Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:08:46 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

CHECK results for Sconify on machv2


To the developers/maintainers of the Sconify package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1734/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Sconify 1.14.0  (landing page)
Tyler J Burns
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/Sconify
git_branch: RELEASE_3_14
git_last_commit: 63a1bff
git_last_commit_date: 2021-10-26 12:42:59 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Sconify
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2022-01-18 17:51:56 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 17:54:51 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 175.3 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/Sconify.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Sconify/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sconify’ version ‘1.14.0’
* 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 R 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   22.979  0.262  23.255
ImputeTesting  5.644  0.027   6.018
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 = 0.969600)!
Learning embedding...
Iteration 50: error is 50.965086 (50 iterations in 0.02 seconds)
Iteration 100: error is 49.388581 (50 iterations in 0.02 seconds)
Iteration 150: error is 51.278556 (50 iterations in 0.02 seconds)
Iteration 200: error is 52.245022 (50 iterations in 0.02 seconds)
Iteration 250: error is 48.763983 (50 iterations in 0.02 seconds)
Iteration 300: error is 1.419485 (50 iterations in 0.02 seconds)
Iteration 350: error is 0.710020 (50 iterations in 0.02 seconds)
Iteration 400: error is 0.173850 (50 iterations in 0.02 seconds)
Iteration 450: error is 0.153788 (50 iterations in 0.02 seconds)
Iteration 500: error is 0.152404 (50 iterations in 0.02 seconds)
Iteration 550: error is 0.153084 (50 iterations in 0.02 seconds)
Iteration 600: error is 0.151382 (50 iterations in 0.02 seconds)
Iteration 650: error is 0.151816 (50 iterations in 0.02 seconds)
Iteration 700: error is 0.151621 (50 iterations in 0.02 seconds)
Iteration 750: error is 0.151487 (50 iterations in 0.02 seconds)
Iteration 800: error is 0.150716 (50 iterations in 0.02 seconds)
Iteration 850: error is 0.151978 (50 iterations in 0.02 seconds)
Iteration 900: error is 0.149945 (50 iterations in 0.02 seconds)
Iteration 950: error is 0.151308 (50 iterations in 0.02 seconds)
Iteration 1000: error is 0.151368 (50 iterations in 0.02 seconds)
Fitting performed in 0.34 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 0.20 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 63.641757 (50 iterations in 0.39 seconds)
Iteration 100: error is 60.643879 (50 iterations in 0.24 seconds)
Iteration 150: error is 60.330637 (50 iterations in 0.22 seconds)
Iteration 200: error is 60.203095 (50 iterations in 0.23 seconds)
Iteration 250: error is 60.135936 (50 iterations in 0.24 seconds)
Iteration 300: error is 1.331182 (50 iterations in 0.23 seconds)
Iteration 350: error is 1.222126 (50 iterations in 0.22 seconds)
Iteration 400: error is 1.196630 (50 iterations in 0.22 seconds)
Iteration 450: error is 1.186443 (50 iterations in 0.21 seconds)
Iteration 500: error is 1.179163 (50 iterations in 0.21 seconds)
Iteration 550: error is 1.173589 (50 iterations in 0.21 seconds)
Iteration 600: error is 1.167913 (50 iterations in 0.22 seconds)
Iteration 650: error is 1.163755 (50 iterations in 0.25 seconds)
Iteration 700: error is 1.162467 (50 iterations in 0.24 seconds)
Iteration 750: error is 1.157432 (50 iterations in 0.24 seconds)
Iteration 800: error is 1.155082 (50 iterations in 0.23 seconds)
Iteration 850: error is 1.153947 (50 iterations in 0.24 seconds)
Iteration 900: error is 1.152103 (50 iterations in 0.23 seconds)
Iteration 950: error is 1.150491 (50 iterations in 0.22 seconds)
Iteration 1000: error is 1.149096 (50 iterations in 0.22 seconds)
Fitting performed in 4.71 seconds.
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 35.936   0.693  36.641 

Example timings

Sconify.Rcheck/Sconify-Ex.timings

nameusersystemelapsed
FcsToTibble0.2990.0080.307
Fnn0.6981.8752.777
GetKnnDe0.1040.0120.115
GetMarkerNames0.0410.0020.043
ImputeTesting5.6440.0276.018
MakeHist0.4530.0100.464
MakeKnnList0.3280.0100.337
MeaningOfLife0.0000.0000.001
ParseMarkers0.3590.0190.380
PostProcessing0.1080.0030.111
ProcessMultipleFiles0.1700.0040.176
QuantNormalizeElements0.2440.0060.251
SconeValues22.979 0.26223.255
SplitFile0.1200.0020.122
StringToNumbers0.0000.0000.001
SubsampleAndTsne2.7440.0052.751
TsneVis0.2530.0040.257