MIMOSA 1.8.1
Greg Finak
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/MIMOSA | | Last Changed Rev: 116621 / Revision: 116712 | | Last Changed Date: 2016-04-20 14:13:54 -0700 (Wed, 20 Apr 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MIMOSA_1.8.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MIMOSA.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-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 ‘1.8.1’
* 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 ... [30s/31s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ... NOTE
MIMOSAExpressionSet: no visible global function definition for
‘ExpressionSet’
MIMOSAExpressionSet: no visible global function definition for
‘AnnotatedDataFrame’
boxplotMIMOSAResultList: no visible global function definition for
‘ldply’
boxplotMIMOSAResultList: no visible global function definition for
‘aes’
boxplotMIMOSAResultList: no visible binding for global variable
‘Proportion’
boxplotMIMOSAResultList: no visible binding for global variable
‘Proportion_REF’
boxplotMIMOSAResultList: no visible global function definition for
‘geom_boxplot’
boxplotMIMOSAResultList: no visible global function definition for
‘coord_trans’
boxplotMIMOSAResultList: no visible global function definition for
‘facet_wrap’
boxplotMIMOSAResultList: no visible global function definition for
‘ggtitle’
boxplotMIMOSAResultList: no visible global function definition for
‘geom_jitter’
boxplotMIMOSAResultList: no visible global function definition for
‘position_jitter’
boxplotMIMOSAResultList: no visible global function definition for
‘scale_fill_brewer’
boxplotMIMOSAResultList: no visible global function definition for
‘scale_color_brewer’
boxplotMIMOSAResultList: no visible global function definition for
‘geom_line’
boxplotMIMOSAResultList: no visible binding for global variable ‘PTID’
huberFilter: no visible global function definition for ‘huber’
refactorPData: no visible global function definition for ‘pData<-’
setpData.icsdata: no visible global function definition for ‘pData<-’
volcanoPlot.MIMOSAResultList: no visible global function definition for
‘is.formula’
volcanoPlot.MIMOSAResultList: no visible global function definition for
‘facet_grid’
MIMOSA,formula-ExpressionSet : .local: no visible binding for global
variable ‘RefTreat’
MIMOSA,formula-ExpressionSet : .local: no visible global function
definition for ‘mclapply’
pData<-,BetaMixResult-data.frame: no visible global function definition
for ‘pData<-’
* 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/18s] OK
* 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
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/MIMOSA.Rcheck/00check.log’
for details.
* installing *source* package ‘MIMOSA’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RcppArmadillo/include" `/home/biocbuild/bbs-3.2-bioc/R/bin/Rscript -e "RcppArmadillo:::CxxFlags()"` -fpic -g -O2 -Wall -c BetaMix.cpp -o BetaMix.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RcppArmadillo/include" `/home/biocbuild/bbs-3.2-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:73:9: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
if(file==NULL|fileP==NULL){
^
MCMC.cpp:88:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(alphas.size()!=stim.ncol()){
^
MCMC.cpp:188:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alphas.size();i++){
^
MCMC.cpp:191:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alphau.size();i++){
^
MCMC.cpp:264:16: warning: null argument where non-null required (argument 1) [-Wnonnull]
newll=nan(0);
^
MCMC.cpp:348:16: warning: null argument where non-null required (argument 1) [-Wnonnull]
newll=nan(0);
^
MCMC.cpp:523:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<p.size();j++){
^
MCMC.cpp:542:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int obs=0;obs<alphas.size();obs++){
^
MCMC.cpp:545:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int obs=0;obs<alphau.size();obs++){
^
MCMC.cpp: In function ‘double lkbeta(const std::vector<double, std::allocator<double> >&)’:
MCMC.cpp:627:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alpha.size();i++){
^
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:677:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i < lnull.size(); i++){
^
MCMC.cpp: In function ‘double normconstIBeta(double, double, double, double)’:
MCMC.cpp:811:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<upper.size();i++){
^
MCMC.cpp: In function ‘double nc(double, double, double, double, double)’:
MCMC.cpp:884:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<(s.size()-1);i++){
^
MCMC.cpp:889:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<s.size();i++){
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c MIMOSA_init.c -o MIMOSA_init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c betaintegral.c -o betaintegral.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RcppArmadillo/include" `/home/biocbuild/bbs-3.2-bioc/R/bin/Rscript -e "RcppArmadillo:::CxxFlags()"` -fpic -g -O2 -Wall -c betaintegralRcpp.cpp -o betaintegralRcpp.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -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-3.2-bioc/R/library/RcppArmadillo/include" -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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)