Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-27 11:45 -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 1003/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
illuminaio 0.47.0 (landing page) Kasper Daniel Hansen
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the illuminaio package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/illuminaio.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: illuminaio |
Version: 0.47.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:illuminaio.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings illuminaio_0.47.0.tar.gz |
StartedAt: 2024-08-26 21:58:50 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 21:59:05 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 15.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: illuminaio.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:illuminaio.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings illuminaio_0.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/illuminaio.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘illuminaio/DESCRIPTION’ ... OK * this is package ‘illuminaio’ version ‘0.47.0’ * 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 ‘illuminaio’ can be installed ... OK * 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 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 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘readBPM.R’ Running ‘readIDAT_370k.R’ Running ‘readIDAT_370k_gz.R’ Running ‘readIDAT_450k.R’ Running ‘readIDAT_450k_gz.R’ Running ‘readIDAT_gs_wg6v2.R’ Running ‘readIDAT_ht12v4.R’ Running ‘readIDAT_wg6v2.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 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/illuminaio.Rcheck/00check.log’ for details.
illuminaio.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL illuminaio ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘illuminaio’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c 000.init.c -o 000.init.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c des.c -o des.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c local_des.c -o local_des.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o illuminaio.so 000.init.o des.o local_des.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-illuminaio/00new/illuminaio/libs ** R ** 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 (illuminaio)
illuminaio.Rcheck/tests/readBPM.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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. > ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > ## System tests for readBPM() > ## > ## Data is automatically downloaded from Illumina (e.g. [1]), if missing. > ## > ## NOTE: These tests will only run if '_R_CHECK_FULL_' is set, i.e. > ## they won't run on Bioconductor or CRAN servers. > ## > ## REFERENCES: > ## [1] http://support.illumina.com/downloads/infinium_bovineld_beadchip_product_files.ilmn > ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > if (FALSE && Sys.getenv("_R_CHECK_FULL_") != "") { + + ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + ## Utility functions + ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + getIlluminaAnnotationFile <- function(chipType, filename, force=FALSE) { + # Share data files across architectures, e.g. tests_i386 and tests_x64. + rootPath <- "../annotationData,illuminaio,tests" + path <- file.path(rootPath, "chipTypes", chipType) + if (!file_test("-d", path)) dir.create(path, recursive=TRUE) + pathname <- file.path(path, filename) + + # Already downloaded? + if (!force && file_test("-f", pathname)) return(pathname) + + # Download from Illumina + urlRoot <- "http://supportres.illumina.com/documents/downloads/productfiles" + url <- file.path(urlRoot, chipType, filename) + download.file(url, destfile=pathname, mode="wb") + if (!file_test("-f", pathname)) stop("Failed to download file: ", url) + + pathname + } # getIlluminaAnnotationFile() + + + ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + ## Tests + ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + ## pathname <- getIlluminaAnnotationFile("bovineld", "bovineld_c.bpm") + + path <- "annotationData/chipTypes/HumanMethylation450" + filename <- "humanmethylation450_15017482_v-1-2.bpm" + pathname <- file.path(path,filename) + data <- illuminaio::readBPM(pathname) + str(data) + + } # if (Sys.getenv("_R_CHECK_FULL_") != "") > > proc.time() user system elapsed 0.073 0.020 0.089
illuminaio.Rcheck/tests/readIDAT_370k.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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. > library(illuminaio) > library(IlluminaDataTestFiles) > > load(file.path(path.package("IlluminaDataTestFiles"), "extdata", "testData", "idat.370k.rda")) > idatFile <- system.file("extdata", "idat", "4019585376_B_Red.idat", + package = "IlluminaDataTestFiles") > idat <- illuminaio::readIDAT(idatFile) > ## FIXME: IlluminaDataTestFiles needs to be updated according > ## to 'RunInfo' bug fix in illuminaio v0.11.2. > if (packageVersion("illuminaio") > "0.11.1") idat$RunInfo[-(1:2),] <- NA > RUnit::checkEquals(idat, idat.370k) [1] TRUE > > proc.time() user system elapsed 0.459 0.032 0.489
illuminaio.Rcheck/tests/readIDAT_370k_gz.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(illuminaio) > library(IlluminaDataTestFiles) > > idatFile1 <- system.file("extdata", "idat", "4019585376_B_Red.idat", + package = "IlluminaDataTestFiles") > idat1 <- illuminaio::readIDAT(idatFile1) > idatFile2 <- system.file("extdata", "idat", "4019585376_B_Red.idat.gz", + package = "IlluminaDataTestFiles") > idat2 <- illuminaio::readIDAT(idatFile2) > idat2$fileSize <- idat1$fileSize <- NULL > RUnit::checkEquals(idat1, idat2) [1] TRUE > > proc.time() user system elapsed 0.366 0.038 0.402
illuminaio.Rcheck/tests/readIDAT_450k.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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. > library(IlluminaDataTestFiles) > > load(file.path(path.package("IlluminaDataTestFiles"), "extdata", "testData", "idat.450k.rda")) > idatFile <- system.file("extdata", "idat", "5723646052_R02C02_Grn.idat", + package = "IlluminaDataTestFiles") > idat <- illuminaio::readIDAT(idatFile) > > ## WORKAROUND: Until 'IlluminaDataTestFiles' is updated, > ## don't test all of the "Unknowns" fields > if ( "Unknown.7" %in% names(idat[["Unknowns"]]) && + ! "Unknown.7" %in% names(idat.450k[["Unknowns"]])) { + unknowns <- idat[["Unknowns"]] + unknowns[["Unknown.6"]] <- NULL + unknowns[["Unknown.7"]] <- NULL + idat[["Unknowns"]] <- unknowns + } > > RUnit::checkEquals(idat, idat.450k) [1] TRUE > > proc.time() user system elapsed 0.801 0.044 0.847
illuminaio.Rcheck/tests/readIDAT_450k_gz.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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. > library(illuminaio) > library(IlluminaDataTestFiles) > > idatFile1 <- system.file("extdata", "idat", "5723646052_R02C02_Grn.idat", + package = "IlluminaDataTestFiles") > idat1 <- illuminaio::readIDAT(idatFile1) > idatFile2 <- system.file("extdata", "idat", "5723646052_R02C02_Grn.idat.gz", + package = "IlluminaDataTestFiles") > idat2 <- illuminaio::readIDAT(idatFile2) > idat2$fileSize <- idat1$fileSize <- NULL > RUnit::checkEquals(idat1, idat2) [1] TRUE > > proc.time() user system elapsed 0.646 0.041 0.686
illuminaio.Rcheck/tests/readIDAT_gs_wg6v2.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(illuminaio) > library(IlluminaDataTestFiles) > > idatFile <- system.file("extdata", "idat", "4343238080_A_Grn.idat", package = "IlluminaDataTestFiles") > idatData <- readIDAT(idatFile)$Quants > gsFile <- system.file("extdata", "gs", "4343238080_A_ProbeSummary.txt.gz", package = "IlluminaDataTestFiles") > gStudio <- read.delim(gzfile(gsFile, open = "r"), sep = "\t", header = TRUE) > > ## not all probes are present in GenomeStudio output, so only select those that are > idatData <- idatData[which(idatData[,"CodesBinData"] %in% gStudio[,"ProbeID"]),] > ## the orders are also different (numeric vs alphabetical) > gStudio <- gStudio[match(idatData[,"CodesBinData"], gStudio[,"ProbeID"]),] > # check each value in GenomeStudio output > ## there are some rounding differences, so we allow slight differences > > ## summarised bead intensities > RUnit::checkEqualsNumeric(idatData[, "MeanBinData"], gStudio[, 3], tolerance = 10e-7) [1] TRUE > ## number of beads > RUnit::checkEquals(idatData[, "NumGoodBeadsBinData"], gStudio[, 5]) [1] TRUE > ## standard errors > RUnit::checkEqualsNumeric(idatData[, "DevBinData"] / sqrt(idatData[, "NumGoodBeadsBinData"]), gStudio[, 4], tolerance = 10e-7) [1] TRUE > > proc.time() user system elapsed 0.509 0.042 0.550
illuminaio.Rcheck/tests/readIDAT_ht12v4.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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. > library(illuminaio) > library(IlluminaDataTestFiles) > > load(file.path(path.package("IlluminaDataTestFiles"), "extdata", "testData", "idat.ht12v4.rda")) > idatFile <- system.file("extdata", "idat", "6016741005_A_Grn.idat", + package = "IlluminaDataTestFiles") > idat <- illuminaio::readIDAT(idatFile) > RUnit::checkEquals(idat, idat.ht12v4) [1] TRUE > > proc.time() user system elapsed 0.476 0.035 0.509
illuminaio.Rcheck/tests/readIDAT_wg6v2.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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. > library(illuminaio) > library(IlluminaDataTestFiles) > > load(file.path(path.package("IlluminaDataTestFiles"), "extdata", "testData", "idat.wg6v2.rda")) > idatFile <- system.file("extdata", "idat", "4343238080_A_Grn.idat", + package = "IlluminaDataTestFiles") > idat <- illuminaio::readIDAT(idatFile) > RUnit::checkEquals(idat, idat.wg6v2) [1] TRUE > > proc.time() user system elapsed 0.472 0.038 0.507
illuminaio.Rcheck/illuminaio-Ex.timings
name | user | system | elapsed | |
readIDAT | 0.029 | 0.003 | 0.034 | |