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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MoleculeExperiment.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MoleculeExperiment_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MoleculeExperiment.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘MoleculeExperiment/DESCRIPTION’ ... OK
* this is package ‘MoleculeExperiment’ version ‘1.6.0’
* 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 ... 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 ... NOTE
  installed size is  8.7Mb
  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 loading without being on the library search path ... 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 ... NOTE
.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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* 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 32.19  0.628  32.819
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/MoleculeExperiment.Rcheck/00check.log’
for details.