Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:47 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 1423/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
oligo 1.69.2 (landing page) Benilton Carvalho
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the oligo package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oligo.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: oligo |
Version: 1.69.2 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:oligo.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings oligo_1.69.2.tar.gz |
StartedAt: 2024-08-27 07:22:40 -0000 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 07:29:24 -0000 (Tue, 27 Aug 2024) |
EllapsedTime: 404.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: oligo.Rcheck |
Warnings: 4 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:oligo.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings oligo_1.69.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/oligo.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘oligo/DESCRIPTION’ ... OK * this is package ‘oligo’ version ‘1.69.2’ * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘doMPI’ * 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 ‘oligo’ can be installed ... OK * used C compiler: ‘gcc (GCC) 10.3.1’ * checking installed package size ... NOTE installed size is 17.1Mb sub-directories of 1Mb or more: scripts 15.7Mb * 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 ... NOTE Warning: no function found corresponding to methods exports from ‘oligo’ for: ‘show’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘Biobase:::annotatedDataFrameFromMatrix’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function calls to a different package: .Call("ReadHeader", ..., PACKAGE = "affyio") .Call("read_abatch", ..., PACKAGE = "affyio") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]): partial argument match of 'nr' to 'nrow' image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]): partial argument match of 'nc' to 'ncol' cloneFS: no visible global function definition for ‘clone’ rmaBgCorrectLDSmaster: no visible global function definition for ‘clone’ backgroundCorrect,matrix: no visible binding for global variable ‘intensities’ normalize,ff_matrix: no visible global function definition for ‘clone’ normalizeToTarget,ff_matrix: no visible global function definition for ‘clone’ pmindex,GenericPDInfo: no visible binding for global variable ‘man_fsetid’ Undefined global functions or variables: clone intensities man_fsetid * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'mm<-' and siglist 'TilingFeatureSet,missing,missing,array' generic 'pm<-' and siglist 'TilingFeatureSet,missing,missing,array' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'boxplot.Rd' ‘target’ Undocumented arguments in Rd file 'hist.Rd' ‘target’ 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 line endings in shell scripts ... 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) ... WARNING apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’ * 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 files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory newer than all files in 'inst/doc': ‘Makefile’ * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed preprocessTools 19.040 0.116 19.189 getProbeInfo 12.120 1.458 13.960 read.celfiles 5.113 0.162 5.375 * 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: 4 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/oligo.Rcheck/00check.log’ for details.
oligo.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL oligo ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘oligo’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c DABG.c -o DABG.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ParserGzXYS.c -o ParserGzXYS.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ParserXYS.c -o ParserXYS.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c baseProfile.c -o baseProfile.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c basecontent.c -o basecontent.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chipbackground.c -o chipbackground.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c mas5calls.c -o mas5calls.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rma2.c -o rma2.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rma_common.c -o rma_common.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c trimmed.c -o trimmed.o gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -lopenblas -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-oligo/00new/oligo/libs ** R ** inst ** byte-compile and prepare package for lazy loading Note: in method for ‘pm<-’ with signature ‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’: expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" Note: in method for ‘mm<-’ with signature ‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’: expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" ** 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 (oligo)
oligo.Rcheck/tests/doRUnit.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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 <- "oligo" + path <- ifelse(Sys.getenv( "RCMDCHECK" ) == "FALSE", + file.path( getwd(), "..", "inst", "unitTests" ), + system.file( package=pkg, "unitTests" )) + + cat( "\nRunning unit tests\n" ) + print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) ) + library( package=pkg, character.only=TRUE ) + + ##Fail on warnings + ##options( warn=2 ) + options(warn=0) + + ## Get the pattern (if there is one?) + patt <- Sys.getenv( "RUNITFILEPATTERN" ) + testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ), + dirs=path, + testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" )) + 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] "oligo" $getwd [1] "/home/biocbuild/bbs-3.20-bioc/meat/oligo.Rcheck/tests" $pathToUnitTests [1] "/home/biocbuild/tmp/Rtmp1dhU7A/RLIBS_86d6a3250d183/oligo/unitTests" 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, aperm, 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, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: oligoClasses Welcome to oligoClasses version 1.67.0 Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: Biostrings Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit ================================================================================ Welcome to oligo version 1.69.2 ================================================================================ Executing test function test_rma ... Getting sample dataset Loading required package: pd.hg18.60mer.expr Loading required package: RSQLite Loading required package: DBI Platform design info loaded. Checking designs for each XYS file... Done. Allocating memory... Done. Reading /home/biocbuild/tmp/Rtmp1dhU7A/RLIBS_86d6a3250d183/maqcExpression4plex/extdata/9868701_532.xys. Reading /home/biocbuild/tmp/Rtmp1dhU7A/RLIBS_86d6a3250d183/maqcExpression4plex/extdata/9868901_532.xys. Reading /home/biocbuild/tmp/Rtmp1dhU7A/RLIBS_86d6a3250d183/maqcExpression4plex/extdata/9869001_532.xys. Reading /home/biocbuild/tmp/Rtmp1dhU7A/RLIBS_86d6a3250d183/maqcExpression4plex/extdata/9870301_532.xys. Reading /home/biocbuild/tmp/Rtmp1dhU7A/RLIBS_86d6a3250d183/maqcExpression4plex/extdata/9870401_532.xys. Reading /home/biocbuild/tmp/Rtmp1dhU7A/RLIBS_86d6a3250d183/maqcExpression4plex/extdata/9870601_532.xys. Running RMA Background correcting Normalizing Calculating Expression Getting reference results done successfully. Executing test function test_selector ... Loading reference data Loading sample dataset: Exon Getting probe info: core Loading required package: pd.huex.1.0.st.v2 Getting probe info: probeset Getting probe info: antigenomic backgroung probes Loading sample dataset: Gene Getting probe info: core Loading required package: pd.hugene.1.0.st.v1 Getting probe info: probeset Getting probe info: antigenomic backgroung probes done successfully. ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Tue Aug 27 07:29:21 2024 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : oligo unit testing - 2 test functions, 0 errors, 0 failures Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry 3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry > > proc.time() user system elapsed 101.259 3.892 107.935
oligo.Rcheck/oligo-Ex.timings
name | user | system | elapsed | |
Index-methods | 0 | 0 | 0 | |
IntensityMatrix-methods | 0.934 | 0.019 | 0.983 | |
MAplot-methods | 1.886 | 0.008 | 1.898 | |
basecontent | 0 | 0 | 0 | |
basicPLM | 1.606 | 0.000 | 1.608 | |
basicRMA | 1.597 | 0.000 | 1.599 | |
colors | 0.025 | 0.000 | 0.025 | |
coordinates | 0.000 | 0.001 | 0.000 | |
fitProbeLevelModel | 4.075 | 0.055 | 4.149 | |
getProbeInfo | 12.120 | 1.458 | 13.960 | |
image | 1.075 | 0.023 | 1.109 | |
justSNPRMA | 0 | 0 | 0 | |
list.xysfiles | 0 | 0 | 0 | |
oligoPLM-class | 0.000 | 0.000 | 0.001 | |
paCalls | 0 | 0 | 0 | |
preprocessTools | 19.040 | 0.116 | 19.189 | |
read.celfiles | 5.113 | 0.162 | 5.375 | |
read.xysfiles | 0.557 | 0.008 | 0.566 | |
rma-methods | 1.834 | 0.020 | 1.857 | |
sequenceDesignMatrix | 0.013 | 0.000 | 0.012 | |