Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:30 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the edge package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/edge.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 565/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
edge 2.26.0 (landing page) John D. Storey
| nebbiolo2 | Linux (Ubuntu 20.04.4 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 | WARNINGS | OK | |||||||||
Package: edge |
Version: 2.26.0 |
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:edge.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings edge_2.26.0.tar.gz |
StartedAt: 2022-04-12 19:01:57 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 19:08:22 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 385.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: edge.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:edge.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings edge_2.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/edge.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'edge/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'edge' version '2.26.0' * 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 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/edge/libs/i386/edge.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/edge/libs/x64/edge.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed apply_snm 10.86 1.01 11.95 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed apply_snm 11.92 0.61 12.54 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/edge.Rcheck/00check.log' for details.
edge.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/edge_2.26.0.tar.gz && rm -rf edge.buildbin-libdir && mkdir edge.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=edge.buildbin-libdir edge_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL edge_2.26.0.zip && rm edge_2.26.0.tar.gz edge_2.26.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 659k 100 659k 0 0 735k 0 --:--:-- --:--:-- --:--:-- 736k 100 659k 100 659k 0 0 735k 0 --:--:-- --:--:-- --:--:-- 735k install for i386 * installing *source* package 'edge' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c edge-init.c -o edge-init.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c edgeKLODP.c -o edgeKLODP.o edgeKLODP.c: In function 'odpScoreCluster': edgeKLODP.c:194:27: warning: 'middle' may be used uninitialized in this function [-Wmaybe-uninitialized] free((FREE_ARG) (v + nl - NR_END)); ~~~~~~~~^~~~~~~~~ edgeKLODP.c:11:19: note: 'middle' was declared here double *first, *middle; ^~~~~~ C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o edge.dll tmp.def edge-init.o edgeKLODP.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/edge.buildbin-libdir/00LOCK-edge/00new/edge/libs/i386 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'edge' finding HTML links ... done apply_jackstraw html finding level-2 HTML links ... done apply_qvalue html apply_snm html apply_sva html betaCoef html build_models html build_study html deFit-class html deSet-class html deSet html edge html endotoxin html fitFull html fitNull html fit_models html fullMatrix html fullModel html gibson html individual html kidney html kl_clust html lrt html nullMatrix html nullModel html odp html qvalueObj html resFull html resNull html sType html show html summary html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'edge' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c edge-init.c -o edge-init.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c edgeKLODP.c -o edgeKLODP.o edgeKLODP.c: In function 'odpScoreCluster': edgeKLODP.c:194:27: warning: 'middle' may be used uninitialized in this function [-Wmaybe-uninitialized] free((FREE_ARG) (v + nl - NR_END)); ~~~~~~~~^~~~~~~~~ edgeKLODP.c:11:19: note: 'middle' was declared here double *first, *middle; ^~~~~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o edge.dll tmp.def edge-init.o edgeKLODP.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/edge.buildbin-libdir/edge/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'edge' as edge_2.26.0.zip * DONE (edge) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'edge' successfully unpacked and MD5 sums checked
edge.Rcheck/tests_i386/testthat.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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 Attaching package: 'BiocGenerics' 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 9.89 0.98 10.90 |
edge.Rcheck/tests_x64/testthat.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 Attaching package: 'BiocGenerics' 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 10.81 0.37 11.45 |
edge.Rcheck/examples_i386/edge-Ex.timings
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edge.Rcheck/examples_x64/edge-Ex.timings
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