##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EWCE.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings EWCE_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/EWCE.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'EWCE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EWCE' version '1.8.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'EWCE' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'EWCE-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filter_ctd_genes
> ### Title: Filter genes in a CellTypeDataset
> ### Aliases: filter_ctd_genes
> 
> ### ** Examples
> 
>  
> ctd <- ewceData::ctd()
see ?ewceData and browseVignettes('ewceData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
Warning in readChar(con, 5L, useBytes = TRUE) :
  truncating string with embedded nuls
Warning: file '16ac463f564a_5419' has magic number 'X'
  Use of save versions prior to 2 is deprecated
Error: failed to load resource
  name: EH5376
  title: ctd
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
    5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
    6.       │ └─base::eval(call, callEnv)
    7.       │   └─base::eval(call, callEnv)
    8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
    9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
   10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
   11.             └─base::tryCatch(...)
   12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   14.                   └─value[[3L]](cond)
  
  [ FAIL 8 | WARN 49 | SKIP 0 | PASS 57 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/EWCE.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL EWCE
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'EWCE' ...
** using staged installation
** R
** 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 (EWCE)

R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 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(EWCE)
Loading required package: RNOmni
> 
> test_check("EWCE")
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Loading required namespace: ggdendro
+ Saving results ==>  F:\biocbuild\bbs-3.17-bioc\tmpdir\Rtmpox5akN/ctd_testthat.rda
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==>  F:\biocbuild\bbs-3.17-bioc\tmpdir\Rtmpox5akN/ctd_testthat.rda
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
Converting to sparse matrix.
1 core(s) assigned as workers (31 reserved).
Processing block [[1/5, 1/1]] ... OK
Processing block [[2/5, 1/1]] ... OK
Processing block [[3/5, 1/1]] ... OK
Processing block [[4/5, 1/1]] ... OK
Processing block [[5/5, 1/1]] ... OK
Processing block [[1/5, 1/1]] ... OK
Processing block [[2/5, 1/1]] ... OK
Processing block [[3/5, 1/1]] ... OK
Processing block [[4/5, 1/1]] ... OK
Processing block [[5/5, 1/1]] ... OK
Loading required namespace: sctransform
Converting to sparse matrix.
Calculating cell attributes from input UMI matrix: log_umi
Variance stabilizing transformation of count matrix of size 17757 by 3005
Model formula is y ~ log_umi
Get Negative Binomial regression parameters per gene
Using 2000 genes, 3005 cells

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  |======================================================================| 100%
Found 12 outliers - those will be ignored in fitting/regularization step

Second step: Get residuals using fitted parameters for 17757 genes

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Calculating gene attributes
Wall clock passed: Time difference of 49.08318 secs
Computing corrected UMI count matrix

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see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Check 1000Check 3005
Warning: sctSpecies not provided. Setting to 'mouse' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
Checking for non-expressed genes.
Checking for cells with no expressed genes.
DGE:: Limma...
248 / 1,000 genes dropped @ DGE adj_pval_thresh < 1e-05
Time difference of 0.8557391 secs
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==>  F:\biocbuild\bbs-3.17-bioc\tmpdir\Rtmpox5akN/ctd_kiCortexOnly.rda
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==>  F:\biocbuild\bbs-3.17-bioc\tmpdir\Rtmpox5akN/ctd_kiCortexOnly.rda
Loading precomputed example bootstrap results.
Aligning celltype names with standardise_ctd format.
7 signficiant enrichment results @ bonferroni < 0.05
14.3% of hits are of the target cell type.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Loading precomputed example bootstrap results.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Check 1000Check 3005
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
Checking for non-expressed genes.
Checking for cells with no expressed genes.
DGE:: Limma...
248 / 1,000 genes dropped @ DGE adj_pval_thresh < 1e-05
Time difference of 0.6674089 secs
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==>  F:\biocbuild\bbs-3.17-bioc\tmpdir\Rtmpox5akN/ctd_kiCortexOnly.rda
+ Processing level 1 ...
Processing mean_exp
Processing specificity
Processing specificity_quantiles
+ Processing level 2 ...
Processing mean_exp
Processing specificity
Processing specificity_quantiles
No input_species provided. Setting to 'mouse'
+ Processing level 1 ...
Processing mean_exp
Processing specificity
Processing specificity_quantiles
+ Processing level 2 ...
Processing mean_exp
Processing specificity
Processing specificity_quantiles
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
trying URL 'http://www.informatics.jax.org/downloads/reports/MRK_List2.rpt'
Content type 'unknown' length 82685770 bytes (78.9 MB)
==================================================
downloaded 78.9 MB

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
10 of 10 are not proper HGNC symbols.
Possible corruption of gene names by excel: Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
10 of 10 are not proper HGNC symbols.
Possible corruption of gene names by excel: Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
10 of 10 are not proper HGNC symbols.
Possible corruption of gene names by excel: Mar-01
Maps last updated on: Thu Oct 24 12:31:05 2019
Maps last updated on: Thu Oct 24 12:31:05 2019
9 of 10 gene symbols corrected.
1 of 10 gene symbols cannot be mapped.
Converting to sparse matrix.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Tm4sf12
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 poorly annotated genes are replicates of existing genes. These are: 
Tspan12
Converting to sparse matrix.
1 rows should have been corrected by checking synonyms.
0 rows STILL do not have proper MGI symbols.

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
0 rows do not have proper MGI symbols

see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
669 rows do not have proper MGI symbols
2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
308 rows do not have proper MGI symbols
2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 poorly annotated genes are replicates of existing genes. These are: 
Hjurp
Converting to sparse matrix.
185 rows should have been corrected by checking synonyms.
126 rows STILL do not have proper MGI symbols.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
308 rows do not have proper MGI symbols
2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 poorly annotated genes are replicates of existing genes. These are: 
Hjurp
Converting to sparse matrix.
185 rows should have been corrected by checking synonyms.
126 rows STILL do not have proper MGI symbols.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 core(s) assigned as workers (31 reserved).
Preparing gene_df.
Dense matrix format detected.
Extracting genes from rownames.
100 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
91 genes extracted.
Extracting genes from ortholog_gene.
91 genes extracted.
Checking for genes without 1:1 orthologs.
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.
Converting obj to sparseMatrix.

=========== REPORT SUMMARY ===========

Total genes dropped after convert_orthologs :
   9 / 100 (9%)
Total genes remaining after convert_orthologs :
   91 / 100 (91%)
Converting to sparse matrix.
Converting to DelayedArray.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==>  F:\biocbuild\bbs-3.17-bioc\tmpdir\Rtmpox5akN/ctd_allKImouse.rda
+ Returning list of CTD file name, and the CTD itself.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Filtering by variance quantiles.
Converting to DelayedArray.
120 / 300 genes dropped @ DGE min_variance_quantile >= 5
Converting to sparse matrix.
Calculating cell attributes from input UMI matrix: log_umi
Variance stabilizing transformation of count matrix of size 300 by 3005
Model formula is y ~ log_umi
Get Negative Binomial regression parameters per gene
Using 300 genes, 3005 cells

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Found 2 outliers - those will be ignored in fitting/regularization step

Second step: Get residuals using fitted parameters for 300 genes

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Calculating gene attributes
Wall clock passed: Time difference of 6.198344 secs
Computing corrected UMI count matrix

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Filtering by variance quantiles.
Converting to DelayedArray.
120 / 300 genes dropped @ DGE min_variance_quantile >= 5
Filtering by variance quantiles.
Converting to DelayedArray.
120 / 300 genes dropped @ DGE min_variance_quantile >= 5
Filtering by variance quantiles.
Converting to DelayedArray.
/ Reading and realizing block 1/1 ... OK
\ Processing it ... OK
120 / 300 genes dropped @ DGE min_variance_quantile >= 5
Retrieving all organisms available in homologene.
Returning table with all species.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
0 non-overlapping gene(s) removed from exp1.
0 non-overlapping gene(s) removed from exp2.
19,972 intersecting genes remain.
Converting to data.frame
Converting to data.frame
Converting to sparse matrix.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
DGE:: Limma...
Loading required namespace: DESeq2
DGE:: DESeq2...
1 core(s) assigned as workers (31 reserved).
converting counts to integer mode
  Note: levels of factors in the design contain characters other than
  letters, numbers, '_' and '.'. It is recommended (but not required) to use
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not a warning or an error]
estimating size factors
  Note: levels of factors in the design contain characters other than
  letters, numbers, '_' and '.'. It is recommended (but not required) to use
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not a warning or an error]
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
   function: y = a/x + b, and a local regression fit was automatically substituted.
   specify fitType='local' or 'mean' to avoid this message next time.
  Note: levels of factors in the design contain characters other than
  letters, numbers, '_' and '.'. It is recommended (but not required) to use
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not a warning or an error]
final dispersion estimates
fitting model and testing
  Note: levels of factors in the design contain characters other than
  letters, numbers, '_' and '.'. It is recommended (but not required) to use
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not a warning or an error]
Loading required namespace: MAST
`fData` has no primerid.  I'll make something up.
`cData` has no wellKey.  I'll make something up.
[ FAIL 8 | WARN 49 | SKIP 0 | PASS 57 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bin_columns_into_quantiles.r:5:9'): bin_columns_into_quantiles works ──
Error: failed to load resource
  name: EH5376
  title: ctd
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─ewceData::ctd() at test-bin_columns_into_quantiles.r:5:8
  2.   ├─eh[["EH5376"]]
  3.   └─eh[["EH5376"]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
── Error ('test-bootstrap_enrichment_test.R:8:9'): bootstrap enrichment runs as expected ──
Error: failed to load resource
  name: EH5376
  title: ctd
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─ewceData::ctd() at test-bootstrap_enrichment_test.R:8:8
  2.   ├─eh[["EH5376"]]
  3.   └─eh[["EH5376"]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
── Error ('test-bootstrap_enrichment_test_2.R:8:9'): bootstrap enrichment function error handling and geneSizeControl runs as expected ──
Error: failed to load resource
  name: EH5376
  title: ctd
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─ewceData::ctd() at test-bootstrap_enrichment_test_2.R:8:8
  2.   ├─eh[["EH5376"]]
  3.   └─eh[["EH5376"]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
── Error ('test-controlled_geneset_enrichment.R:6:9'): Correct controlled & uncontrolled geneset enrichment calculations ──
Error: failed to load resource
  name: EH5376
  title: ctd
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─ewceData::ctd() at test-controlled_geneset_enrichment.R:6:8
  2.   ├─eh[["EH5376"]]
  3.   └─eh[["EH5376"]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
── Error ('test-ewce_expression_data.R:10:9'): EWCE expression data creation ───
Error: failed to load resource
  name: EH5376
  title: ctd
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─ewceData::ctd() at test-ewce_expression_data.R:10:8
  2.   ├─eh[["EH5376"]]
  3.   └─eh[["EH5376"]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
── Error ('test-ewce_plot.r:4:5'): ewce_plot works ─────────────────────────────
Error: failed to load resource
  name: EH5376
  title: ctd
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─ewceData::ctd() at test-ewce_plot.r:4:4
  2.   ├─eh[["EH5376"]]
  3.   └─eh[["EH5376"]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
── Error ('test-filter_ctd_genes.R:3:5'): filter_ctd_genes works ───────────────
Error: failed to load resource
  name: EH5376
  title: ctd
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─ewceData::ctd() at test-filter_ctd_genes.R:3:4
  2.   ├─eh[["EH5376"]]
  3.   └─eh[["EH5376"]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
── Error ('test-merge_ctd.R:3:9'): merge_sce works ─────────────────────────────
Error: failed to load resource
  name: EH5376
  title: ctd
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─ewceData::ctd() at test-merge_ctd.R:3:8
  2.   ├─eh[["EH5376"]]
  3.   └─eh[["EH5376"]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)

[ FAIL 8 | WARN 49 | SKIP 0 | PASS 57 ]
Error: Test failures
Execution halted