Greg Finak
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/MIMOSA |
| Branch: RELEASE_3_11 |
| Last Commit: 37a7580 |
| Last Changed Date: 2020-04-27 14:38:21 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:10 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE MIMOSA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1082/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MIMOSA 1.26.0 Greg Finak
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: MIMOSA |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MIMOSA.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MIMOSA_1.26.0.tar.gz |
| StartedAt: 2020-10-17 03:14:00 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:15:57 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 117.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MIMOSA.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MIMOSA.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MIMOSA_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/MIMOSA.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.26.0’
* 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-3.11-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 6.211 0.02 6.231
* 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-3.11-bioc/meat/MIMOSA.Rcheck/00check.log’
for details.
MIMOSA.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL MIMOSA
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘MIMOSA’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include `/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include `/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include `/home/biocbuild/bbs-3.11-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-3.11-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-3.11-bioc/R/library/RcppArmadillo/include" -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-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)
MIMOSA.Rcheck/tests/test-all.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
⠙ | 1 1 | MIMOSA fitting
✔ | 3 1 | MIMOSA fitting [2.4 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.
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | getZ
✔ | 3 | getZ
⠏ | 0 | getW
✔ | 4 | getW
⠏ | 0 | countsTable
✔ | 8 | countsTable
⠏ | 0 | volcanoPlot
✔ | 2 | volcanoPlot
⠏ | 0 | pData
✖ | 3 1 | pData
────────────────────────────────────────────────────────────────────────────────
test-MIMOSA.R:52: failure: (unknown)
`x` inherits from `data.frame` not `data.table`.
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 2.7 s
OK: 23
Failed: 1
Warnings: 1
Skipped: 0
>
> proc.time()
user system elapsed
8.020 0.239 8.267
MIMOSA.Rcheck/MIMOSA-Ex.timings
| name | user | system | elapsed | |
| ConstructMIMOSAExpressionSet | 0.514 | 0.004 | 0.518 | |
| MIMOSA-accessors | 6.211 | 0.020 | 6.231 | |
| MIMOSA | 1.891 | 0.004 | 1.895 | |
| MIMOSAExpressionSet | 0.226 | 0.000 | 0.226 | |
| countsTable | 2.108 | 0.000 | 2.107 | |
| fdr | 2.045 | 0.000 | 2.045 | |
| volcanoPlot | 2.370 | 0.004 | 2.374 | |