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This page was generated on 2022-01-17 13:05:39 -0500 (Mon, 17 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 nebbiolo2


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: 2022-01-16 01:55:05 -0500 (Sun, 16 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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Sconify_1.14.0.tar.gz
StartedAt: 2022-01-16 09:41:30 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 09:42:58 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 87.7 seconds
RetCode: 0
Status:   OK  
CheckDir: Sconify.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Sconify_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/Sconify.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (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 11.916  0.124   12.04
* 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:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Sconify
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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-pc-linux-gnu (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!
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 = 0.971400)!
Learning embedding...
Iteration 50: error is 55.319718 (50 iterations in 0.01 seconds)
Iteration 100: error is 51.641010 (50 iterations in 0.01 seconds)
Iteration 150: error is 49.955580 (50 iterations in 0.01 seconds)
Iteration 200: error is 52.183307 (50 iterations in 0.01 seconds)
Iteration 250: error is 54.903274 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.665367 (50 iterations in 0.01 seconds)
Iteration 350: error is 1.143634 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.604331 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.268229 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.211268 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.177549 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.172401 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.168510 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.158843 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.155463 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.153753 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.152349 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.154211 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.154428 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.155204 (50 iterations in 0.01 seconds)
Fitting performed in 0.16 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 0.11 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 63.528463 (50 iterations in 0.27 seconds)
Iteration 100: error is 60.638993 (50 iterations in 0.16 seconds)
Iteration 150: error is 60.285388 (50 iterations in 0.16 seconds)
Iteration 200: error is 60.163033 (50 iterations in 0.16 seconds)
Iteration 250: error is 60.104226 (50 iterations in 0.17 seconds)
Iteration 300: error is 1.327005 (50 iterations in 0.14 seconds)
Iteration 350: error is 1.225030 (50 iterations in 0.13 seconds)
Iteration 400: error is 1.200055 (50 iterations in 0.14 seconds)
Iteration 450: error is 1.183362 (50 iterations in 0.14 seconds)
Iteration 500: error is 1.174166 (50 iterations in 0.14 seconds)
Iteration 550: error is 1.167504 (50 iterations in 0.14 seconds)
Iteration 600: error is 1.163127 (50 iterations in 0.14 seconds)
Iteration 650: error is 1.158514 (50 iterations in 0.13 seconds)
Iteration 700: error is 1.155577 (50 iterations in 0.13 seconds)
Iteration 750: error is 1.151616 (50 iterations in 0.13 seconds)
Iteration 800: error is 1.148190 (50 iterations in 0.14 seconds)
Iteration 850: error is 1.146082 (50 iterations in 0.13 seconds)
Iteration 900: error is 1.144706 (50 iterations in 0.13 seconds)
Iteration 950: error is 1.142425 (50 iterations in 0.13 seconds)
Iteration 1000: error is 1.140865 (50 iterations in 0.13 seconds)
Fitting performed in 2.94 seconds.
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 16.947   0.347  17.294 

Example timings

Sconify.Rcheck/Sconify-Ex.timings

nameusersystemelapsed
FcsToTibble0.1420.0010.142
Fnn0.2430.2510.495
GetKnnDe0.0680.0040.071
GetMarkerNames0.0220.0000.022
ImputeTesting2.6860.0242.711
MakeHist0.2340.0000.234
MakeKnnList0.2090.0000.210
MeaningOfLife000
ParseMarkers0.2410.0120.267
PostProcessing0.0940.0040.098
ProcessMultipleFiles0.1040.0000.105
QuantNormalizeElements0.1250.0000.125
SconeValues11.916 0.12412.040
SplitFile0.0640.0080.072
StringToNumbers000
SubsampleAndTsne1.6030.0281.630
TsneVis0.1350.0120.147