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This page was generated on 2024-07-18 11:41 -0400 (Thu, 18 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4683
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4379
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4450
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4399
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 1861/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Sconify 1.25.0  (landing page)
Tyler J Burns
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/Sconify
git_branch: devel
git_last_commit: 49aeaa1
git_last_commit_date: 2024-04-30 11:04:59 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 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  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for Sconify on lconway

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: 1.25.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Sconify.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Sconify_1.25.0.tar.gz
StartedAt: 2024-07-18 00:08:14 -0400 (Thu, 18 Jul 2024)
EndedAt: 2024-07-18 00:10:28 -0400 (Thu, 18 Jul 2024)
EllapsedTime: 133.2 seconds
RetCode: 0
Status:   OK  
CheckDir: Sconify.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Sconify.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Sconify_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Sconify.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Sconify/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sconify’ version ‘1.25.0’
* 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 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 14.46   0.19  14.742
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Sconify
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘Sconify’ ...
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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!
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.01 seconds (sparsity = 0.968400)!
Learning embedding...
Iteration 50: error is 53.015006 (50 iterations in 0.01 seconds)
Iteration 100: error is 53.399325 (50 iterations in 0.01 seconds)
Iteration 150: error is 53.665208 (50 iterations in 0.01 seconds)
Iteration 200: error is 51.443306 (50 iterations in 0.01 seconds)
Iteration 250: error is 50.948931 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.493183 (50 iterations in 0.01 seconds)
Iteration 350: error is 1.043024 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.451501 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.259487 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.205544 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.193949 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.193703 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.195147 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.195331 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.195123 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.195259 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.193049 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.191889 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.194624 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.192629 (50 iterations in 0.01 seconds)
Fitting performed in 0.18 seconds.
Read the 1000 x 27 data matrix successfully!
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.13 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 63.743666 (50 iterations in 0.21 seconds)
Iteration 100: error is 60.647760 (50 iterations in 0.16 seconds)
Iteration 150: error is 60.297664 (50 iterations in 0.15 seconds)
Iteration 200: error is 60.169303 (50 iterations in 0.16 seconds)
Iteration 250: error is 60.119159 (50 iterations in 0.16 seconds)
Iteration 300: error is 1.340284 (50 iterations in 0.13 seconds)
Iteration 350: error is 1.235949 (50 iterations in 0.12 seconds)
Iteration 400: error is 1.205429 (50 iterations in 0.12 seconds)
Iteration 450: error is 1.191408 (50 iterations in 0.12 seconds)
Iteration 500: error is 1.182408 (50 iterations in 0.11 seconds)
Iteration 550: error is 1.175562 (50 iterations in 0.12 seconds)
Iteration 600: error is 1.171681 (50 iterations in 0.13 seconds)
Iteration 650: error is 1.168220 (50 iterations in 0.12 seconds)
Iteration 700: error is 1.164610 (50 iterations in 0.12 seconds)
Iteration 750: error is 1.161993 (50 iterations in 0.12 seconds)
Iteration 800: error is 1.160037 (50 iterations in 0.13 seconds)
Iteration 850: error is 1.159004 (50 iterations in 0.13 seconds)
Iteration 900: error is 1.156878 (50 iterations in 0.13 seconds)
Iteration 950: error is 1.154808 (50 iterations in 0.13 seconds)
Iteration 1000: error is 1.152970 (50 iterations in 0.12 seconds)
Fitting performed in 2.70 seconds.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 22.049   0.730  23.060 

Example timings

Sconify.Rcheck/Sconify-Ex.timings

nameusersystemelapsed
FcsToTibble0.1620.0070.172
Fnn0.3310.9751.329
GetKnnDe0.0620.0050.070
GetMarkerNames0.0280.0020.030
ImputeTesting3.8940.0303.953
MakeHist0.3860.0120.399
MakeKnnList0.3650.0090.376
MeaningOfLife0.0010.0010.001
ParseMarkers0.3080.0310.355
PostProcessing0.1450.0040.149
ProcessMultipleFiles0.1410.0060.149
QuantNormalizeElements0.2290.0030.232
SconeValues14.460 0.19014.742
SplitFile0.1010.0040.105
StringToNumbers0.0000.0010.000
SubsampleAndTsne1.4530.0511.510
TsneVis0.2020.0050.208