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CHECK report for MIMOSA on malbec2

This page was generated on 2019-10-16 12:03:54 -0400 (Wed, 16 Oct 2019).

Package 1000/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MIMOSA 1.22.0
Greg Finak
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MIMOSA
Branch: RELEASE_3_9
Last Commit: 47aebc2
Last Changed Date: 2019-05-02 11:53:47 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MIMOSA
Version: 1.22.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MIMOSA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MIMOSA_1.22.0.tar.gz
StartedAt: 2019-10-16 03:11:09 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:14:05 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 176.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MIMOSA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MIMOSA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MIMOSA_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MIMOSA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.22.0’
* 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-3.9-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
* 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 : : no visible global function definition for
  ‘read.table’
BetaMix: no visible global function definition for ‘optim’
BetaMix : : no visible binding for global variable ‘par’
ConstructMIMOSAExpressionSet : MIMOSAReshape: no visible global
  function definition for ‘as.formula’
MDMix :  : : no visible global function
  definition for ‘fisher.test’
MDMix: no visible global function definition for ‘p.adjust’
MDMix : : 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 : : no visible global function definition for
  ‘pbeta’
betaintegral_R : : 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 : : 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 : : no visible global function definition for
  ‘fisher.test’
initBetaMix: no visible global function definition for ‘p.adjust’
initBetaMix : : no visible binding for global variable ‘par’
integrand : : no visible global function definition for
  ‘dbeta’
integrand : : 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 : : 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 : : 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 : : no visible global function
  definition for ‘quantile’
MIMOSA,formula-ExpressionSet :  : : no visible
  global function definition for ‘quantile’
MIMOSA,formula-ExpressionSet: no visible global function definition for
  ‘mclapply’
MIMOSA,formula-ExpressionSet :  :  : :
  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
  : : no visible global function definition for ‘p.adjust’
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric
  : : 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/MIMOSA.Rcheck/00check.log’
for details.

Installation output

MIMOSA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MIMOSA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘MIMOSA’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include `/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include `/home/biocbuild/bbs-3.9-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:188:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i&)’:
MCMC.cpp:627:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i&, std::vector&, std::vector&, std::vector&, std::vector&, 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

Tests output

MIMOSA.Rcheck/tests/test-all.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, 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")
✔ |  OK F W S | Context

⠏ |   0       | MIMOSA fitting
⠋ |   0   1   | MIMOSA fitting
⠙ |   0   2   | MIMOSA fitting
⠏ |   1   9   | MIMOSA fitting
✔ |   3   9   | MIMOSA fitting [3.2 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
✔ |   3       | getZ

⠏ |   0       | getW
✔ |   4       | getW

⠏ |   0       | countsTable
✔ |   8       | countsTable

⠏ |   0       | volcanoPlot
✔ |   2       | volcanoPlot

⠏ |   0       | pData
✔ |   4       | pData

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 3.3 s

OK:       24
Failed:   0
Warnings: 9
Skipped:  0
> 
> proc.time()
   user  system elapsed 
 10.946   0.392  11.423

Example timings

MIMOSA.Rcheck/MIMOSA-Ex.timings

nameusersystemelapsed
ConstructMIMOSAExpressionSet0.4150.0640.479
MIMOSA-accessors3.6520.0443.696
MIMOSA1.8030.0001.803
MIMOSAExpressionSet0.2660.0000.266
countsTable2.7340.0002.738
fdr3.2930.0003.402
volcanoPlot2.8120.0082.828