Andrzej Oleś
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/RBioFormats |
| git_branch: RELEASE_3_17 |
| git_last_commit: 5660c9d |
| git_last_commit_date: 2023-04-25 11:42:03 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1636/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RBioFormats 1.0.0 (landing page) Andrzej Oleś
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the RBioFormats package: - 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: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2023-10-18 17:25:23 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 17:27:35 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 131.9 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/RBioFormats.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RBioFormats/DESCRIPTION’ ... OK
* this is package ‘RBioFormats’ version ‘1.0.0’
* 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 R 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 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 in ‘inst/doc’ ... 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/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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 6.12.0
>
> 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
3.704 0.269 5.475
RBioFormats.Rcheck/tests/reader.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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 6.12.0
> 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
3.688 0.274 5.569
RBioFormats.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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 6.12.0
>
> 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
8.235 1.175 11.430
RBioFormats.Rcheck/RBioFormats-Ex.timings
| name | user | system | elapsed | |
| AnnotatedImage-class | 0.901 | 0.099 | 1.052 | |
| AnnotatedImageList-class | 0.057 | 0.007 | 0.066 | |
| FormatTools | 0.032 | 0.002 | 0.040 | |
| ImageMetadata-class | 0.057 | 0.005 | 0.129 | |
| RBioFormats | 0 | 0 | 0 | |
| checkJavaMemory | 0.001 | 0.000 | 0.001 | |
| dimorder | 0.538 | 0.052 | 0.854 | |
| metadataAccessors | 0.732 | 0.163 | 1.010 | |
| mockFile | 0.016 | 0.001 | 0.023 | |
| read.image | 0.327 | 0.021 | 0.329 | |
| read.metadata | 0.099 | 0.021 | 0.172 | |
| read.omexml | 0.440 | 0.059 | 0.512 | |
| seriesCount | 0.036 | 0.002 | 0.040 | |
| write.image | 0.091 | 0.009 | 0.112 | |