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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1876/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scFeatures 1.6.0  (landing page)
Yue Cao
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/scFeatures
git_branch: RELEASE_3_20
git_last_commit: 73ee2f1
git_last_commit_date: 2024-10-29 11:17:33 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
merida1macOS 12.7.5 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 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: 1.6.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scFeatures_1.6.0.tar.gz
StartedAt: 2024-12-20 05:11:05 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 05:18:16 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 431.4 seconds
RetCode: 0
Status:   OK  
CheckDir: scFeatures.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scFeatures_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scFeatures.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 ‘scFeatures/DESCRIPTION’ ... OK
* this is package ‘scFeatures’ version ‘1.6.0’
* 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 ... 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 5.178  0.301   5.479
* 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-3.20-bioc/meat/scFeatures.Rcheck/00check.log’
for details.


Installation output

scFeatures.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL scFeatures
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘scFeatures’ ...
** 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_spot0.1630.0140.177
remove_mito_ribo1.5400.1131.654
run_CCI2.5570.1252.682
run_L_function0.3150.0450.360
run_Morans_I0.3320.0180.351
run_association_study_report000
run_celltype_interaction0.2090.0220.230
run_gene_cor0.3620.0150.378
run_gene_cor_celltype0.2910.0100.301
run_gene_mean0.3200.0270.347
run_gene_mean_celltype0.4330.0130.446
run_gene_prop0.3130.0070.320
run_gene_prop_celltype0.3230.0230.347
run_nn_correlation0.2540.0120.266
run_pathway_gsva5.1780.3015.479
run_pathway_mean1.450.121.57
run_pathway_prop3.1550.0413.196
run_proportion_logit0.1990.0110.210
run_proportion_ratio0.2390.0100.248
run_proportion_raw0.2010.0080.208
scFeatures0.5700.0370.607