##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RBioFormats.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RBioFormats_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RBioFormats.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RBioFormats/DESCRIPTION’ ... OK
* this is package ‘RBioFormats’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AnnotatedImage-class.Rd: Image-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/RBioFormats.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL RBioFormats
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.21-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)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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 
  2.831   0.214   2.409 

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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 
  2.995   0.218   2.422 

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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 
  8.059   0.633   4.141