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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:easier.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings easier_1.12.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/easier.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'easier/DESCRIPTION' ... OK
* this is package 'easier' version '1.12.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'easier' 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 code 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'reannotate_genes'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compute_TF_activity: no visible binding for global variable 'condition'
compute_TF_activity: no visible binding for global variable 'score'
Undefined global functions or variables:
  condition score
* 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 'easier-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assess_immune_response
> ### Title: Assess easier score as predictor of patients' immune response
> ### Aliases: assess_immune_response
> 
> ### ** Examples
> 
> # using a SummarizedExperiment object
> library(SummarizedExperiment)
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> # Using example exemplary dataset (Mariathasan et al., Nature, 2018)
> # from easierData. Original processed data is available from
> # IMvigor210CoreBiologies package.
> library("easierData")
> 
> dataset_mariathasan <- easierData::get_Mariathasan2018_PDL1_treatment()
Retrieving Mariathasan2018_PDL1_treatment dataset...
see ?easierData and browseVignettes('easierData') for documentation
loading from cache
> RNA_tpm <- assays(dataset_mariathasan)[["tpm"]]
> cancer_type <- metadata(dataset_mariathasan)[["cancertype"]]
> 
> # Select a subset of patients to reduce vignette building time.
> pat_subset <- c(
+   "SAM76a431ba6ce1", "SAMd3bd67996035", "SAMd3601288319e",
+   "SAMba1a34b5a060", "SAM18a4dabbc557"
+ )
> RNA_tpm <- RNA_tpm[, colnames(RNA_tpm) %in% pat_subset]
> 
> # Computation of TF activity (Garcia-Alonso et al., Genome Res, 2019)
> tf_activities <- compute_TF_activity(
+   RNA_tpm = RNA_tpm
+ )
Regulated transcripts found in data set: 3084/3254 (94.8%)
TF activity computed! 

> 
> # Predict patients' immune response
> predictions <- predict_immune_response(
+   tfs = tf_activities,
+   cancer_type = cancer_type,
+   verbose = TRUE
+ )
Warning: download failed
  web resource path: 'https://experimenthub.bioconductor.org/fetch/6722'
  local file path: 'F:\biocbuild\ExperimentHub_cache\file160dc40d95552'
  reason: Internal Server Error (HTTP 500).
Warning: bfcdownload() failed
  rid: BFC111
  file: 'https://experimenthub.bioconductor.org/fetch/6722'
  reason: download failed
Warning: download failed
  hub path: 'https://experimenthub.bioconductor.org/fetch/6722'
  cache resource: 'EH6679 : 6722'
  reason: download failed; see warnings()
Warning: download failed
  web resource path: 'https://experimenthub.bioconductor.org/fetch/6722'
  local file path: 'F:\biocbuild\ExperimentHub_cache\file160dc3cba6d37'
  reason: Internal Server Error (HTTP 500).
Warning: bfcdownload() failed
  rid: BFC111
  file: 'https://experimenthub.bioconductor.org/fetch/6722'
  reason: download failed
Warning: download failed
  hub path: 'https://experimenthub.bioconductor.org/fetch/6722'
  cache resource: 'EH6679 : 6722'
  reason: download failed; see warnings()
Error: failed to load resource
  name: EH6679
  title: opt_xtrain_stats
  reason: 1 resources failed to download
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:
  Error: unable to find an inherited method for function 'assays' for signature 'x = "GRanges"'
  Backtrace:
      ▆
   1. └─SummarizedExperiment::assays(dataset_mariathasan) at test-easier_run.R:12:3
   2.   └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
  ── Error ('test-easier_run.R:40:3'): easier fails to run on cancer type with non-available cancer-specific model ──
  Error: unable to find an inherited method for function 'assays' for signature 'x = "GRanges"'
  Backtrace:
      ▆
   1. └─SummarizedExperiment::assays(dataset_mariathasan) at test-easier_run.R:40:3
   2.   └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/easier.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL easier
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'easier' ...
** 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 (easier)

R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(easier)
> 
> test_check("easier")
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Retrieving Mariathasan2018_PDL1_treatment dataset...
see ?easierData and browseVignettes('easierData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
Retrieving Mariathasan2018_PDL1_treatment dataset...
see ?easierData and browseVignettes('easierData') for documentation
loading from cache
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-easier_run.R:12:3'): easier runs on cancer type with available cancer-specific model ──
Error: unable to find an inherited method for function 'assays' for signature 'x = "GRanges"'
Backtrace:
    ▆
 1. └─SummarizedExperiment::assays(dataset_mariathasan) at test-easier_run.R:12:3
 2.   └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-easier_run.R:40:3'): easier fails to run on cancer type with non-available cancer-specific model ──
Error: unable to find an inherited method for function 'assays' for signature 'x = "GRanges"'
Backtrace:
    ▆
 1. └─SummarizedExperiment::assays(dataset_mariathasan) at test-easier_run.R:40:3
 2.   └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted