##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MIMOSA.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MIMOSA_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/MIMOSA.Rcheck'
* using R Under development (unstable) (2023-01-10 r83596 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MIMOSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MIMOSA' version '1.37.0'
* package encoding: UTF-8
* 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:73:16: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'F:/biocbuild/bbs-3.17-bioc/meat/MIMOSA.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 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 LazyData ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/MIMOSA/libs/x64/MIMOSA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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, 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/MIMOSA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL MIMOSA
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'MIMOSA' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I"F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c BetaMix.cpp -o BetaMix.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I"F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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:73:16: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   73 |         if(file==NULL|fileP==NULL){
      |                ^
MCMC.cpp:88:25: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   88 |         if(alphas.size()!=stim.ncol()){
      |            ~~~~~~~~~~~~~^~~~~~~~~~~~~
MCMC.cpp:189:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  189 |         for(int i=0;i<alphas.size();i++){
      |                     ~^~~~~~~~~~~~~~
MCMC.cpp:192:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  192 |         for(int i=0;i<alphau.size();i++){
      |                     ~^~~~~~~~~~~~~~
MCMC.cpp:524:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  524 |                         for(int j=0;j<p.size();j++){
      |                                     ~^~~~~~~~~
MCMC.cpp:544:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  544 |                         for(int obs=0;obs<alphas.size();obs++){
      |                                       ~~~^~~~~~~~~~~~~~
MCMC.cpp:547:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  547 |                         for(int obs=0;obs<alphau.size();obs++){
      |                                       ~~~^~~~~~~~~~~~~~
MCMC.cpp: In function 'double lkbeta(const std::vector<double>&)':
MCMC.cpp:631:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  631 |         for(int i=0;i<alpha.size();i++){
      |                     ~^~~~~~~~~~~~~
MCMC.cpp: In function 'void simZ(double&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<bool>&, int, int)':
MCMC.cpp:681:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  681 |         for(i=0;i < lnull.size(); i++){
      |                 ~~^~~~~~~~~~~~~~
MCMC.cpp: In function 'double normconstIBeta(double, double, double, double)':
MCMC.cpp:815:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  815 |         for(int i=0;i<upper.size();i++){
      |                     ~^~~~~~~~~~~~~
MCMC.cpp: In function 'double nc(double, double, double, double, double)':
MCMC.cpp:888:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  888 |         for(int i=0;i<(s.size()-1);i++){
      |                     ~^~~~~~~~~~~~~
MCMC.cpp:893:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  893 |         for(int i=0;i<s.size();i++){
      |                     ~^~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MIMOSA_init.c -o MIMOSA_init.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c betaintegral.c -o betaintegral.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I"F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c betaintegralRcpp.cpp -o betaintegralRcpp.o
g++ -std=gnu++14 -shared -s -static-libgcc -o MIMOSA.dll tmp.def BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -lm -lstdc++ -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -IF:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-MIMOSA/00new/MIMOSA/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (MIMOSA)

R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 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

Attaching package: 'BiocGenerics'

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, aperm, append,
    as.data.frame, basename, cbind, 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, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, 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")
✔ | F W S  OK | Context

⠏ |         0 | MIMOSA                                                          
⠏ |         0 | MIMOSA fitting                                                  
⠋ |   1     0 | MIMOSA fitting                                                  
⠙ |   1     1 | MIMOSA fitting                                                  
✔ |   1     3 | MIMOSA fitting [1.5s]
────────────────────────────────────────────────────────────────────────────────
Warning ('test-MIMOSA.R:6'): (code run outside of `test_that()`)
Formula does not contain the RefTreat variable. It will be added automatically. Set RT=FALSE to disable this.
Backtrace:
 1. MIMOSA::MIMOSA(...)
      at test-MIMOSA.R:6:0
 2. MIMOSA::MIMOSA(...)
 3. MIMOSA (local) .local(formula, data, ...)
────────────────────────────────────────────────────────────────────────────────

⠏ |         0 | getZ                                                            
✔ |         3 | getZ

⠏ |         0 | getW                                                            
✔ |         4 | getW

⠏ |         0 | countsTable                                                     
✔ |         8 | countsTable

⠏ |         0 | volcanoPlot                                                     
✔ |         2 | volcanoPlot

⠏ |         0 | pData                                                           
✔ |         3 | pData

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.7 s

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
   6.07    0.48    6.50