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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1924/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Sconify 1.28.1  (landing page)
Tyler J Burns
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/Sconify
git_branch: RELEASE_3_21
git_last_commit: c9a356a
git_last_commit_date: 2025-10-08 04:01:42 -0400 (Wed, 08 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for Sconify on nebbiolo1

To the developers/maintainers of the Sconify package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Sconify.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: Sconify
Version: 1.28.1
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Sconify_1.28.1.tar.gz
StartedAt: 2025-10-16 03:22:33 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 03:24:49 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 136.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Sconify.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Sconify_1.28.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Sconify.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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Sconify/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sconify’ version ‘1.28.1’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Sconify’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 LazyData ... 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
SconeValues 11.766  0.132  11.908
* 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: OK


Installation output

Sconify.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Sconify
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘Sconify’ ...
** this is package ‘Sconify’ version ‘1.28.1’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '/' 
Note: wrong number of arguments to 'asinh' 
** 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 (Sconify)

Tests output

Sconify.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> library(testthat)
> library(Sconify)
> 
> test_check("Sconify")
Read the 100 x 27 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.01 seconds (sparsity = 0.967400)!
Learning embedding...
Iteration 50: error is 52.604365 (50 iterations in 0.01 seconds)
Iteration 100: error is 52.941963 (50 iterations in 0.01 seconds)
Iteration 150: error is 54.547214 (50 iterations in 0.01 seconds)
Iteration 200: error is 55.475063 (50 iterations in 0.01 seconds)
Iteration 250: error is 52.546360 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.226017 (50 iterations in 0.01 seconds)
Iteration 350: error is 0.729698 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.248717 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.217112 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.212353 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.210103 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.211386 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.212954 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.215807 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.217222 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.216356 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.215537 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.216193 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.216553 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.215007 (50 iterations in 0.01 seconds)
Fitting performed in 0.17 seconds.
Read the 1000 x 27 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.12 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 66.983609 (50 iterations in 0.21 seconds)
Iteration 100: error is 60.747735 (50 iterations in 0.16 seconds)
Iteration 150: error is 60.313309 (50 iterations in 0.16 seconds)
Iteration 200: error is 60.182912 (50 iterations in 0.17 seconds)
Iteration 250: error is 60.124605 (50 iterations in 0.17 seconds)
Iteration 300: error is 1.334607 (50 iterations in 0.14 seconds)
Iteration 350: error is 1.231727 (50 iterations in 0.13 seconds)
Iteration 400: error is 1.202211 (50 iterations in 0.14 seconds)
Iteration 450: error is 1.187785 (50 iterations in 0.14 seconds)
Iteration 500: error is 1.180237 (50 iterations in 0.14 seconds)
Iteration 550: error is 1.176652 (50 iterations in 0.13 seconds)
Iteration 600: error is 1.173632 (50 iterations in 0.14 seconds)
Iteration 650: error is 1.171729 (50 iterations in 0.14 seconds)
Iteration 700: error is 1.169637 (50 iterations in 0.14 seconds)
Iteration 750: error is 1.168604 (50 iterations in 0.14 seconds)
Iteration 800: error is 1.166284 (50 iterations in 0.14 seconds)
Iteration 850: error is 1.164540 (50 iterations in 0.14 seconds)
Iteration 900: error is 1.163144 (50 iterations in 0.14 seconds)
Iteration 950: error is 1.161478 (50 iterations in 0.14 seconds)
Iteration 1000: error is 1.159731 (50 iterations in 0.14 seconds)
Fitting performed in 2.93 seconds.
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 72 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 18.426   0.439  18.857 

Example timings

Sconify.Rcheck/Sconify-Ex.timings

nameusersystemelapsed
FcsToTibble0.1060.0060.114
Fnn0.3091.0911.400
GetKnnDe0.0760.0090.085
GetMarkerNames0.0260.0060.033
ImputeTesting3.2570.0433.300
MakeHist0.5390.0210.559
MakeKnnList0.2820.0490.331
MeaningOfLife0.0000.0000.001
ParseMarkers0.2360.0150.251
PostProcessing0.0750.0040.079
ProcessMultipleFiles0.0950.0050.099
QuantNormalizeElements0.1630.0010.164
SconeValues11.766 0.13211.908
SplitFile0.0710.0020.073
StringToNumbers000
SubsampleAndTsne1.6850.0111.696
TsneVis0.1950.0140.210