Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 |
Package 2258/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
XDE 2.53.0 (landing page) Robert Scharpf
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the XDE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/XDE.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: XDE |
Version: 2.53.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:XDE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings XDE_2.53.0.tar.gz |
StartedAt: 2024-12-23 22:00:49 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 22:02:00 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 70.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: XDE.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:XDE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings XDE_2.53.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/XDE.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘XDE/DESCRIPTION’ ... OK * this is package ‘XDE’ version ‘2.53.0’ * 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 ‘XDE’ can be installed ... WARNING Found the following significant warnings: ./Matrix_v2.h:4:17: warning: using directive refers to implicitly-defined namespace 'std' Potential_v2.cpp:374:34: warning: equality comparison result unused [-Wunused-comparison] See ‘/Users/biocbuild/bbs-3.21-bioc/meat/XDE.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 code 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 whether startup messages can be suppressed ... 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 include directives 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘doRUnit.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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, 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/XDE.Rcheck/00check.log’ for details.
XDE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL XDE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘XDE’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Cholesky.cpp -o Cholesky.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Matrix_v2.cpp -o Matrix_v2.o In file included from Matrix_v2.cpp:1: ./Matrix_v2.h:4:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ Matrix_v2.cpp:148:7: warning: variable 'signDet' set but not used [-Wunused-but-set-variable] int signDet = 1; ^ Matrix_v2.cpp:244:7: warning: unused variable 'k' [-Wunused-variable] int k = 1; ^ Matrix_v2.cpp:246:9: warning: unused variable 'j' [-Wunused-variable] int i,j,r; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Potential_v2.cpp -o Potential_v2.o Potential_v2.cpp:374:34: warning: equality comparison result unused [-Wunused-comparison] if (theGene[k][i] == 1) include == 1; ~~~~~~~~^~~~ Potential_v2.cpp:374:34: note: use '=' to turn this equality comparison into an assignment if (theGene[k][i] == 1) include == 1; ^~ = 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Random_v2.cpp -o Random_v2.o Random_v2.cpp:12:16: warning: variable 'temp' set but not used [-Wunused-but-set-variable] unsigned int temp = UINT_MAX - 1; ^ Random_v2.cpp:1847:10: warning: unused variable 'x' [-Wunused-variable] double x,y,tt,sum; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Rinterface_v2.cpp -o Rinterface_v2.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Structure.cpp -o Structure.o Structure.cpp:528:8: warning: unused variable 'c' [-Wunused-variable] char c; ^ Structure.cpp:1642:8: warning: unused variable 'nRead' [-Wunused-variable] int nRead = sscanf(var1,"%d",&value); ^ Structure.cpp:1668:12: warning: unused variable 'nRead' [-Wunused-variable] int nRead = sscanf(var2,"%le",&value); ^ Structure.cpp:1579:12: warning: unused variable 'c' [-Wunused-variable] char c; ^ Structure.cpp:1728:12: warning: unused variable 'c' [-Wunused-variable] char c; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Update_v2.cpp -o Update_v2.o Update_v2.cpp:2314:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:2464:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:3293:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:3404:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:3919:10: warning: unused variable 'pot' [-Wunused-variable] double pot = - OmegaGibbs(df,D,oldClique,oldComponents,Q,G,Delta, ^ Update_v2.cpp:3973:10: warning: unused variable 'pot' [-Wunused-variable] double pot = DeltaStarGibbs(oldClique,oldComponents,Q,G,S,newValues, ^ Update_v2.cpp:4526:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:4657:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Utility_v2.cpp -o Utility_v2.o Utility_v2.cpp:221:12: warning: unused variable 'detPrior' [-Wunused-variable] double detPrior = inverse(var,varInv); ^ Utility_v2.cpp:228:12: warning: unused variable 'detPosterior' [-Wunused-variable] double detPosterior = 1.0 /inverse(varInv,var); ^ Utility_v2.cpp:303:9: warning: unused variable 's' [-Wunused-variable] int s; ^ Utility_v2.cpp:328:12: warning: unused variable 'detPrior' [-Wunused-variable] double detPrior = inverse(var,varInv); ^ Utility_v2.cpp:334:12: warning: unused variable 'detPosterior' [-Wunused-variable] double detPosterior = 1.0 / inverse(varInv,var); ^ Utility_v2.cpp:764:6: warning: unused variable 'ngg' [-Wunused-variable] int ngg = neighbour[gg].size(); ^ Utility_v2.cpp:954:8: warning: unused variable 'ngg' [-Wunused-variable] int ngg = neighbour[gg].size(); ^ Utility_v2.cpp:1463:33: warning: unused variable 'itextra' [-Wunused-variable] map<int,double>::iterator itextra = VinvSparse[k].end(); ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c diffExpressed_main.cpp -o diffExpressed_main.o In file included from diffExpressed_main.cpp:38: ./UpdateGamma2Gibbs.h:112:14: warning: variable 'pot' set but not used [-Wunused-but-set-variable] double pot = - model->potential(ran); ^ In file included from diffExpressed_main.cpp:42: ./UpdateXiGibbs.h:95:11: warning: variable 'pot' set but not used [-Wunused-but-set-variable] double pot = - model->potential(ran); ^ ./UpdateXiGibbs.h:162:15: warning: variable 'pot' set but not used [-Wunused-but-set-variable] double pot = - model->potential(ran); ^ 3 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o registerDynamicSymbol.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-XDE/00new/XDE/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘qqplot’ in package ‘XDE’ ** 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 (XDE)
XDE.Rcheck/tests/doRUnit.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > ## from xmapcore package > if( require( "RUnit", quietly=TRUE ) ) { + pkg <- "XDE" + + if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) { + path <- file.path( getwd(), "..", "inst", "unitTests" ) + } else { + path <- system.file( package=pkg, "unitTests" ) + } + + cat( "\nRunning unit tests\n" ) + print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) ) + library( package=pkg, character.only=TRUE ) + + ##xmap.clear.cache() + + ##Fail on warnings + options( warn=2 ) + + ## Get the pattern (if there is one?) + patt <- Sys.getenv( "RUNITFILEPATTERN" ) + if( is.null( patt ) || nchar( patt ) == 0 ) { + testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ), + dirs=path, + testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" )) + } else { + ##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path ) + testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ), + testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ), + dirs=path ) + } + tests <- runTestSuite( testSuite ) + + pathReport <- file.path( path, "report" ) + + cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" ) + printTextProtocol( tests, showDetails=FALSE ) + printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) ) + printTextProtocol( tests, showDetails=TRUE, fileName=paste( pathReport, ".txt", sep="" ) ) + + printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) ) + + tmp <- getErrors( tests ) + if( tmp$nFail > 0 | tmp$nErr > 0 ){ + stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ", tmp$nErr, ")\n\n", sep="")) + } + } else { + warning( "cannot run unit tests -- package RUnit is not available" ) + } Running unit tests $pkg [1] "XDE" $getwd [1] "/Users/biocbuild/bbs-3.21-bioc/meat/XDE.Rcheck/tests" $pathToUnitTests [1] "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpDvvwCh/RLIBS_16327586773fc/XDE/unitTests" Loading required package: Biobase Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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")'. Welcome to XDE version 2.53.0 ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Mon Dec 23 22:01:56 2024 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : XDE unit testing - 0 test functions, 0 errors, 0 failures > > proc.time() user system elapsed 2.374 0.137 2.524
XDE.Rcheck/XDE-Ex.timings
name | user | system | elapsed | |
ExpressionSetList-class | 0.008 | 0.002 | 0.010 | |
Parameters-class | 0.000 | 0.001 | 0.001 | |
XdeMcmc-class | 0 | 0 | 0 | |
XdeParameter-class | 0.000 | 0.000 | 0.001 | |
burnin | 0 | 0 | 0 | |
empiricalStart | 0.049 | 0.005 | 0.057 | |
expressionSetList | 0.007 | 0.001 | 0.009 | |
firstMcmc | 0.047 | 0.003 | 0.061 | |
geneCenter | 0.014 | 0.002 | 0.016 | |
hyperparameters | 0.031 | 0.001 | 0.032 | |
lastMcmc | 0 | 0 | 0 | |
output | 0.027 | 0.002 | 0.028 | |
ssStatistic | 0.185 | 0.013 | 0.197 | |
studyCenter | 0.016 | 0.001 | 0.017 | |
symbolsInteresting | 0.060 | 0.004 | 0.063 | |
xde | 0 | 0 | 0 | |
xmcmc | 0.031 | 0.002 | 0.033 | |
xsScores | 0.015 | 0.001 | 0.016 | |