Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-12-24 11:43 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1296/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MoleculeExperiment 1.7.0  (landing page)
Shila Ghazanfar
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/MoleculeExperiment
git_branch: devel
git_last_commit: d50404d
git_last_commit_date: 2024-10-29 11:20:12 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped


CHECK results for MoleculeExperiment on lconway

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: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2024-12-23 21:42:43 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 21:48:58 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 374.7 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MoleculeExperiment.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MoleculeExperiment/DESCRIPTION’ ... OK
* this is package ‘MoleculeExperiment’ version ‘1.7.0’
* 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 ... 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 39.813  0.252  40.272
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-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/4.5-x86_64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 60 ]
> 
> proc.time()
   user  system elapsed 
 18.140   0.790  19.034 

Example timings

MoleculeExperiment.Rcheck/MoleculeExperiment-Ex.timings

nameusersystemelapsed
MoleculeExperiment0.1070.0060.114
accessors0.2960.0210.322
bufferBoundaries0.7250.0310.768
countMolecules1.5300.0211.562
dataframeToMEList0.0820.0020.083
plotting-functions0.5220.0140.541
readBoundaries0.1830.0040.189
readCosmx0.6170.0480.694
readMerscope0.6150.0230.649
readMolecules0.0420.0020.045
readSegMask0.5240.0170.546
readXenium0.0730.0030.076
subset_by_extent39.813 0.25240.272
summarization0.0740.0050.079