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This page was generated on 2025-08-04 12:13 -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 1902/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Sconify 1.29.0  (landing page)
Tyler J Burns
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for Sconify on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Sconify
Version: 1.29.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Sconify_1.29.0.tar.gz
StartedAt: 2025-08-01 11:00:49 -0000 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 11:03:53 -0000 (Fri, 01 Aug 2025)
EllapsedTime: 184.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Sconify.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Sconify_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Sconify.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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   17.744  0.119  20.063
ImputeTesting  5.120  0.040   5.749
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Sconify
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 = 0.968600)!
Learning embedding...
Iteration 50: error is 51.247494 (50 iterations in 0.01 seconds)
Iteration 100: error is 51.642341 (50 iterations in 0.01 seconds)
Iteration 150: error is 50.110691 (50 iterations in 0.01 seconds)
Iteration 200: error is 50.062861 (50 iterations in 0.02 seconds)
Iteration 250: error is 49.356539 (50 iterations in 0.02 seconds)
Iteration 300: error is 1.330722 (50 iterations in 0.01 seconds)
Iteration 350: error is 0.608375 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.275074 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.216606 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.195229 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.195731 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.196957 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.196245 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.196581 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.197302 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.195747 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.195375 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.194945 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.195847 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.196130 (50 iterations in 0.01 seconds)
Fitting performed in 0.25 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 0.16 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 65.899965 (50 iterations in 0.40 seconds)
Iteration 100: error is 60.686444 (50 iterations in 0.27 seconds)
Iteration 150: error is 60.293081 (50 iterations in 0.28 seconds)
Iteration 200: error is 60.163614 (50 iterations in 0.29 seconds)
Iteration 250: error is 60.104534 (50 iterations in 0.30 seconds)
Iteration 300: error is 1.328850 (50 iterations in 0.24 seconds)
Iteration 350: error is 1.224982 (50 iterations in 0.23 seconds)
Iteration 400: error is 1.198632 (50 iterations in 0.24 seconds)
Iteration 450: error is 1.185743 (50 iterations in 0.26 seconds)
Iteration 500: error is 1.177301 (50 iterations in 0.27 seconds)
Iteration 550: error is 1.170526 (50 iterations in 0.28 seconds)
Iteration 600: error is 1.166848 (50 iterations in 0.27 seconds)
Iteration 650: error is 1.161611 (50 iterations in 0.27 seconds)
Iteration 700: error is 1.156992 (50 iterations in 0.27 seconds)
Iteration 750: error is 1.154728 (50 iterations in 0.27 seconds)
Iteration 800: error is 1.150951 (50 iterations in 0.26 seconds)
Iteration 850: error is 1.148994 (50 iterations in 0.26 seconds)
Iteration 900: error is 1.147175 (50 iterations in 0.26 seconds)
Iteration 950: error is 1.144277 (50 iterations in 0.25 seconds)
Iteration 1000: error is 1.142301 (50 iterations in 0.26 seconds)
Fitting performed in 5.44 seconds.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 30.458   0.444  37.696 

Example timings

Sconify.Rcheck/Sconify-Ex.timings

nameusersystemelapsed
FcsToTibble0.1780.0030.368
Fnn0.2760.1600.438
GetKnnDe0.1100.0030.172
GetMarkerNames0.0240.0150.040
ImputeTesting5.1200.0405.749
MakeHist0.4350.0000.437
MakeKnnList0.4950.0000.527
MeaningOfLife000
ParseMarkers0.3040.0080.324
PostProcessing0.1170.0040.121
ProcessMultipleFiles0.1560.0120.191
QuantNormalizeElements0.3130.0120.327
SconeValues17.744 0.11920.063
SplitFile0.1100.0040.114
StringToNumbers000
SubsampleAndTsne2.8270.0004.775
TsneVis0.2350.0240.259