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This page was generated on 2023-01-16 11:05:45 -0500 (Mon, 16 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4509
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4287
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4316
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MIMOSA on nebbiolo2


To the developers/maintainers of the MIMOSA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MIMOSA.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1204/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MIMOSA 1.36.0  (landing page)
Greg Finak
Snapshot Date: 2023-01-15 14:00:06 -0500 (Sun, 15 Jan 2023)
git_url: https://git.bioconductor.org/packages/MIMOSA
git_branch: RELEASE_3_16
git_last_commit: aedd0eb
git_last_commit_date: 2022-11-01 11:09:12 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MIMOSA
Version: 1.36.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MIMOSA.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings MIMOSA_1.36.0.tar.gz
StartedAt: 2023-01-15 21:50:01 -0500 (Sun, 15 Jan 2023)
EndedAt: 2023-01-15 21:52:08 -0500 (Sun, 15 Jan 2023)
EllapsedTime: 126.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MIMOSA.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MIMOSA.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings MIMOSA_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/MIMOSA.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘MIMOSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MIMOSA’ version ‘1.36.0’
* 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 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-3.16-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 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 is not available
* 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 ...
  ‘MIMOSA.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/MIMOSA.Rcheck/00check.log’
for details.



Installation output

MIMOSA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL MIMOSA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘MIMOSA’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  `/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript -e "RcppArmadillo:::CxxFlags()"`   -fpic  -g -O2  -Wall -c BetaMix.cpp -o BetaMix.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  `/home/biocbuild/bbs-3.16-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]
   73 |  if(file==NULL|fileP==NULL){
      |         ^
MCMC.cpp:88:18: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   88 |  if(alphas.size()!=stim.ncol()){
      |     ~~~~~~~~~~~~~^~~~~~~~~~~~~
MCMC.cpp:189:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  189 |  for(int i=0;i<alphas.size();i++){
      |              ~^~~~~~~~~~~~~~
MCMC.cpp:192:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  192 |  for(int i=0;i<alphau.size();i++){
      |              ~^~~~~~~~~~~~~~
MCMC.cpp:524:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  524 |    for(int j=0;j<p.size();j++){
      |                ~^~~~~~~~~
MCMC.cpp:544:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  544 |    for(int obs=0;obs<alphas.size();obs++){
      |                  ~~~^~~~~~~~~~~~~~
MCMC.cpp:547:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘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:631:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘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:681:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘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:815:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘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:888:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  888 |  for(int i=0;i<(s.size()-1);i++){
      |              ~^~~~~~~~~~~~~
MCMC.cpp:893:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  893 |  for(int i=0;i<s.size();i++){
      |              ~^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c betaintegral.c -o betaintegral.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  `/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript -e "RcppArmadillo:::CxxFlags()"`   -fpic  -g -O2  -Wall -c betaintegralRcpp.cpp -o betaintegralRcpp.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-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-3.16-bioc/R/library/RcppArmadillo/include" -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/library/00LOCK-MIMOSA/00new/MIMOSA/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MIMOSA)

Tests output

MIMOSA.Rcheck/tests/test-all.Rout


R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 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

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 [1.7s]
────────────────────────────────────────────────────────────────────────────────
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: 1.8 s

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
  6.445   0.371   6.803 

Example timings

MIMOSA.Rcheck/MIMOSA-Ex.timings

nameusersystemelapsed
ConstructMIMOSAExpressionSet0.2730.0010.273
MIMOSA-accessors3.1560.0713.228
MIMOSA1.4770.0231.501
MIMOSAExpressionSet0.1930.0200.214
countsTable1.5910.0471.640
fdr1.5170.0361.553
volcanoPlot1.7620.0551.818