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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --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 09:31:26 -0400 (Sat, 08 May 2021) |
EndedAt: 2021-05-08 10:23:11 -0400 (Sat, 08 May 2021) |
EllapsedTime: 3105.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ChromSCape.Rcheck |
Warnings: NA |
ChromSCape.Rcheck/tests/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-apple-darwin17.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(ChromSCape) > > test_check("ChromSCape") Read the 300 x 50 data matrix successfully! Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000 Computing input similarities... Symmetrizing... Done in 0.02 seconds! Learning embedding... Iteration 50: error is 61.387038 (50 iterations in 0.05 seconds) Iteration 100: error is 60.213185 (50 iterations in 0.06 seconds) Iteration 150: error is 61.274730 (50 iterations in 0.05 seconds) Iteration 200: error is 59.714483 (50 iterations in 0.06 seconds) Iteration 250: error is 59.804889 (50 iterations in 0.06 seconds) Iteration 300: error is 0.794957 (50 iterations in 0.05 seconds) Iteration 350: error is 0.731237 (50 iterations in 0.06 seconds) Iteration 400: error is 0.713576 (50 iterations in 0.06 seconds) Iteration 450: error is 0.700977 (50 iterations in 0.05 seconds) Iteration 500: error is 0.689412 (50 iterations in 0.05 seconds) Iteration 550: error is 0.683384 (50 iterations in 0.05 seconds) Iteration 600: error is 0.672235 (50 iterations in 0.06 seconds) Iteration 650: error is 0.670558 (50 iterations in 0.06 seconds) Iteration 700: error is 0.666880 (50 iterations in 0.06 seconds) Iteration 750: error is 0.665984 (50 iterations in 0.06 seconds) Iteration 800: error is 0.665225 (50 iterations in 0.06 seconds) Iteration 850: error is 0.664715 (50 iterations in 0.06 seconds) Iteration 900: error is 0.664409 (50 iterations in 0.06 seconds) Iteration 950: error is 0.664299 (50 iterations in 0.06 seconds) Iteration 1000: error is 0.664246 (50 iterations in 0.06 seconds) Fitting performed in 1.11 seconds. Read the 300 x 50 data matrix successfully! Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000 Computing input similarities... Symmetrizing... Done in 0.03 seconds! Learning embedding... Iteration 50: error is 62.244770 (50 iterations in 0.06 seconds) Iteration 100: error is 60.930018 (50 iterations in 0.06 seconds) Iteration 150: error is 59.077449 (50 iterations in 0.06 seconds) Iteration 200: error is 62.880987 (50 iterations in 0.06 seconds) Iteration 250: error is 61.059820 (50 iterations in 0.06 seconds) Iteration 300: error is 0.766336 (50 iterations in 0.06 seconds) Iteration 350: error is 0.688107 (50 iterations in 0.06 seconds) Iteration 400: error is 0.661303 (50 iterations in 0.06 seconds) Iteration 450: error is 0.653369 (50 iterations in 0.06 seconds) Iteration 500: error is 0.648102 (50 iterations in 0.06 seconds) Iteration 550: error is 0.646022 (50 iterations in 0.06 seconds) Iteration 600: error is 0.643693 (50 iterations in 0.06 seconds) Iteration 650: error is 0.640896 (50 iterations in 0.06 seconds) Iteration 700: error is 0.637783 (50 iterations in 0.06 seconds) Iteration 750: error is 0.636772 (50 iterations in 0.06 seconds) Iteration 800: error is 0.636272 (50 iterations in 0.06 seconds) Iteration 850: error is 0.634549 (50 iterations in 0.06 seconds) Iteration 900: error is 0.634087 (50 iterations in 0.06 seconds) Iteration 950: error is 0.633911 (50 iterations in 0.06 seconds) Iteration 1000: error is 0.633772 (50 iterations in 0.06 seconds) Fitting performed in 1.15 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. [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! Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000 Computing input similarities... Symmetrizing... Done in 0.03 seconds! Learning embedding... Iteration 50: error is 60.002960 (50 iterations in 0.06 seconds) Iteration 100: error is 62.272369 (50 iterations in 0.06 seconds) Iteration 150: error is 61.736430 (50 iterations in 0.06 seconds) Iteration 200: error is 59.807325 (50 iterations in 0.06 seconds) Iteration 250: error is 60.689361 (50 iterations in 0.06 seconds) Iteration 300: error is 0.769445 (50 iterations in 0.06 seconds) Iteration 350: error is 0.682849 (50 iterations in 0.06 seconds) Iteration 400: error is 0.663524 (50 iterations in 0.06 seconds) Iteration 450: error is 0.650254 (50 iterations in 0.06 seconds) Iteration 500: error is 0.640166 (50 iterations in 0.06 seconds) Iteration 550: error is 0.635179 (50 iterations in 0.06 seconds) Iteration 600: error is 0.631540 (50 iterations in 0.06 seconds) Iteration 650: error is 0.628213 (50 iterations in 0.06 seconds) Iteration 700: error is 0.626821 (50 iterations in 0.06 seconds) Iteration 750: error is 0.626699 (50 iterations in 0.06 seconds) Iteration 800: error is 0.626525 (50 iterations in 0.06 seconds) Iteration 850: error is 0.626505 (50 iterations in 0.06 seconds) Iteration 900: error is 0.626493 (50 iterations in 0.06 seconds) Iteration 950: error is 0.626479 (50 iterations in 0.06 seconds) Iteration 1000: error is 0.626416 (50 iterations in 0.06 seconds) Fitting performed in 1.15 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! Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000 Computing input similarities... Symmetrizing... Done in 0.02 seconds! Learning embedding... Iteration 50: error is 62.251201 (50 iterations in 0.05 seconds) Iteration 100: error is 63.316683 (50 iterations in 0.05 seconds) Iteration 150: error is 63.272710 (50 iterations in 0.05 seconds) Iteration 200: error is 64.941412 (50 iterations in 0.05 seconds) Iteration 250: error is 63.678978 (50 iterations in 0.05 seconds) Iteration 300: error is 1.318203 (50 iterations in 0.05 seconds) Iteration 350: error is 0.962986 (50 iterations in 0.05 seconds) Iteration 400: error is 0.850926 (50 iterations in 0.05 seconds) Iteration 450: error is 0.769669 (50 iterations in 0.05 seconds) Iteration 500: error is 0.764725 (50 iterations in 0.05 seconds) Iteration 550: error is 0.762310 (50 iterations in 0.05 seconds) Iteration 600: error is 0.761070 (50 iterations in 0.05 seconds) Iteration 650: error is 0.758293 (50 iterations in 0.05 seconds) Iteration 700: error is 0.754977 (50 iterations in 0.05 seconds) Iteration 750: error is 0.752902 (50 iterations in 0.05 seconds) Iteration 800: error is 0.752572 (50 iterations in 0.05 seconds) Iteration 850: error is 0.751399 (50 iterations in 0.05 seconds) Iteration 900: error is 0.750943 (50 iterations in 0.05 seconds) Iteration 950: error is 0.749628 (50 iterations in 0.05 seconds) Iteration 1000: error is 0.749601 (50 iterations in 0.05 seconds) Fitting performed in 0.96 seconds. Read the 300 x 50 data matrix successfully! Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000 Computing input similarities... Symmetrizing... Done in 0.02 seconds! Learning embedding... Iteration 50: error is 63.708712 (50 iterations in 0.05 seconds) Iteration 100: error is 62.958279 (50 iterations in 0.05 seconds) Iteration 150: error is 67.162279 (50 iterations in 0.05 seconds) Iteration 200: error is 66.143913 (50 iterations in 0.05 seconds) Iteration 250: error is 63.502742 (50 iterations in 0.05 seconds) Iteration 300: error is 1.397072 (50 iterations in 0.05 seconds) Iteration 350: error is 1.263138 (50 iterations in 0.05 seconds) Iteration 400: error is 1.199851 (50 iterations in 0.05 seconds) Iteration 450: error is 1.147400 (50 iterations in 0.05 seconds) Iteration 500: error is 0.874397 (50 iterations in 0.05 seconds) Iteration 550: error is 0.847991 (50 iterations in 0.05 seconds) Iteration 600: error is 0.832676 (50 iterations in 0.05 seconds) Iteration 650: error is 0.821099 (50 iterations in 0.05 seconds) Iteration 700: error is 0.809725 (50 iterations in 0.05 seconds) Iteration 750: error is 0.794456 (50 iterations in 0.05 seconds) Iteration 800: error is 0.788231 (50 iterations in 0.05 seconds) Iteration 850: error is 0.786411 (50 iterations in 0.05 seconds) Iteration 900: error is 0.786030 (50 iterations in 0.05 seconds) Iteration 950: error is 0.785805 (50 iterations in 0.05 seconds) Iteration 1000: error is 0.784449 (50 iterations in 0.05 seconds) Fitting performed in 1.08 seconds. ══ Failed tests ════════════════════════════════════════════════════════════════ ── 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 6 | WARN 1800 | SKIP 0 | PASS 131 ] Error: Test failures Execution halted
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --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 ‘/Users/biocbuild/bbs-3.12-bioc-longtests/meat/ChromSCape.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * 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 for sufficient/correct file permissions ... 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 * 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 ‘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 6 | WARN 1800 | SKIP 0 | PASS 131 ] Error: Test failures Execution halted * DONE Status: 1 ERROR, 1 NOTE See ‘/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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ChromSCape)