Back to Long Tests report for BioC 3.12 |
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 4/10 | Hostname | OS / Arch | CHECK | |||||||
ChromSCape 1.0.0 (landing page) Pacome Prompsy
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | ERROR | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | ERROR | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | ERROR | ||||||||
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 |
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 |
############################################################################## ############################################################################## ### ### 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.
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)