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This page was generated on 2024-07-12 17:42 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 1316/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MoleculeExperiment 1.4.1  (landing page)
Shila Ghazanfar
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/MoleculeExperiment
git_branch: RELEASE_3_19
git_last_commit: 7b1b477
git_last_commit_date: 2024-05-29 19:49:20 -0400 (Wed, 29 May 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for MoleculeExperiment on kjohnson1

To the developers/maintainers of the MoleculeExperiment package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MoleculeExperiment.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: MoleculeExperiment
Version: 1.4.1
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_1.4.1.tar.gz
StartedAt: 2024-07-12 02:09:13 -0400 (Fri, 12 Jul 2024)
EndedAt: 2024-07-12 02:15:19 -0400 (Fri, 12 Jul 2024)
EllapsedTime: 366.0 seconds
RetCode: 0
Status:   OK  
CheckDir: MoleculeExperiment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MoleculeExperiment.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MoleculeExperiment/DESCRIPTION’ ... OK
* this is package ‘MoleculeExperiment’ version ‘1.4.1’
* 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 ... NOTE
  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 ... 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 37.75  0.387  38.159
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/MoleculeExperiment.Rcheck/00check.log’
for details.


Installation output

MoleculeExperiment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MoleculeExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘MoleculeExperiment’ ...
** using staged installation
** R
** data
** 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 (MoleculeExperiment)

Tests output

MoleculeExperiment.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> # 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)
> 
> test_check("MoleculeExperiment")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 70 ]
> 
> proc.time()
   user  system elapsed 
 18.019   0.609  18.637 

Example timings

MoleculeExperiment.Rcheck/MoleculeExperiment-Ex.timings

nameusersystemelapsed
MoleculeExperiment0.1110.0060.116
accessors0.3020.0170.323
bufferBoundaries1.6080.0241.633
countMolecules1.3810.0881.470
dataframeToMEList0.0630.0000.063
plotting-functions0.4520.0100.462
readBoundaries0.1400.0050.144
readCosmx0.5650.0360.611
readMerscope0.5220.0180.546
readMolecules0.0410.0020.043
readSegMask0.4190.0140.435
readXenium0.0640.0030.068
subset_by_extent37.750 0.38738.159
summarization0.0680.0040.072