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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MoleculeExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MoleculeExperiment_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/MoleculeExperiment.Rcheck’
* using R Under development (unstable) (2026-03-01 r89506)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-16 23:28:49 UTC
* using option ‘--no-vignettes’
* checking for file ‘MoleculeExperiment/DESCRIPTION’ ... OK
* this is package ‘MoleculeExperiment’ version ‘1.11.0’
* 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 ... NOTE
Found the following non-portable file path:
  MoleculeExperiment/inst/extdata/vizgen_HumanOvarianCancerPatient2Slice2/cell_boundaries/feature_data_1753.hdf5

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MoleculeExperiment’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      3.4Mb
    extdata   4.8Mb
* 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 dependencies in R code ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
* checking S3 generic/method consistency ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
.get_sample_id: no visible binding for global variable ‘.’
countMolecules: no visible binding for global variable ‘sample_id’
countMolecules: no visible binding for global variable ‘x_location’
countMolecules: no visible binding for global variable ‘y_location’
geom_point_me: no visible binding for global variable ‘feature_id’
geom_raster_img: no visible global function definition for ‘ftable’
geom_raster_img: no visible binding for global variable ‘x’
geom_raster_img: no visible binding for global variable ‘y’
geom_raster_img: no visible binding for global variable ‘value’
geom_raster_img: no visible global function definition for
  ‘scale_fill_gradient’
readSegMask: no visible binding for global variable ‘num’
subset_by_extent: no visible binding for global variable ‘x_location’
subset_by_extent: no visible binding for global variable ‘y_location’
Undefined global functions or variables:
  . feature_id ftable num sample_id scale_fill_gradient value x
  x_location y y_location
Consider adding
  importFrom("stats", "ftable")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
* checking Rd \usage sections ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... INFO
  proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
  proj_create: no database context specified
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
subset_by_extent 13.542  0.177  13.882
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 4 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/MoleculeExperiment.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MoleculeExperiment
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘MoleculeExperiment’ ...
** this is package ‘MoleculeExperiment’ version ‘1.11.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
** testing if installed package can be loaded from final location
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
** testing if installed package keeps a record of temporary installation path
* DONE (MoleculeExperiment)

R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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.

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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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(MoleculeExperiment)
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
> 
> test_check("MoleculeExperiment")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 70 ]
> 
> proc.time()
   user  system elapsed 
  6.487   0.219   6.809