Greg Finak
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/MIMOSA |
| git_branch: RELEASE_3_13 |
| git_last_commit: 8910727 |
| git_last_commit_date: 2021-05-19 12:02:48 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:42 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1136/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MIMOSA 1.30.0 (landing page) Greg Finak
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.30.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MIMOSA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MIMOSA_1.30.0.tar.gz |
| StartedAt: 2021-10-14 21:09:01 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:11:37 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 155.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MIMOSA.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MIMOSA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MIMOSA_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MIMOSA.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.30.0’
* 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:
.git_fetch_output.txt
.git_merge_output.txt
.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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MIMOSA-accessors 6.823 0.083 6.916
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/MIMOSA.Rcheck/00check.log’
for details.
MIMOSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MIMOSA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘MIMOSA’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "RcppArmadillo:::CxxFlags()"` -fPIC -Wall -g -O2 -c BetaMix.cpp -o BetaMix.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "RcppArmadillo:::CxxFlags()"` -fPIC -Wall -g -O2 -c MCMC.cpp -o MCMC.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MIMOSA_init.c -o MIMOSA_init.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c betaintegral.c -o betaintegral.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "RcppArmadillo:::CxxFlags()"` -fPIC -Wall -g -O2 -c betaintegralRcpp.cpp -o betaintegralRcpp.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o MIMOSA.so BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -O3 -lm -lstdc++ -I"/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include" -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
> 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 [4.0s]
────────────────────────────────────────────────────────────────────────────────
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: 4.2 s
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ]
>
> proc.time()
user system elapsed
10.267 0.395 11.423
MIMOSA.Rcheck/MIMOSA-Ex.timings
| name | user | system | elapsed | |
| ConstructMIMOSAExpressionSet | 0.387 | 0.011 | 0.399 | |
| MIMOSA-accessors | 6.823 | 0.083 | 6.916 | |
| MIMOSA | 3.397 | 0.022 | 3.438 | |
| MIMOSAExpressionSet | 0.326 | 0.001 | 0.327 | |
| countsTable | 3.375 | 0.025 | 3.429 | |
| fdr | 3.243 | 0.021 | 3.282 | |
| volcanoPlot | 3.695 | 0.016 | 3.722 | |