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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MIMOSA.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MIMOSA_1.28.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/MIMOSA.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.28.1’
* 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 for sufficient/correct file permissions ... 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 ‘/home/biocbuild/bbs-3.12-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
* 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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
MIMOSA-accessors 5.664      0   5.676
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/MIMOSA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL MIMOSA
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘MIMOSA’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  `/home/biocbuild/bbs-3.12-bioc/R/bin/Rscript -e "RcppArmadillo:::CxxFlags()"`   -fpic  -g -O2  -Wall -c BetaMix.cpp -o BetaMix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  `/home/biocbuild/bbs-3.12-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:88:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if(alphas.size()!=stim.ncol()){
     ~~~~~~~~~~~~~^~~~~~~~~~~~~
MCMC.cpp:189:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<alphas.size();i++){
              ~^~~~~~~~~~~~~~
MCMC.cpp:192:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<alphau.size();i++){
              ~^~~~~~~~~~~~~~
MCMC.cpp:524:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int j=0;j<p.size();j++){
                ~^~~~~~~~~
MCMC.cpp:544:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int obs=0;obs<alphas.size();obs++){
                  ~~~^~~~~~~~~~~~~~
MCMC.cpp:547:21: 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>&)’:
MCMC.cpp:631:15: 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::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<bool>&, int, int)’:
MCMC.cpp:681:12: 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:815:15: 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:888:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<(s.size()-1);i++){
              ~^~~~~~~~~~~~~
MCMC.cpp:893:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<s.size();i++){
              ~^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c MIMOSA_init.c -o MIMOSA_init.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c betaintegral.c -o betaintegral.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  `/home/biocbuild/bbs-3.12-bioc/R/bin/Rscript -e "RcppArmadillo:::CxxFlags()"`   -fpic  -g -O2  -Wall -c betaintegralRcpp.cpp -o betaintegralRcpp.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/RcppArmadillo/include" -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-MIMOSA/00new/MIMOSA/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package keeps a record of temporary installation path
* DONE (MIMOSA)

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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
Warning message:
In .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
> test_dir("testthat")
✔ |  OK F W S | Context

⠏ |   0       | MIMOSA                                                          
⠏ |   0       | MIMOSA fitting                                                  
⠋ |   0   1   | MIMOSA fitting                                                  
⠙ |   1   1   | MIMOSA fitting                                                  
✔ |   3   1   | MIMOSA fitting [2.9 s]
────────────────────────────────────────────────────────────────────────────────
Warning (test-MIMOSA.R:6:1): (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(...) test-MIMOSA.R:6:0
 2. MIMOSA::MIMOSA(...)
 3. MIMOSA:::.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: 3.0 s

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
  8.656   0.144   8.820