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This page was generated on 2024-05-04 11:41:05 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1907/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Sconify 1.24.0  (landing page)
Tyler J Burns
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/Sconify
git_branch: RELEASE_3_19
git_last_commit: 6552cc4
git_last_commit_date: 2024-04-30 11:04:59 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for Sconify on kunpeng2


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: 1.24.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings Sconify_1.24.0.tar.gz
StartedAt: 2024-05-04 11:46:55 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 11:49:14 -0000 (Sat, 04 May 2024)
EllapsedTime: 139.2 seconds
RetCode: 0
Status:   OK  
CheckDir: Sconify.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings Sconify_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Sconify.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Sconify/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sconify’ version ‘1.24.0’
* 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   18.037  0.199  18.273
ImputeTesting  5.058  0.056   5.125
* 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-beta-2024-04-15_r86425/bin/R CMD INSTALL Sconify
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 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 = 0.966000)!
Learning embedding...
Iteration 50: error is 48.663462 (50 iterations in 0.02 seconds)
Iteration 100: error is 51.089175 (50 iterations in 0.02 seconds)
Iteration 150: error is 50.343253 (50 iterations in 0.02 seconds)
Iteration 200: error is 50.396771 (50 iterations in 0.02 seconds)
Iteration 250: error is 50.576304 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.175761 (50 iterations in 0.01 seconds)
Iteration 350: error is 0.614834 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.210623 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.162508 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.162710 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.160978 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.162011 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.162439 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.160896 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.161440 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.161488 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.161094 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.161050 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.161075 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.161351 (50 iterations in 0.01 seconds)
Fitting performed in 0.24 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 64.052898 (50 iterations in 0.47 seconds)
Iteration 100: error is 60.649681 (50 iterations in 0.36 seconds)
Iteration 150: error is 60.324652 (50 iterations in 0.37 seconds)
Iteration 200: error is 60.206073 (50 iterations in 0.37 seconds)
Iteration 250: error is 60.136996 (50 iterations in 0.38 seconds)
Iteration 300: error is 1.346069 (50 iterations in 0.33 seconds)
Iteration 350: error is 1.236590 (50 iterations in 0.30 seconds)
Iteration 400: error is 1.209675 (50 iterations in 0.30 seconds)
Iteration 450: error is 1.191626 (50 iterations in 0.30 seconds)
Iteration 500: error is 1.182975 (50 iterations in 0.31 seconds)
Iteration 550: error is 1.176363 (50 iterations in 0.30 seconds)
Iteration 600: error is 1.171474 (50 iterations in 0.29 seconds)
Iteration 650: error is 1.167769 (50 iterations in 0.28 seconds)
Iteration 700: error is 1.164198 (50 iterations in 0.26 seconds)
Iteration 750: error is 1.161317 (50 iterations in 0.27 seconds)
Iteration 800: error is 1.159109 (50 iterations in 0.29 seconds)
Iteration 850: error is 1.156401 (50 iterations in 0.30 seconds)
Iteration 900: error is 1.153984 (50 iterations in 0.29 seconds)
Iteration 950: error is 1.151347 (50 iterations in 0.31 seconds)
Iteration 1000: error is 1.149752 (50 iterations in 0.30 seconds)
Fitting performed in 6.39 seconds.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 31.794   0.353  32.193 

Example timings

Sconify.Rcheck/Sconify-Ex.timings

nameusersystemelapsed
FcsToTibble0.1900.0000.191
Fnn0.3040.1360.439
GetKnnDe0.1050.0000.105
GetMarkerNames0.0340.0000.035
ImputeTesting5.0580.0565.125
MakeHist0.4390.0280.468
MakeKnnList0.5060.0040.510
MeaningOfLife0.0000.0000.001
ParseMarkers0.3200.0120.331
PostProcessing0.1510.0080.160
ProcessMultipleFiles0.1500.0000.151
QuantNormalizeElements0.3020.0000.303
SconeValues18.037 0.19918.273
SplitFile0.1040.0080.112
StringToNumbers000
SubsampleAndTsne3.1580.0003.164
TsneVis0.2460.0040.251