John D. Storey
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/edge |
| Branch: RELEASE_3_8 |
| Last Commit: 17fa86d |
| Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:58:41 -0400 (Tue, 16 Apr 2019).
| Package 457/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| edge 2.14.0 John D. Storey
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: edge |
| Version: 2.14.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:edge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings edge_2.14.0.tar.gz |
| StartedAt: 2019-04-15 23:43:03 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:46:29 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 205.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: edge.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:edge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings edge_2.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/edge.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘edge’ version ‘2.14.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘edge’ 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 ... NOTE
build_study: no visible global function definition for ‘as.formula’
createSet: no visible global function definition for ‘model.matrix’
deSetCheck: no visible global function definition for ‘model.matrix’
fitFDist: no visible global function definition for ‘median’
fitFDist: no visible global function definition for ‘lm.fit’
fitFDist: no visible global function definition for ‘predict’
fit_wmodels: no visible global function definition for ‘model.matrix’
fit_wmodels: no visible global function definition for ‘lm.wfit’
null: no visible global function definition for ‘model.matrix’
apply_sva,deSet: no visible global function definition for ‘as.formula’
apply_sva,deSet: no visible global function definition for ‘terms’
fit_models,deSet: no visible global function definition for
‘model.matrix’
fullModel<-,deSet: no visible global function definition for
‘model.matrix’
lrt,deSet-deFit: no visible global function definition for ‘pf’
nullModel<-,deSet: no visible global function definition for
‘model.matrix’
Undefined global functions or variables:
as.formula lm.fit lm.wfit median model.matrix pf predict terms
Consider adding
importFrom("stats", "as.formula", "lm.fit", "lm.wfit", "median",
"model.matrix", "pf", "predict", "terms")
to your NAMESPACE file.
* 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 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 or elapsed time > 5s
user system elapsed
apply_snm 15.842 1.547 17.562
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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-3.8-bioc/meat/edge.Rcheck/00check.log’
for details.
edge.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL edge ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘edge’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c edge-init.c -o edge-init.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c edgeKLODP.c -o edgeKLODP.o clang -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 edge.so edge-init.o edgeKLODP.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/edge/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 * DONE (edge)
edge.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(edge)
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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")'.
>
> test_check("edge")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 29 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
11.400 0.498 11.995
edge.Rcheck/edge-Ex.timings
| name | user | system | elapsed | |
| apply_jackstraw | 2.285 | 0.110 | 2.416 | |
| apply_qvalue | 0.970 | 0.021 | 1.011 | |
| apply_snm | 15.842 | 1.547 | 17.562 | |
| apply_sva | 3.024 | 0.274 | 3.328 | |
| betaCoef | 0.477 | 0.007 | 0.493 | |
| build_models | 0.446 | 0.014 | 0.463 | |
| build_study | 0.346 | 0.003 | 0.349 | |
| deSet | 0.852 | 0.085 | 0.942 | |
| edge | 0 | 0 | 0 | |
| endotoxin | 1.054 | 0.093 | 1.152 | |
| fitFull | 0.417 | 0.007 | 0.432 | |
| fitNull | 0.390 | 0.007 | 0.399 | |
| fit_models | 0.416 | 0.013 | 0.433 | |
| fullMatrix | 0.442 | 0.015 | 0.467 | |
| fullModel | 0.710 | 0.014 | 0.727 | |
| gibson | 1.029 | 0.076 | 1.120 | |
| individual | 0.435 | 0.003 | 0.442 | |
| kidney | 1.120 | 0.098 | 1.235 | |
| kl_clust | 0.645 | 0.026 | 0.674 | |
| lrt | 1.354 | 0.124 | 1.511 | |
| nullMatrix | 0.397 | 0.005 | 0.411 | |
| nullModel | 0.832 | 0.032 | 0.873 | |
| odp | 1.980 | 0.277 | 2.282 | |
| qvalueObj | 1.273 | 0.119 | 1.409 | |
| resFull | 0.395 | 0.007 | 0.406 | |
| resNull | 0.470 | 0.022 | 0.497 | |
| sType | 0.433 | 0.007 | 0.443 | |
| show | 1.141 | 0.115 | 1.267 | |
| summary | 1.201 | 0.137 | 1.359 | |