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This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1875/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Sconify 1.27.0  (landing page)
Tyler J Burns
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/Sconify
git_branch: devel
git_last_commit: e6f83c2
git_last_commit_date: 2024-10-29 10:26:42 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


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: 1.27.0
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_1.27.0.tar.gz
StartedAt: 2024-12-23 23:01:56 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 23:03:59 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 123.1 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_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Sconify.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Sconify/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sconify’ version ‘1.27.0’
* 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 12.828   0.18  13.061
* 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/4.5-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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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 = 0.965200)!
Learning embedding...
Iteration 50: error is 49.647446 (50 iterations in 0.01 seconds)
Iteration 100: error is 49.234719 (50 iterations in 0.01 seconds)
Iteration 150: error is 54.421226 (50 iterations in 0.01 seconds)
Iteration 200: error is 51.628886 (50 iterations in 0.01 seconds)
Iteration 250: error is 51.295089 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.365824 (50 iterations in 0.01 seconds)
Iteration 350: error is 0.852475 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.245659 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.193541 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.189553 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.188320 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.188390 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.181393 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.184057 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.183400 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.183209 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.183087 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.184347 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.183906 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.183177 (50 iterations in 0.01 seconds)
Fitting performed in 0.17 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 65.589775 (50 iterations in 0.23 seconds)
Iteration 100: error is 60.670846 (50 iterations in 0.15 seconds)
Iteration 150: error is 60.284058 (50 iterations in 0.13 seconds)
Iteration 200: error is 60.143124 (50 iterations in 0.14 seconds)
Iteration 250: error is 60.093439 (50 iterations in 0.14 seconds)
Iteration 300: error is 1.334293 (50 iterations in 0.11 seconds)
Iteration 350: error is 1.228432 (50 iterations in 0.10 seconds)
Iteration 400: error is 1.198397 (50 iterations in 0.12 seconds)
Iteration 450: error is 1.186260 (50 iterations in 0.12 seconds)
Iteration 500: error is 1.177182 (50 iterations in 0.10 seconds)
Iteration 550: error is 1.171685 (50 iterations in 0.11 seconds)
Iteration 600: error is 1.168242 (50 iterations in 0.11 seconds)
Iteration 650: error is 1.166152 (50 iterations in 0.11 seconds)
Iteration 700: error is 1.164314 (50 iterations in 0.11 seconds)
Iteration 750: error is 1.162384 (50 iterations in 0.11 seconds)
Iteration 800: error is 1.160709 (50 iterations in 0.11 seconds)
Iteration 850: error is 1.157943 (50 iterations in 0.12 seconds)
Iteration 900: error is 1.155160 (50 iterations in 0.12 seconds)
Iteration 950: error is 1.152678 (50 iterations in 0.12 seconds)
Iteration 1000: error is 1.150554 (50 iterations in 0.11 seconds)
Fitting performed in 2.48 seconds.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 20.075   0.700  20.924 

Example timings

Sconify.Rcheck/Sconify-Ex.timings

nameusersystemelapsed
FcsToTibble0.1390.0060.146
Fnn0.3060.8971.213
GetKnnDe0.0600.0050.066
GetMarkerNames0.0320.0030.034
ImputeTesting3.4200.0263.463
MakeHist0.3340.0100.345
MakeKnnList0.3660.0090.376
MeaningOfLife000
ParseMarkers0.2710.0310.413
PostProcessing0.1240.0040.128
ProcessMultipleFiles0.1050.0050.110
QuantNormalizeElements0.2300.0040.233
SconeValues12.828 0.18013.061
SplitFile0.0890.0030.092
StringToNumbers0.0000.0010.000
SubsampleAndTsne1.4370.0551.502
TsneVis0.1860.0080.194