R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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Platform: x86_64-apple-darwin17.0 (64-bit)

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> 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.

* 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)