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This page was generated on 2025-08-04 12:06 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 1887/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scFeatures 1.9.0  (landing page)
Yue Cao
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/scFeatures
git_branch: devel
git_last_commit: 0d8daf3
git_last_commit_date: 2025-04-15 13:02:06 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for scFeatures on nebbiolo2

To the developers/maintainers of the scFeatures package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scFeatures.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: scFeatures
Version: 1.9.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scFeatures_1.9.0.tar.gz
StartedAt: 2025-08-04 02:31:18 -0400 (Mon, 04 Aug 2025)
EndedAt: 2025-08-04 02:39:50 -0400 (Mon, 04 Aug 2025)
EllapsedTime: 512.4 seconds
RetCode: 0
Status:   OK  
CheckDir: scFeatures.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scFeatures_1.9.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scFeatures.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘scFeatures/DESCRIPTION’ ... OK
* this is package ‘scFeatures’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘scFeatures’ 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'DT' 'Seurat'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
helper_CCI: no visible global function definition for 'data'
helper_CCI: no visible binding for global variable 'LRdb'
helper_CCI: no visible global function definition for 'capture.output'
helper_pathway_gsva: no visible global function definition for
  'capture.output'
run_pathway_gsva: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  LRdb capture.output data
Consider adding
  importFrom("utils", "capture.output", "data")
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
run_pathway_gsva 45.493  0.899  46.394
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/scFeatures.Rcheck/00check.log’
for details.


Installation output

scFeatures.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scFeatures
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scFeatures’ ...
** this is package ‘scFeatures’ version ‘1.9.0’
** 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 (scFeatures)

Tests output


Example timings

scFeatures.Rcheck/scFeatures-Ex.timings

nameusersystemelapsed
get_num_cell_per_spot0.1630.0190.182
remove_mito_ribo1.5590.0751.633
run_CCI2.7330.1562.889
run_L_function0.3590.0260.385
run_Morans_I0.3400.0240.364
run_association_study_report000
run_celltype_interaction0.2100.0280.238
run_gene_cor0.3700.0260.396
run_gene_cor_celltype0.3170.0080.325
run_gene_mean0.3840.0140.397
run_gene_mean_celltype0.4420.0110.453
run_gene_prop0.3180.0110.329
run_gene_prop_celltype0.3580.0180.376
run_nn_correlation0.2650.0130.278
run_pathway_gsva45.493 0.89946.394
run_pathway_mean3.1650.1643.329
run_pathway_prop3.3900.2513.641
run_proportion_logit0.1920.0170.209
run_proportion_ratio0.2550.0060.261
run_proportion_raw0.2100.0180.227
scFeatures0.5260.0470.573