Greg Finak
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/MIMOSA |
| Branch: master |
| Last Commit: 6c2aa33 |
| Last Changed Date: 2019-01-04 13:39:22 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:16:18 -0400 (Tue, 09 Apr 2019).
| Package 983/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MIMOSA 1.21.1 Greg Finak
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: MIMOSA |
| Version: 1.21.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MIMOSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MIMOSA_1.21.1.tar.gz |
| StartedAt: 2019-04-09 04:15:33 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:19:51 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 258.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MIMOSA.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MIMOSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MIMOSA_1.21.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MIMOSA.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MIMOSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MIMOSA' version '1.21.1'
* 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 whether package 'MIMOSA' can be installed ... WARNING
Found the following significant warnings:
MCMC.cpp:73:9: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MIMOSA.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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
.fitMCMC : <anonymous>: no visible global function definition for
'read.table'
BetaMix: no visible global function definition for 'optim'
BetaMix : <anonymous>: no visible binding for global variable 'par'
ConstructMIMOSAExpressionSet : MIMOSAReshape: no visible global
function definition for 'as.formula'
MDMix : <anonymous> : <anonymous>: no visible global function
definition for 'fisher.test'
MDMix: no visible global function definition for 'p.adjust'
MDMix : <anonymous>: no visible global function definition for
'fisher.test'
MDMix : f: no visible global function definition for 'dbeta'
MDMix: no visible global function definition for 'optim'
MIMOSAExpressionSet: no visible global function definition for
'ExpressionSet'
MIMOSAExpressionSet: no visible global function definition for
'AnnotatedDataFrame'
alphaProp1: no visible global function definition for 'rnorm'
betaintegral_R : <anonymous>: no visible global function definition for
'pbeta'
betaintegral_R : <anonymous>: no visible global function definition for
'rbeta'
betaintegral_R2: no visible global function definition for 'dbeta'
betaintegral_R2: no visible global function definition for 'pbeta'
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'
contourPlot : <anonymous>: no visible global function definition for
'rbinom'
contourPlot: no visible global function definition for 'contour'
contourPlot: no visible global function definition for 'points'
estimate_logZus: no visible global function definition for 'rbeta'
estimate_logZus: no visible global function definition for 'pbeta'
f1: no visible global function definition for 'dbeta'
f1: no visible global function definition for 'pbeta'
f1.log: no visible global function definition for 'dbeta'
f1.log: no visible global function definition for 'pbeta'
f2: no visible global function definition for 'dbeta'
f2: no visible global function definition for 'pbeta'
f2.log: no visible global function definition for 'dbeta'
f2.log: no visible global function definition for 'pbeta'
gibbsPsPu: no visible global function definition for 'rbeta'
gibbsPsPu: no visible global function definition for 'qbeta'
gibbsPsPu: no visible global function definition for 'runif'
gibbsPsPu: no visible global function definition for 'pbeta'
gibbsPsPu: no visible global function definition for 'ecdf'
huberFilter: no visible global function definition for 'huber'
initBetaMix: no visible global function definition for 'var'
initBetaMix: no visible global function definition for 'optim'
initBetaMix : <anonymous>: no visible global function definition for
'fisher.test'
initBetaMix: no visible global function definition for 'p.adjust'
initBetaMix : <anonymous>: no visible binding for global variable 'par'
integrand : <anonymous>: no visible global function definition for
'dbeta'
integrand : <anonymous>: no visible global function definition for
'pbeta'
match.elispot.antigens: no visible global function definition for
'na.omit'
plot.BetaMixResult: no visible global function definition for 'plot'
plotPriors: no visible global function definition for 'qbeta'
plotPriors: no visible global function definition for 'dbeta'
plotPriors: no visible global function definition for 'pbeta'
plotPriors: no visible global function definition for 'plot'
plotPriors: no visible global function definition for 'lines'
plotPriors: no visible global function definition for 'legend'
plotPriors: no visible global function definition for 'title'
posteriorSample : <anonymous>: no visible global function definition
for 'rbinom'
refactorPData: no visible global function definition for 'pData<-'
setpData.icsdata: no visible global function definition for 'pData<-'
simAlpha.s: no visible global function definition for 'dexp'
simAlpha.s: no visible global function definition for 'runif'
simAlpha.u: no visible global function definition for 'dexp'
simAlpha.u: no visible global function definition for 'runif'
simMD: no visible global function definition for 'runif'
simMD : <anonymous>: no visible global function definition for
'rmultinom'
simQ: no visible global function definition for 'rbeta'
simulate2: no visible global function definition for 'rbeta'
simulate2: no visible global function definition for 'rnorm'
simulate2: no visible global function definition for 'rbinom'
test: no visible global function definition for 'optim'
volcanoPlot.MIMOSAResultList: no visible global function definition for
'is.formula'
volcanoPlot.MIMOSAResultList: no visible global function definition for
'facet_grid'
MIMOSA,formula-ExpressionSet: no visible binding for global variable
'RefTreat'
MIMOSA,formula-ExpressionSet: no visible global function definition for
'terms'
MIMOSA,formula-ExpressionSet: no visible global function definition for
'model.frame'
MIMOSA,formula-ExpressionSet : <anonymous>: no visible global function
definition for 'quantile'
MIMOSA,formula-ExpressionSet : <anonymous> : <anonymous>: no visible
global function definition for 'quantile'
MIMOSA,formula-ExpressionSet: no visible global function definition for
'mclapply'
MIMOSA,formula-ExpressionSet : <anonymous> : <anonymous> : <anonymous>:
no visible global function definition for 'quantile'
initialize,MIMOSAResult: no visible global function definition for
'callNextMethod'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric:
no visible global function definition for 'image'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric:
no visible global function definition for 'gray.colors'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric:
no visible global function definition for 'contour'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric:
no visible global function definition for 'points'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric
: <anonymous>: no visible global function definition for 'p.adjust'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric
: <anonymous>: no visible global function definition for
'fisher.test'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric:
no visible global function definition for 'lines'
pData<-,BetaMixResult-data.frame: no visible global function definition
for 'pData<-'
summary,BetaMixResult: no visible global function definition for 'show'
Undefined global functions or variables:
AnnotatedDataFrame ExpressionSet PTID Proportion Proportion_REF
RefTreat aes as.formula callNextMethod contour coord_trans dbeta dexp
ecdf facet_grid facet_wrap fisher.test geom_boxplot geom_jitter
geom_line ggtitle gray.colors huber image is.formula ldply legend
lines mclapply model.frame na.omit optim p.adjust pData<- par pbeta
plot points position_jitter qbeta quantile rbeta rbinom read.table
rmultinom rnorm runif scale_color_brewer scale_fill_brewer show terms
title var
Consider adding
importFrom("grDevices", "gray.colors")
importFrom("graphics", "contour", "image", "legend", "lines", "par",
"plot", "points", "title")
importFrom("methods", "callNextMethod", "show")
importFrom("stats", "as.formula", "dbeta", "dexp", "ecdf",
"fisher.test", "model.frame", "na.omit", "optim",
"p.adjust", "pbeta", "qbeta", "quantile", "rbeta", "rbinom",
"rmultinom", "rnorm", "runif", "terms", "var")
importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/MIMOSA/libs/i386/MIMOSA.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/MIMOSA/libs/x64/MIMOSA.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R'
OK
** running tests for arch 'x64' ...
Running 'test-all.R'
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: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/MIMOSA.Rcheck/00check.log'
for details.
MIMOSA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MIMOSA_1.21.1.tar.gz && rm -rf MIMOSA.buildbin-libdir && mkdir MIMOSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MIMOSA.buildbin-libdir MIMOSA_1.21.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MIMOSA_1.21.1.zip && rm MIMOSA_1.21.1.tar.gz MIMOSA_1.21.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 73935 100 73935 0 0 1037k 0 --:--:-- --:--:-- --:--:-- 1164k
install for i386
* installing *source* package 'MIMOSA' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c BetaMix.cpp -o BetaMix.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -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:88:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(alphas.size()!=stim.ncol()){
^
MCMC.cpp:188:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alphas.size();i++){
^
MCMC.cpp:191:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alphau.size();i++){
^
MCMC.cpp:523:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<p.size();j++){
^
MCMC.cpp:542:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int obs=0;obs<alphas.size();obs++){
^
MCMC.cpp:545:21: 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:627:15: 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:677:12: 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:811:15: 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:884:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<(s.size()-1);i++){
^
MCMC.cpp:889:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<s.size();i++){
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c MIMOSA_init.c -o MIMOSA_init.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c betaintegral.c -o betaintegral.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c betaintegralRcpp.cpp -o betaintegralRcpp.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o MIMOSA.dll tmp.def BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -lm -lstdc++ -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -IC:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/MIMOSA.buildbin-libdir/00LOCK-MIMOSA/00new/MIMOSA/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MIMOSA'
finding HTML links ... done
BetaMixResult-class html
ConstructMIMOSAExpressionSet html
ICS html
MDMix html
MIMOSA-accessors html
MIMOSA-package html
MIMOSA html
MIMOSAExpressionSet html
MIMOSAResult-class html
MIMOSAResult html
asinh_trans html
boxplotMIMOSAResultList html
combine.MIMOSA html
countsTable html
fdr html
fitMCMC html
pData html
print html
show html
volcanoPlot html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'MIMOSA' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c BetaMix.cpp -o BetaMix.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -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:88:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(alphas.size()!=stim.ncol()){
^
MCMC.cpp:188:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alphas.size();i++){
^
MCMC.cpp:191:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alphau.size();i++){
^
MCMC.cpp:523:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<p.size();j++){
^
MCMC.cpp:542:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int obs=0;obs<alphas.size();obs++){
^
MCMC.cpp:545:21: 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:627:15: 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:677:12: 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:811:15: 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:884:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<(s.size()-1);i++){
^
MCMC.cpp:889:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<s.size();i++){
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c MIMOSA_init.c -o MIMOSA_init.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c betaintegral.c -o betaintegral.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c betaintegralRcpp.cpp -o betaintegralRcpp.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o MIMOSA.dll tmp.def BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -lm -lstdc++ -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -IC:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/MIMOSA.buildbin-libdir/MIMOSA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MIMOSA' as MIMOSA_1.21.1.zip
* DONE (MIMOSA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MIMOSA' successfully unpacked and MD5 sums checked
|
MIMOSA.Rcheck/tests_i386/test-all.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(MIMOSA)
Loading required package: MASS
Loading required package: plyr
Loading required package: reshape
Attaching package: 'reshape'
The following objects are masked from 'package:plyr':
rename, round_any
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ggplot2
> test_dir("testthat")
v | OK F W S | Context
/ | 0 | MIMOSA fitting
- | 0 1 | MIMOSA fitting
\ | 0 2 | MIMOSA fitting
| | 0 3 | MIMOSA fitting
/ | 0 4 | MIMOSA fitting
- | 0 5 | MIMOSA fitting
\ | 0 6 | MIMOSA fitting
| | 0 7 | MIMOSA fitting
/ | 0 8 | MIMOSA fitting
- | 0 9 | MIMOSA fitting
\ | 1 9 | MIMOSA fitting
| | 2 9 | MIMOSA fitting
/ | 3 9 | MIMOSA fitting
v | 3 9 | MIMOSA fitting [2.3 s]
--------------------------------------------------------------------------------
test-MIMOSA.R:6: warning: (unknown)
Formula does not contain the RefTreat variable. It will be added automatically. Set RT=FALSE to disable this.
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
--------------------------------------------------------------------------------
/ | 0 | getZ
- | 1 | getZ
\ | 2 | getZ
| | 3 | getZ
v | 3 | getZ
/ | 0 | getW
- | 1 | getW
\ | 2 | getW
| | 3 | getW
/ | 4 | getW
v | 4 | getW
/ | 0 | countsTable
- | 1 | countsTable
\ | 2 | countsTable
| | 3 | countsTable
/ | 4 | countsTable
- | 5 | countsTable
\ | 6 | countsTable
| | 7 | countsTable
/ | 8 | countsTable
v | 8 | countsTable
/ | 0 | volcanoPlot
- | 1 | volcanoPlot
\ | 2 | volcanoPlot
v | 2 | volcanoPlot
/ | 0 | pData
- | 1 | pData
\ | 2 | pData
| | 3 | pData
/ | 4 | pData
v | 4 | pData
== Results =====================================================================
Duration: 2.5 s
OK: 24
Failed: 0
Warnings: 9
Skipped: 0
>
> proc.time()
user system elapsed
9.29 0.92 10.20
|
MIMOSA.Rcheck/tests_x64/test-all.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(MIMOSA)
Loading required package: MASS
Loading required package: plyr
Loading required package: reshape
Attaching package: 'reshape'
The following objects are masked from 'package:plyr':
rename, round_any
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ggplot2
> test_dir("testthat")
v | OK F W S | Context
/ | 0 | MIMOSA fitting
- | 0 1 | MIMOSA fitting
\ | 0 2 | MIMOSA fitting
| | 0 3 | MIMOSA fitting
/ | 0 4 | MIMOSA fitting
- | 0 5 | MIMOSA fitting
\ | 0 6 | MIMOSA fitting
| | 0 7 | MIMOSA fitting
/ | 0 8 | MIMOSA fitting
- | 0 9 | MIMOSA fitting
\ | 1 9 | MIMOSA fitting
| | 2 9 | MIMOSA fitting
/ | 3 9 | MIMOSA fitting
v | 3 9 | MIMOSA fitting [2.1 s]
--------------------------------------------------------------------------------
test-MIMOSA.R:6: warning: (unknown)
Formula does not contain the RefTreat variable. It will be added automatically. Set RT=FALSE to disable this.
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
test-MIMOSA.R:6: warning: (unknown)
NaNs produced
--------------------------------------------------------------------------------
/ | 0 | getZ
- | 1 | getZ
\ | 2 | getZ
| | 3 | getZ
v | 3 | getZ
/ | 0 | getW
- | 1 | getW
\ | 2 | getW
| | 3 | getW
/ | 4 | getW
v | 4 | getW
/ | 0 | countsTable
- | 1 | countsTable
\ | 2 | countsTable
| | 3 | countsTable
/ | 4 | countsTable
- | 5 | countsTable
\ | 6 | countsTable
| | 7 | countsTable
/ | 8 | countsTable
v | 8 | countsTable
/ | 0 | volcanoPlot
- | 1 | volcanoPlot
\ | 2 | volcanoPlot
v | 2 | volcanoPlot
/ | 0 | pData
- | 1 | pData
\ | 2 | pData
| | 3 | pData
/ | 4 | pData
v | 4 | pData
== Results =====================================================================
Duration: 2.2 s
OK: 24
Failed: 0
Warnings: 9
Skipped: 0
>
> proc.time()
user system elapsed
8.68 0.42 9.09
|
|
MIMOSA.Rcheck/examples_i386/MIMOSA-Ex.timings
|
MIMOSA.Rcheck/examples_x64/MIMOSA-Ex.timings
|