Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1670/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RBioFormats 1.6.0 (landing page) Andrzej Oleś
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the RBioFormats package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RBioFormats.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: RBioFormats |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RBioFormats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RBioFormats_1.6.0.tar.gz |
StartedAt: 2024-12-20 08:13:06 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 08:15:54 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 168.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RBioFormats.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RBioFormats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RBioFormats_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RBioFormats.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RBioFormats/DESCRIPTION’ ... OK * this is package ‘RBioFormats’ version ‘1.6.0’ * package encoding: UTF-8 * 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 ‘RBioFormats’ 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 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘read.image.R’ Running ‘reader.R’ Running ‘testthat.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: OK
RBioFormats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RBioFormats ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘RBioFormats’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RBioFormats)
RBioFormats.Rcheck/tests/read.image.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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("RBioFormats") BioFormats library version 7.3.0 > > parameters = list ( + sizeX = 32L, + sizeY = 32L, + sizeZ = 5L, + sizeC = 1L, + sizeT = 2L, + dimOrder = "XYTZC", + interleaved = TRUE, + indexed = FALSE + ) > > img = read.image(do.call(mockFile, parameters)) > > metadata = coreMetadata(img) > # metadata$indexed > # metadata > stopifnot(metadata$sizeC == 1L) > stopifnot(metadata$rgb == FALSE) > # stopifnot(.jcall(reader, "Z", "isIndexed") == FALSE) > # stopifnot(.jcall(reader, "I", "getImageCount") == 30) > # stopifnot(.jcall(reader, "S", "getDimensionOrder") == "XYCZT") > # > # metadata2 = .metadata(reader) > # metadata = RBioFormats:::.getCoreMetadata(reader) > > proc.time() user system elapsed 6.774 0.536 7.795
RBioFormats.Rcheck/tests/reader.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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("RBioFormats") BioFormats library version 7.3.0 > library("rJava") > > parameters = list ( + sizeX = 32L, + sizeY = 32L, + sizeZ = 5L, + sizeC = 3L, + sizeT = 2L, + dimOrder = "XYTZC", + interleaved = TRUE, + rgb = 1L, + indexed = TRUE + ) > > file = do.call(mockFile, parameters) > > # reduce verbosity > .jcall("loci.common.DebugTools", "Z", "enableLogging", "ERROR") [1] TRUE > > ## raw reader > reader = .jnew("loci.formats.ImageReader") > > # initialize file > .jcall(reader, , "setId", file) > > metadata = list ( + sizeX = .jcall(reader, "I", "getSizeX"), + sizeY = .jcall(reader, "I", "getSizeY"), + sizeZ = .jcall(reader, "I", "getSizeZ"), + sizeC = .jcall(reader, "I", "getSizeC"), + sizeT = .jcall(reader, "I", "getSizeT"), + dimOrder = .jcall(reader, "S", "getDimensionOrder"), + interleaved = .jcall(reader, "Z", "isInterleaved"), + rgb = .jcall(reader, "I", "getRGBChannelCount"), + indexed = .jcall(reader, "Z", "isIndexed") + ) > > stopifnot(identical(names(parameters), names(metadata))) > stopifnot(identical(parameters, metadata)) > > proc.time() user system elapsed 6.778 0.551 7.648
RBioFormats.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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(testthat) > library(RBioFormats) BioFormats library version 7.3.0 > > test_check("RBioFormats") [ FAIL 0 | WARN 0 | SKIP 1 | PASS 61 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-pixelType.R:23:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 61 ] > > proc.time() user system elapsed 15.050 2.435 15.448
RBioFormats.Rcheck/RBioFormats-Ex.timings
name | user | system | elapsed | |
AnnotatedImage-class | 1.325 | 0.164 | 2.314 | |
AnnotatedImageList-class | 0.115 | 0.014 | 0.086 | |
FormatTools | 0.051 | 0.006 | 0.047 | |
ImageMetadata-class | 0.077 | 0.007 | 0.063 | |
RBioFormats | 0.001 | 0.001 | 0.001 | |
checkJavaMemory | 0.003 | 0.000 | 0.001 | |
dimorder | 0.787 | 0.183 | 0.965 | |
metadataAccessors | 2.658 | 0.203 | 1.308 | |
mockFile | 0.024 | 0.004 | 0.029 | |
read.image | 0.531 | 0.061 | 0.322 | |
read.metadata | 0.169 | 0.042 | 0.162 | |
read.omexml | 0.506 | 0.076 | 0.496 | |
seriesCount | 0.041 | 0.003 | 0.037 | |
write.image | 0.121 | 0.011 | 0.091 | |