Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:34 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the edge package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/edge.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 556/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
edge 2.24.0 (landing page) John D. Storey
| 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 | WARNINGS | OK | |||||||||
Package: edge |
Version: 2.24.0 |
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_2.24.0.tar.gz |
StartedAt: 2021-10-14 18:40:02 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 18:44:20 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 258.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: edge.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_2.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/edge.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 ‘edge/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘edge’ version ‘2.24.0’ * 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: .git_fetch_output.txt .git_merge_output.txt 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 ‘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 ... WARNING Documented arguments not in \usage in documentation object 'show': ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 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 apply_snm 15.388 1.152 16.568 * 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: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-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/4.1/Resources/library’ * installing *source* package ‘edge’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c edgeKLODP.c -o edgeKLODP.o clang -mmacosx-version-min=10.13 -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/4.1/Resources/library/00LOCK-edge/00new/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 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 (edge)
edge.Rcheck/tests/testthat.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(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, 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")'. > > test_check("edge") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ] > > proc.time() user system elapsed 13.114 0.527 13.650
edge.Rcheck/edge-Ex.timings
name | user | system | elapsed | |
apply_jackstraw | 2.826 | 0.063 | 2.892 | |
apply_qvalue | 0.837 | 0.018 | 0.857 | |
apply_snm | 15.388 | 1.152 | 16.568 | |
apply_sva | 3.223 | 0.288 | 3.513 | |
betaCoef | 0.470 | 0.008 | 0.481 | |
build_models | 0.516 | 0.024 | 0.544 | |
build_study | 0.357 | 0.004 | 0.363 | |
deSet | 0.846 | 0.007 | 0.854 | |
edge | 0 | 0 | 0 | |
endotoxin | 1.108 | 0.053 | 1.164 | |
fitFull | 0.364 | 0.003 | 0.367 | |
fitNull | 0.442 | 0.005 | 0.446 | |
fit_models | 0.335 | 0.009 | 0.344 | |
fullMatrix | 0.447 | 0.003 | 0.450 | |
fullModel | 0.717 | 0.014 | 0.735 | |
gibson | 1.066 | 0.014 | 1.081 | |
individual | 0.392 | 0.004 | 0.396 | |
kidney | 1.171 | 0.059 | 1.230 | |
kl_clust | 0.636 | 0.004 | 0.639 | |
lrt | 1.297 | 0.068 | 1.367 | |
nullMatrix | 0.430 | 0.004 | 0.434 | |
nullModel | 0.983 | 0.017 | 1.001 | |
odp | 1.941 | 0.205 | 2.153 | |
qvalueObj | 1.219 | 0.086 | 1.307 | |
resFull | 0.454 | 0.006 | 0.462 | |
resNull | 0.475 | 0.030 | 0.507 | |
sType | 0.321 | 0.002 | 0.322 | |
show | 1.021 | 0.051 | 1.072 | |
summary | 1.160 | 0.174 | 1.338 | |