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 11:40 -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 1648/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RBioFormats 1.5.1 (landing page) Andrzej Oleś
| 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 | ERROR | ERROR | skipped | ||||||||||
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: 1.5.1 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RBioFormats.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RBioFormats_1.5.1.tar.gz |
StartedAt: 2024-08-27 02:56:17 -0400 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 02:57:32 -0400 (Tue, 27 Aug 2024) |
EllapsedTime: 75.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RBioFormats.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RBioFormats.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RBioFormats_1.5.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RBioFormats.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘RBioFormats/DESCRIPTION’ ... OK * this is package ‘RBioFormats’ version ‘1.5.1’ * 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
RBioFormats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RBioFormats ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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. > 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 3.419 0.188 2.745
RBioFormats.Rcheck/tests/reader.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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. > 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 3.456 0.242 2.885
RBioFormats.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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. > 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 9.016 0.476 4.561
RBioFormats.Rcheck/RBioFormats-Ex.timings
name | user | system | elapsed | |
AnnotatedImage-class | 1.071 | 0.064 | 0.557 | |
AnnotatedImageList-class | 0.057 | 0.012 | 0.036 | |
FormatTools | 0.016 | 0.000 | 0.013 | |
ImageMetadata-class | 0.047 | 0.000 | 0.022 | |
RBioFormats | 0.000 | 0.000 | 0.001 | |
checkJavaMemory | 0.001 | 0.000 | 0.000 | |
dimorder | 0.600 | 0.140 | 0.683 | |
metadataAccessors | 1.080 | 0.066 | 0.363 | |
mockFile | 0.013 | 0.000 | 0.013 | |
read.image | 0.420 | 0.044 | 0.207 | |
read.metadata | 0.057 | 0.024 | 0.067 | |
read.omexml | 0.513 | 0.041 | 0.282 | |
seriesCount | 0.043 | 0.008 | 0.024 | |
write.image | 0.065 | 0.005 | 0.050 | |