -o BetaMix.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppArmadillo/include" `/home/biocbuild/bbs-2.14-bioc/R/bin/Rscript -e "RcppArmadillo:::CxxFlags()"` -fpic -g -O2 -Wall -c MCMC.cpp -o MCMC.o
MCMC.cpp: In function ‘SEXPREC* fitMCMC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
MCMC.cpp:73:23: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
MCMC.cpp:88:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:188:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:191:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:267:16: warning: null argument where non-null required (argument 1) [-Wnonnull]
MCMC.cpp:351:16: warning: null argument where non-null required (argument 1) [-Wnonnull]
MCMC.cpp:526:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:545:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:548:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp: In function ‘double lkbeta(const std::vector<double, std::allocator<double> >&)’:
MCMC.cpp:630:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp: In function ‘void simZ(double&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<bool>&, int, int)’:
MCMC.cpp:680:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp: In function ‘double normconstIBeta(double, double, double, double)’:
MCMC.cpp:812:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp: In function ‘double nc(double, double, double, double, double)’:
MCMC.cpp:890:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c MIMOSA_init.c -o MIMOSA_init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c betaintegral.c -o betaintegral.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppArmadillo/include" `/home/biocbuild/bbs-2.14-bioc/R/bin/Rscript -e "RcppArmadillo:::CxxFlags()"` -fpic -g -O2 -Wall -c betaintegralRcpp.cpp -o betaintegralRcpp.o
g++ -shared -L/usr/local/lib -o MIMOSA.so BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -O3 -lm -lstdc++ -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppArmadillo/include" -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/MIMOSA.Rcheck/MIMOSA/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘MIMOSA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MIMOSA)