Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (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 1636/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBioFormats 1.0.0  (landing page)
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)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for RBioFormats on kjohnson2


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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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


Installation output

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)

Tests output

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 

Example timings

RBioFormats.Rcheck/RBioFormats-Ex.timings

nameusersystemelapsed
AnnotatedImage-class0.9010.0991.052
AnnotatedImageList-class0.0570.0070.066
FormatTools0.0320.0020.040
ImageMetadata-class0.0570.0050.129
RBioFormats000
checkJavaMemory0.0010.0000.001
dimorder0.5380.0520.854
metadataAccessors0.7320.1631.010
mockFile0.0160.0010.023
read.image0.3270.0210.329
read.metadata0.0990.0210.172
read.omexml0.4400.0590.512
seriesCount0.0360.0020.040
write.image0.0910.0090.112