Back to Long Tests report for BioC 3.12

CHECK report for ChromSCape on tokay1

This page was generated on 2021-05-08 14:20:33 -0400 (Sat, 08 May 2021).

To the developers/maintainers of the ChromSCape package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 4/10HostnameOS / ArchCHECK
ChromSCape 1.0.0  (landing page)
Pacome Prompsy
Snapshot Date: 2021-05-08 09:00:02 -0400 (Sat, 08 May 2021)
URL: https://git.bioconductor.org/packages/ChromSCape
Branch: RELEASE_3_12
Last Commit: c84df0d
Last Changed Date: 2020-10-27 12:02:02 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  ERROR  
tokay1Windows Server 2012 R2 Standard / x64  ERROR  
merida1macOS 10.14.6 Mojave / x86_64  ERROR  

Summary

Package: ChromSCape
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no ChromSCape_1.0.0.tar.gz
StartedAt: 2021-05-08 09:33:25 -0400 (Sat, 08 May 2021)
EndedAt: 2021-05-08 11:02:50 -0400 (Sat, 08 May 2021)
EllapsedTime: 5365.3 seconds
RetCode: 1
Status:   ERROR   
CheckDir: ChromSCape.Rcheck
Warnings: NA

Tests output

ChromSCape.Rcheck/tests_i386/testthat.Rout.fail


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(ChromSCape)
> 
> test_check("ChromSCape")
Read the 300 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000
Computing input similarities...
Symmetrizing...
Done in 0.14 seconds!
Learning embedding...
Iteration 50: error is 62.409205 (50 iterations in 0.08 seconds)
Iteration 100: error is 62.345294 (50 iterations in 0.08 seconds)
Iteration 150: error is 61.615651 (50 iterations in 0.08 seconds)
Iteration 200: error is 63.951338 (50 iterations in 0.08 seconds)
Iteration 250: error is 63.390381 (50 iterations in 0.08 seconds)
Iteration 300: error is 1.073014 (50 iterations in 0.08 seconds)
Iteration 350: error is 0.751635 (50 iterations in 0.08 seconds)
Iteration 400: error is 0.722227 (50 iterations in 0.08 seconds)
Iteration 450: error is 0.712948 (50 iterations in 0.08 seconds)
Iteration 500: error is 0.708160 (50 iterations in 0.08 seconds)
Iteration 550: error is 0.707512 (50 iterations in 0.08 seconds)
Iteration 600: error is 0.706860 (50 iterations in 0.08 seconds)
Iteration 650: error is 0.706508 (50 iterations in 0.08 seconds)
Iteration 700: error is 0.706426 (50 iterations in 0.08 seconds)
Iteration 750: error is 0.706358 (50 iterations in 0.08 seconds)
Iteration 800: error is 0.706324 (50 iterations in 0.08 seconds)
Iteration 850: error is 0.706051 (50 iterations in 0.08 seconds)
Iteration 900: error is 0.706002 (50 iterations in 0.08 seconds)
Iteration 950: error is 0.705989 (50 iterations in 0.08 seconds)
Iteration 1000: error is 0.705984 (50 iterations in 0.08 seconds)
Fitting performed in 1.56 seconds.
Read the 300 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000
Computing input similarities...
Symmetrizing...
Done in 0.12 seconds!
Learning embedding...
Iteration 50: error is 59.767075 (50 iterations in 0.08 seconds)
Iteration 100: error is 60.473030 (50 iterations in 0.08 seconds)
Iteration 150: error is 63.451806 (50 iterations in 0.09 seconds)
Iteration 200: error is 63.821595 (50 iterations in 0.08 seconds)
Iteration 250: error is 63.583202 (50 iterations in 0.08 seconds)
Iteration 300: error is 0.994891 (50 iterations in 0.08 seconds)
Iteration 350: error is 0.733793 (50 iterations in 0.09 seconds)
Iteration 400: error is 0.715841 (50 iterations in 0.08 seconds)
Iteration 450: error is 0.704571 (50 iterations in 0.08 seconds)
Iteration 500: error is 0.692120 (50 iterations in 0.09 seconds)
Iteration 550: error is 0.681591 (50 iterations in 0.08 seconds)
Iteration 600: error is 0.679901 (50 iterations in 0.08 seconds)
Iteration 650: error is 0.679237 (50 iterations in 0.09 seconds)
Iteration 700: error is 0.679171 (50 iterations in 0.08 seconds)
Iteration 750: error is 0.679134 (50 iterations in 0.08 seconds)
Iteration 800: error is 0.679108 (50 iterations in 0.09 seconds)
Iteration 850: error is 0.678947 (50 iterations in 0.08 seconds)
Iteration 900: error is 0.678915 (50 iterations in 0.08 seconds)
Iteration 950: error is 0.678900 (50 iterations in 0.08 seconds)
Iteration 1000: error is 0.678878 (50 iterations in 0.09 seconds)
Fitting performed in 1.66 seconds.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
Read the 300 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000
Computing input similarities...
Symmetrizing...
Done in 0.12 seconds!
Learning embedding...
Iteration 50: error is 60.464158 (50 iterations in 0.09 seconds)
Iteration 100: error is 61.021894 (50 iterations in 0.09 seconds)
Iteration 150: error is 62.605160 (50 iterations in 0.09 seconds)
Iteration 200: error is 59.527058 (50 iterations in 0.09 seconds)
Iteration 250: error is 63.167891 (50 iterations in 0.09 seconds)
Iteration 300: error is 1.143978 (50 iterations in 0.09 seconds)
Iteration 350: error is 0.920406 (50 iterations in 0.09 seconds)
Iteration 400: error is 0.703426 (50 iterations in 0.09 seconds)
Iteration 450: error is 0.680638 (50 iterations in 0.09 seconds)
Iteration 500: error is 0.660157 (50 iterations in 0.09 seconds)
Iteration 550: error is 0.651307 (50 iterations in 0.09 seconds)
Iteration 600: error is 0.647862 (50 iterations in 0.09 seconds)
Iteration 650: error is 0.646997 (50 iterations in 0.08 seconds)
Iteration 700: error is 0.646642 (50 iterations in 0.09 seconds)
Iteration 750: error is 0.646615 (50 iterations in 0.09 seconds)
Iteration 800: error is 0.646377 (50 iterations in 0.09 seconds)
Iteration 850: error is 0.646372 (50 iterations in 0.09 seconds)
Iteration 900: error is 0.646371 (50 iterations in 0.09 seconds)
Iteration 950: error is 0.646371 (50 iterations in 0.09 seconds)
Iteration 1000: error is 0.646371 (50 iterations in 0.08 seconds)
Fitting performed in 1.84 seconds.
[1] "Comparing C2 versus C1"
[1] "Comparing C3 versus C1"
[1] "Comparing C4 versus C1"
[1] "Comparing C3 versus C2"
[1] "Comparing C4 versus C2"
[1] "Comparing C4 versus C3"
[1] "Comparing notC1 versus C1"
[1] "Comparing notC2 versus C2"
[1] "Comparing notC3 versus C3"
[1] "Comparing notC4 versus C4"
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Running Batch Correction ..."
Read the 285 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000
Computing input similarities...
Symmetrizing...
Done in 0.11 seconds!
Learning embedding...
Iteration 50: error is 62.250764 (50 iterations in 0.09 seconds)
Iteration 100: error is 61.437720 (50 iterations in 0.09 seconds)
Iteration 150: error is 59.512223 (50 iterations in 0.09 seconds)
Iteration 200: error is 62.208378 (50 iterations in 0.09 seconds)
Iteration 250: error is 64.578855 (50 iterations in 0.09 seconds)
Iteration 300: error is 1.304942 (50 iterations in 0.09 seconds)
Iteration 350: error is 0.847566 (50 iterations in 0.08 seconds)
Iteration 400: error is 0.810426 (50 iterations in 0.08 seconds)
Iteration 450: error is 0.794791 (50 iterations in 0.09 seconds)
Iteration 500: error is 0.780322 (50 iterations in 0.09 seconds)
Iteration 550: error is 0.767948 (50 iterations in 0.09 seconds)
Iteration 600: error is 0.761637 (50 iterations in 0.09 seconds)
Iteration 650: error is 0.760618 (50 iterations in 0.09 seconds)
Iteration 700: error is 0.759591 (50 iterations in 0.09 seconds)
Iteration 750: error is 0.758671 (50 iterations in 0.09 seconds)
Iteration 800: error is 0.757025 (50 iterations in 0.09 seconds)
Iteration 850: error is 0.756037 (50 iterations in 0.09 seconds)
Iteration 900: error is 0.755671 (50 iterations in 0.09 seconds)
Iteration 950: error is 0.754037 (50 iterations in 0.09 seconds)
Iteration 1000: error is 0.753390 (50 iterations in 0.09 seconds)
Fitting performed in 1.84 seconds.
Read the 300 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000
Computing input similarities...
Symmetrizing...
Done in 0.12 seconds!
Learning embedding...
Iteration 50: error is 63.708607 (50 iterations in 0.09 seconds)
Iteration 100: error is 63.799896 (50 iterations in 0.09 seconds)
Iteration 150: error is 64.379459 (50 iterations in 0.11 seconds)
Iteration 200: error is 63.393703 (50 iterations in 0.09 seconds)
Iteration 250: error is 62.738061 (50 iterations in 0.09 seconds)
Iteration 300: error is 1.161648 (50 iterations in 0.09 seconds)
Iteration 350: error is 0.854257 (50 iterations in 0.09 seconds)
Iteration 400: error is 0.825087 (50 iterations in 0.11 seconds)
Iteration 450: error is 0.816358 (50 iterations in 0.09 seconds)
Iteration 500: error is 0.808408 (50 iterations in 0.09 seconds)
Iteration 550: error is 0.800645 (50 iterations in 0.09 seconds)
Iteration 600: error is 0.794758 (50 iterations in 0.09 seconds)
Iteration 650: error is 0.787013 (50 iterations in 0.11 seconds)
Iteration 700: error is 0.784119 (50 iterations in 0.09 seconds)
Iteration 750: error is 0.782492 (50 iterations in 0.09 seconds)
Iteration 800: error is 0.782231 (50 iterations in 0.09 seconds)
Iteration 850: error is 0.782095 (50 iterations in 0.09 seconds)
Iteration 900: error is 0.781850 (50 iterations in 0.11 seconds)
Iteration 950: error is 0.781756 (50 iterations in 0.09 seconds)
Iteration 1000: error is 0.781670 (50 iterations in 0.11 seconds)
Fitting performed in 1.95 seconds.
== Failed tests ================================================================
-- Failure (test_diff_analysis_gene_set_enrichment.R:105:3): GSEA - Right inputs.  n = 2 --
length(scExp_cf@metadata$enr$Underexpressed) not equal to length(unique(SingleCellExperiment::colData(scExp_cf)$cell_cluster)).
1/1 mismatches
[1] 1 - 2 == -1
-- Failure (test_processing_filtering.R:54:5): Some cells are empty ------------
`create_scExp(mat., annot.)` produced no output
-- Failure (test_processing_filtering.R:63:5): Some features are empty ---------
`create_scExp(mat., annot.)` produced no output
-- Failure (test_processing_filtering.R:70:5): Removing chrM - non canonical ---
`create_scExp(mat., annot)` produced no output
-- Failure (test_processing_filtering.R:80:5): Removing chrM - non canonical ---
`create_scExp(mat., annot)` produced no output
-- Failure (test_processing_filtering.R:127:5): Verbose is on /off -------------
`filter_scExp(scExp, verbose = TRUE)` produced no output
-- Failure (test_processing_filtering.R:128:5): Verbose is on /off -------------
`filter_scExp(scExp, verbose = TRUE)` produced no output

[ FAIL 7 | WARN 600 | SKIP 0 | PASS 130 ]
Error: Test failures
Execution halted

ChromSCape.Rcheck/tests_x64/testthat.Rout.fail


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(ChromSCape)
> 
> test_check("ChromSCape")
Read the 300 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000
Computing input similarities...
Symmetrizing...
Done in 0.14 seconds!
Learning embedding...
Iteration 50: error is 60.831272 (50 iterations in 0.03 seconds)
Iteration 100: error is 59.067020 (50 iterations in 0.03 seconds)
Iteration 150: error is 60.360675 (50 iterations in 0.05 seconds)
Iteration 200: error is 62.538816 (50 iterations in 0.05 seconds)
Iteration 250: error is 59.226182 (50 iterations in 0.05 seconds)
Iteration 300: error is 0.899140 (50 iterations in 0.05 seconds)
Iteration 350: error is 0.695260 (50 iterations in 0.05 seconds)
Iteration 400: error is 0.681333 (50 iterations in 0.05 seconds)
Iteration 450: error is 0.676608 (50 iterations in 0.05 seconds)
Iteration 500: error is 0.674493 (50 iterations in 0.05 seconds)
Iteration 550: error is 0.673041 (50 iterations in 0.05 seconds)
Iteration 600: error is 0.672269 (50 iterations in 0.05 seconds)
Iteration 650: error is 0.671977 (50 iterations in 0.05 seconds)
Iteration 700: error is 0.671753 (50 iterations in 0.05 seconds)
Iteration 750: error is 0.671563 (50 iterations in 0.05 seconds)
Iteration 800: error is 0.668643 (50 iterations in 0.05 seconds)
Iteration 850: error is 0.668305 (50 iterations in 0.05 seconds)
Iteration 900: error is 0.668183 (50 iterations in 0.05 seconds)
Iteration 950: error is 0.668041 (50 iterations in 0.05 seconds)
Iteration 1000: error is 0.667844 (50 iterations in 0.05 seconds)
Fitting performed in 0.91 seconds.
Read the 300 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000
Computing input similarities...
Symmetrizing...
Done in 0.12 seconds!
Learning embedding...
Iteration 50: error is 60.996253 (50 iterations in 0.03 seconds)
Iteration 100: error is 58.083754 (50 iterations in 0.05 seconds)
Iteration 150: error is 59.382045 (50 iterations in 0.05 seconds)
Iteration 200: error is 61.262512 (50 iterations in 0.05 seconds)
Iteration 250: error is 59.493230 (50 iterations in 0.05 seconds)
Iteration 300: error is 0.798125 (50 iterations in 0.05 seconds)
Iteration 350: error is 0.671534 (50 iterations in 0.05 seconds)
Iteration 400: error is 0.651449 (50 iterations in 0.05 seconds)
Iteration 450: error is 0.643685 (50 iterations in 0.05 seconds)
Iteration 500: error is 0.631401 (50 iterations in 0.05 seconds)
Iteration 550: error is 0.627199 (50 iterations in 0.05 seconds)
Iteration 600: error is 0.623835 (50 iterations in 0.05 seconds)
Iteration 650: error is 0.623023 (50 iterations in 0.05 seconds)
Iteration 700: error is 0.622920 (50 iterations in 0.05 seconds)
Iteration 750: error is 0.622747 (50 iterations in 0.05 seconds)
Iteration 800: error is 0.621928 (50 iterations in 0.05 seconds)
Iteration 850: error is 0.621598 (50 iterations in 0.05 seconds)
Iteration 900: error is 0.621506 (50 iterations in 0.05 seconds)
Iteration 950: error is 0.621475 (50 iterations in 0.05 seconds)
Iteration 1000: error is 0.621462 (50 iterations in 0.03 seconds)
Fitting performed in 0.90 seconds.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
Read the 300 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000
Computing input similarities...
Symmetrizing...
Done in 0.12 seconds!
Learning embedding...
Iteration 50: error is 57.294299 (50 iterations in 0.06 seconds)
Iteration 100: error is 57.916756 (50 iterations in 0.06 seconds)
Iteration 150: error is 59.015957 (50 iterations in 0.08 seconds)
Iteration 200: error is 59.192911 (50 iterations in 0.06 seconds)
Iteration 250: error is 58.131246 (50 iterations in 0.06 seconds)
Iteration 300: error is 0.948052 (50 iterations in 0.08 seconds)
Iteration 350: error is 0.728945 (50 iterations in 0.08 seconds)
Iteration 400: error is 0.655138 (50 iterations in 0.06 seconds)
Iteration 450: error is 0.639723 (50 iterations in 0.06 seconds)
Iteration 500: error is 0.635586 (50 iterations in 0.06 seconds)
Iteration 550: error is 0.629763 (50 iterations in 0.08 seconds)
Iteration 600: error is 0.625963 (50 iterations in 0.08 seconds)
Iteration 650: error is 0.615896 (50 iterations in 0.06 seconds)
Iteration 700: error is 0.615386 (50 iterations in 0.06 seconds)
Iteration 750: error is 0.613941 (50 iterations in 0.08 seconds)
Iteration 800: error is 0.613434 (50 iterations in 0.06 seconds)
Iteration 850: error is 0.611104 (50 iterations in 0.06 seconds)
Iteration 900: error is 0.610991 (50 iterations in 0.06 seconds)
Iteration 950: error is 0.610088 (50 iterations in 0.08 seconds)
Iteration 1000: error is 0.609285 (50 iterations in 0.08 seconds)
Fitting performed in 1.37 seconds.
[1] "Comparing C2 versus C1"
[1] "Comparing C3 versus C1"
[1] "Comparing C4 versus C1"
[1] "Comparing C3 versus C2"
[1] "Comparing C4 versus C2"
[1] "Comparing C4 versus C3"
[1] "Comparing notC1 versus C1"
[1] "Comparing notC2 versus C2"
[1] "Comparing notC3 versus C3"
[1] "Comparing notC4 versus C4"
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Warning: some of the gene sets have no intersection \n            with possibleIds"
NB : enrichment tests are based on 32937 distinct ids.
[1] "Running Batch Correction ..."
Read the 285 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000
Computing input similarities...
Symmetrizing...
Done in 0.11 seconds!
Learning embedding...
Iteration 50: error is 62.250764 (50 iterations in 0.03 seconds)
Iteration 100: error is 61.437720 (50 iterations in 0.03 seconds)
Iteration 150: error is 59.512223 (50 iterations in 0.05 seconds)
Iteration 200: error is 62.208378 (50 iterations in 0.05 seconds)
Iteration 250: error is 64.578855 (50 iterations in 0.03 seconds)
Iteration 300: error is 1.304942 (50 iterations in 0.03 seconds)
Iteration 350: error is 0.847566 (50 iterations in 0.05 seconds)
Iteration 400: error is 0.810426 (50 iterations in 0.05 seconds)
Iteration 450: error is 0.794791 (50 iterations in 0.03 seconds)
Iteration 500: error is 0.780322 (50 iterations in 0.03 seconds)
Iteration 550: error is 0.767948 (50 iterations in 0.05 seconds)
Iteration 600: error is 0.761637 (50 iterations in 0.05 seconds)
Iteration 650: error is 0.760618 (50 iterations in 0.03 seconds)
Iteration 700: error is 0.759591 (50 iterations in 0.03 seconds)
Iteration 750: error is 0.758671 (50 iterations in 0.05 seconds)
Iteration 800: error is 0.757025 (50 iterations in 0.03 seconds)
Iteration 850: error is 0.756037 (50 iterations in 0.03 seconds)
Iteration 900: error is 0.755671 (50 iterations in 0.05 seconds)
Iteration 950: error is 0.754037 (50 iterations in 0.05 seconds)
Iteration 1000: error is 0.753390 (50 iterations in 0.03 seconds)
Fitting performed in 0.77 seconds.
Read the 300 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000
Computing input similarities...
Symmetrizing...
Done in 0.12 seconds!
Learning embedding...
Iteration 50: error is 63.708607 (50 iterations in 0.05 seconds)
Iteration 100: error is 63.799896 (50 iterations in 0.05 seconds)
Iteration 150: error is 64.379459 (50 iterations in 0.05 seconds)
Iteration 200: error is 63.393703 (50 iterations in 0.05 seconds)
Iteration 250: error is 62.738061 (50 iterations in 0.05 seconds)
Iteration 300: error is 1.161648 (50 iterations in 0.05 seconds)
Iteration 350: error is 0.854257 (50 iterations in 0.05 seconds)
Iteration 400: error is 0.825087 (50 iterations in 0.05 seconds)
Iteration 450: error is 0.816358 (50 iterations in 0.05 seconds)
Iteration 500: error is 0.808408 (50 iterations in 0.05 seconds)
Iteration 550: error is 0.800645 (50 iterations in 0.05 seconds)
Iteration 600: error is 0.794758 (50 iterations in 0.05 seconds)
Iteration 650: error is 0.787013 (50 iterations in 0.05 seconds)
Iteration 700: error is 0.784119 (50 iterations in 0.05 seconds)
Iteration 750: error is 0.782492 (50 iterations in 0.05 seconds)
Iteration 800: error is 0.782231 (50 iterations in 0.05 seconds)
Iteration 850: error is 0.782095 (50 iterations in 0.05 seconds)
Iteration 900: error is 0.781850 (50 iterations in 0.05 seconds)
Iteration 950: error is 0.781756 (50 iterations in 0.03 seconds)
Iteration 1000: error is 0.781670 (50 iterations in 0.03 seconds)
Fitting performed in 0.90 seconds.
== Failed tests ================================================================
-- Failure (test_diff_analysis_gene_set_enrichment.R:104:3): GSEA - Right inputs.  n = 2 --
length(scExp_cf@metadata$enr$Overexpressed) not equal to length(unique(SingleCellExperiment::colData(scExp_cf)$cell_cluster)).
1/1 mismatches
[1] 1 - 2 == -1
-- Failure (test_processing_filtering.R:54:5): Some cells are empty ------------
`create_scExp(mat., annot.)` produced no output
-- Failure (test_processing_filtering.R:63:5): Some features are empty ---------
`create_scExp(mat., annot.)` produced no output
-- Failure (test_processing_filtering.R:70:5): Removing chrM - non canonical ---
`create_scExp(mat., annot)` produced no output
-- Failure (test_processing_filtering.R:80:5): Removing chrM - non canonical ---
`create_scExp(mat., annot)` produced no output
-- Failure (test_processing_filtering.R:127:5): Verbose is on /off -------------
`filter_scExp(scExp, verbose = TRUE)` produced no output
-- Failure (test_processing_filtering.R:128:5): Verbose is on /off -------------
`filter_scExp(scExp, verbose = TRUE)` produced no output

[ FAIL 7 | WARN 600 | SKIP 0 | PASS 130 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no ChromSCape_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/ChromSCape.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'ChromSCape/DESCRIPTION' ... OK
* this is package 'ChromSCape' version '1.0.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ChromSCape' can be installed ... OK
* checking installed package size ... OK
* checking package 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... SKIPPED
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
  `create_scExp(mat., annot.)` produced no output
  -- Failure (test_processing_filtering.R:63:5): Some features are empty ---------
  `create_scExp(mat., annot.)` produced no output
  -- Failure (test_processing_filtering.R:70:5): Removing chrM - non canonical ---
  `create_scExp(mat., annot)` produced no output
  -- Failure (test_processing_filtering.R:80:5): Removing chrM - non canonical ---
  `create_scExp(mat., annot)` produced no output
  -- Failure (test_processing_filtering.R:127:5): Verbose is on /off -------------
  `filter_scExp(scExp, verbose = TRUE)` produced no output
  -- Failure (test_processing_filtering.R:128:5): Verbose is on /off -------------
  `filter_scExp(scExp, verbose = TRUE)` produced no output
  
  [ FAIL 7 | WARN 600 | SKIP 0 | PASS 130 ]
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
  `create_scExp(mat., annot.)` produced no output
  -- Failure (test_processing_filtering.R:63:5): Some features are empty ---------
  `create_scExp(mat., annot.)` produced no output
  -- Failure (test_processing_filtering.R:70:5): Removing chrM - non canonical ---
  `create_scExp(mat., annot)` produced no output
  -- Failure (test_processing_filtering.R:80:5): Removing chrM - non canonical ---
  `create_scExp(mat., annot)` produced no output
  -- Failure (test_processing_filtering.R:127:5): Verbose is on /off -------------
  `filter_scExp(scExp, verbose = TRUE)` produced no output
  -- Failure (test_processing_filtering.R:128:5): Verbose is on /off -------------
  `filter_scExp(scExp, verbose = TRUE)` produced no output
  
  [ FAIL 7 | WARN 600 | SKIP 0 | PASS 130 ]
  Error: Test failures
  Execution halted
* DONE

Status: 2 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/ChromSCape.Rcheck/00check.log'
for details.


Installation output

ChromSCape.Rcheck/00install.out

* installing *source* package 'ChromSCape' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (ChromSCape)