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This page was generated on 2025-08-09 12:07 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 1905/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Sconify 1.29.0  (landing page)
Tyler J Burns
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/Sconify
git_branch: devel
git_last_commit: d0d3ac0
git_last_commit_date: 2025-04-15 11:19:48 -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  NO, package depends on 'flowCore' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'flowCore' which is only available as a source package that needs compilation


CHECK results for Sconify on palomino8

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: 1.29.0
Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Sconify.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings Sconify_1.29.0.tar.gz
StartedAt: 2025-08-09 06:30:28 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 06:32:44 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 136.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Sconify.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Sconify.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings Sconify_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/Sconify.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Sconify/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Sconify' version '1.29.0'
* 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 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 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 17.33   0.59   17.92
* 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: OK


Installation output

Sconify.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL Sconify
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'Sconify' ...
** this is package 'Sconify' version '1.29.0'
** 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 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 0.02 seconds (sparsity = 0.966400)!
Learning embedding...
Iteration 50: error is 52.817186 (50 iterations in 0.01 seconds)
Iteration 100: error is 50.151830 (50 iterations in 0.01 seconds)
Iteration 150: error is 53.145310 (50 iterations in 0.01 seconds)
Iteration 200: error is 51.078984 (50 iterations in 0.01 seconds)
Iteration 250: error is 52.880057 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.174008 (50 iterations in 0.01 seconds)
Iteration 350: error is 0.675403 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.233299 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.212158 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.193986 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.176168 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.174439 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.163317 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.164023 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.165073 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.163841 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.162375 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.162010 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.161431 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.157998 (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 0.24 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 66.611640 (50 iterations in 0.19 seconds)
Iteration 100: error is 60.780575 (50 iterations in 0.17 seconds)
Iteration 150: error is 60.355563 (50 iterations in 0.19 seconds)
Iteration 200: error is 60.214786 (50 iterations in 0.19 seconds)
Iteration 250: error is 60.149699 (50 iterations in 0.19 seconds)
Iteration 300: error is 1.348569 (50 iterations in 0.17 seconds)
Iteration 350: error is 1.232828 (50 iterations in 0.13 seconds)
Iteration 400: error is 1.202373 (50 iterations in 0.14 seconds)
Iteration 450: error is 1.188034 (50 iterations in 0.13 seconds)
Iteration 500: error is 1.181176 (50 iterations in 0.15 seconds)
Iteration 550: error is 1.176010 (50 iterations in 0.15 seconds)
Iteration 600: error is 1.173280 (50 iterations in 0.13 seconds)
Iteration 650: error is 1.171325 (50 iterations in 0.10 seconds)
Iteration 700: error is 1.168649 (50 iterations in 0.15 seconds)
Iteration 750: error is 1.165818 (50 iterations in 0.15 seconds)
Iteration 800: error is 1.162798 (50 iterations in 0.15 seconds)
Iteration 850: error is 1.160287 (50 iterations in 0.15 seconds)
Iteration 900: error is 1.158351 (50 iterations in 0.15 seconds)
Iteration 950: error is 1.156938 (50 iterations in 0.14 seconds)
Iteration 1000: error is 1.154781 (50 iterations in 0.10 seconds)
Fitting performed in 3.04 seconds.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
  24.20    1.28   26.60 

Example timings

Sconify.Rcheck/Sconify-Ex.timings

nameusersystemelapsed
FcsToTibble0.160.020.17
Fnn0.880.551.43
GetKnnDe0.080.000.08
GetMarkerNames0.050.000.04
ImputeTesting4.470.124.61
MakeHist0.390.000.39
MakeKnnList0.430.000.44
MeaningOfLife000
ParseMarkers0.300.051.13
PostProcessing0.130.000.12
ProcessMultipleFiles0.170.000.17
QuantNormalizeElements0.260.030.30
SconeValues17.33 0.5917.92
SplitFile0.060.030.10
StringToNumbers000
SubsampleAndTsne1.580.021.59
TsneVis0.170.020.19