Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-08-04 11:41 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1.28.0  (landing page)
Tyler J Burns
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/Sconify
git_branch: RELEASE_3_21
git_last_commit: 77b3a46
git_last_commit_date: 2025-04-15 11:19:48 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 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
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
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: 1.28.0
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_1.28.0.tar.gz
StartedAt: 2025-08-04 02:32:05 -0400 (Mon, 04 Aug 2025)
EndedAt: 2025-08-04 02:34:16 -0400 (Mon, 04 Aug 2025)
EllapsedTime: 131.1 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_1.28.0.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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘Sconify/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sconify’ version ‘1.28.0’
* 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 ‘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 12.031  0.173  12.204
* 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 ‘1.28.0’
** 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 = 0.966000)!
Learning embedding...
Iteration 50: error is 48.016751 (50 iterations in 0.01 seconds)
Iteration 100: error is 47.977205 (50 iterations in 0.01 seconds)
Iteration 150: error is 49.492736 (50 iterations in 0.01 seconds)
Iteration 200: error is 48.828568 (50 iterations in 0.01 seconds)
Iteration 250: error is 47.195953 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.088604 (50 iterations in 0.01 seconds)
Iteration 350: error is 0.307624 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.180719 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.165472 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.162605 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.162278 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.160225 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.159685 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.154697 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.152403 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.153066 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.153311 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.153126 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.152458 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.154094 (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 65.250216 (50 iterations in 0.21 seconds)
Iteration 100: error is 60.714451 (50 iterations in 0.16 seconds)
Iteration 150: error is 60.321804 (50 iterations in 0.18 seconds)
Iteration 200: error is 60.188681 (50 iterations in 0.20 seconds)
Iteration 250: error is 60.120655 (50 iterations in 0.20 seconds)
Iteration 300: error is 1.334231 (50 iterations in 0.15 seconds)
Iteration 350: error is 1.229222 (50 iterations in 0.13 seconds)
Iteration 400: error is 1.202539 (50 iterations in 0.14 seconds)
Iteration 450: error is 1.188181 (50 iterations in 0.14 seconds)
Iteration 500: error is 1.180855 (50 iterations in 0.14 seconds)
Iteration 550: error is 1.173732 (50 iterations in 0.14 seconds)
Iteration 600: error is 1.167453 (50 iterations in 0.15 seconds)
Iteration 650: error is 1.164093 (50 iterations in 0.14 seconds)
Iteration 700: error is 1.161100 (50 iterations in 0.14 seconds)
Iteration 750: error is 1.156931 (50 iterations in 0.14 seconds)
Iteration 800: error is 1.155715 (50 iterations in 0.14 seconds)
Iteration 850: error is 1.154971 (50 iterations in 0.14 seconds)
Iteration 900: error is 1.153607 (50 iterations in 0.14 seconds)
Iteration 950: error is 1.152026 (50 iterations in 0.14 seconds)
Iteration 1000: error is 1.150521 (50 iterations in 0.14 seconds)
Fitting performed in 3.09 seconds.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 18.486   0.380  18.854 

Example timings

Sconify.Rcheck/Sconify-Ex.timings

nameusersystemelapsed
FcsToTibble0.1140.0020.117
Fnn0.2521.1151.366
GetKnnDe0.0730.0110.085
GetMarkerNames0.0230.0080.030
ImputeTesting3.1750.0573.235
MakeHist0.2850.0030.288
MakeKnnList0.3020.0030.305
MeaningOfLife0.0000.0000.001
ParseMarkers0.2430.0130.256
PostProcessing0.0760.0020.078
ProcessMultipleFiles0.0980.0020.101
QuantNormalizeElements0.1850.0010.186
SconeValues12.031 0.17312.204
SplitFile0.0690.0040.073
StringToNumbers0.0000.0000.001
SubsampleAndTsne1.6920.0031.694
TsneVis0.1630.0020.165