##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RNAmodR.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings RNAmodR_1.23.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/RNAmodR.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RNAmodR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RNAmodR' version '1.23.1'
* 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 'RNAmodR' 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
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'Biostrings:::XString'
  'IRanges:::.valid.CompressedList' 'IRanges:::coerceToCompressedList'
  'S4Vectors:::.valid.DataFrame' 'S4Vectors:::labeledLine'
  'S4Vectors:::make_zero_col_DataFrame'
  'S4Vectors:::prepare_objects_to_bind'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.get_inosine_score'
* 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 ... NOTE
checkRd: (-1) ModInosine-functions.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModInosine-functions.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModInosine-functions.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModInosine-functions.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModInosine-functions.Rd:47-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModInosine-functions.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModInosine-functions.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModInosine.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModInosine.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModInosine.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:124-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:127-128: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:129-130: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:78-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:83-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:103-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:194-195: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:196-197: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:198-199: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-functions.Rd:138-139: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:140-141: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:142-143: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:144: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:145: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:146-147: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:148: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:149: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:150-151: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:152: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:153-154: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:155-156: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModifierSet-class.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModifierSet-class.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModifierSet-class.Rd:54-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModifierSet-class.Rd:74-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-development.Rd:49-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RNAmodR-development.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SequenceData-class.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SequenceData-class.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SequenceData-class.Rd:60-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SequenceData-class.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SequenceData-class.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SequenceData-class.Rd:76-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SequenceData-functions.Rd:159: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SequenceData-functions.Rd:160-161: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SequenceData-functions.Rd:162-163: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SequenceData-functions.Rd:164-165: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aggregate.Rd:64-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aggregate.Rd:69-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aggregate.Rd:73-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aggregate.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aggregate.Rd:82-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aggregate.Rd:85-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compareByCoord.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compareByCoord.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compareByCoord.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compareByCoord.Rd:51-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compareByCoord.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compareByCoord.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) modify.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modify.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotData.Rd:122-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotData.Rd:125-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotData.Rd:128-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotData.Rd:130-131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subsetByCoord.Rd:99-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subsetByCoord.Rd:106-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subsetByCoord.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subsetByCoord.Rd:111-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subsetByCoord.Rd:124-125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) subsetByCoord.Rd:128-129: Lost braces in \itemize; \value handles \item{}{} directly
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'RNAmodR-internals.Rd':
  'object' 'range' 'data' 'modType' 'scoreFun' 'source' 'type' 'j'
  'value'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... OK
* checking examples ... ERROR
Running examples in 'RNAmodR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CoverageSequenceData-class
> ### Title: CoverageSequenceData
> ### Aliases: CoverageSequenceData-class CoverageSequenceData
> ###   CoverageSequenceDataFrame CoverageSequenceDataFrame-class
> ###   getData,CoverageSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method
> ###   aggregateData,CoverageSequenceData-method
> ###   getDataTrack,CoverageSequenceData-method
> 
> ### ** Examples
> 
> # Construction of a CoverageSequenceData objectobject
> library(RNAmodR.Data)
Loading required package: ExperimentHub
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: ExperimentHubData
Loading required package: AnnotationHubData
No methods found in package 'rtracklayer' for request: 'trackName<-' when loading 'AnnotationHubData'
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'ExperimentHubData'
> library(rtracklayer)

Attaching package: 'rtracklayer'

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

    hubUrl

> annotation <- GFF3File(RNAmodR.Data.example.man.gff3())
see ?RNAmodR.Data and browseVignettes('RNAmodR.Data') for documentation
loading from cache
> sequences <- RNAmodR.Data.example.man.fasta()
see ?RNAmodR.Data and browseVignettes('RNAmodR.Data') for documentation
loading from cache
require("Rsamtools")
> files <- c(treated = RNAmodR.Data.example.wt.1())
see ?RNAmodR.Data and browseVignettes('RNAmodR.Data') for documentation
loading from cache
> csd <- CoverageSequenceData(files, annotation = annotation,
+                             sequences = sequences)
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Warning in .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
OK
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/22ecc627f4101_2545'
[E::fai_read] Could not understand FASTA index F:\biocbuild\ExperimentHub_cache/1114c3f1a132b_2551 line 1
[E::fai_load3_core] Failed to read FASTA index F:\biocbuild\ExperimentHub_cache/1114c3f1a132b_2551
Error in value[[3L]](cond) : 'open' index failed
  file: F:\biocbuild\ExperimentHub_cache/1114c55a31869_2550
Calls: CoverageSequenceData ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
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.       ├─Biostrings::getSeq(sequences, unlist(grl))
    5.       └─Biostrings::getSeq(sequences, unlist(grl))
    6.         └─Rsamtools (local) .local(x, ...)
    7.           ├─Rsamtools::scanFa(x, param, ...)
    8.           └─Rsamtools::scanFa(x, param, ...)
    9.             ├─base::open(file)
   10.             └─Rsamtools::open.FaFile(file)
   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 1 | WARN 2 | SKIP 8 | PASS 177 ]
  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, 3 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/RNAmodR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL RNAmodR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'RNAmodR' ...
** this is package 'RNAmodR' version '1.23.1'
** using staged installation
** R
** data
** 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 (RNAmodR)

R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 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(RNAmodR)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


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: GenomicRanges
Loading required package: Seqinfo
Loading required package: Modstrings
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'RNAmodR'

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

    compare

> 
> test_check("RNAmodR")
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/22ecc129642d8_2547'
[E::fai_read] Could not understand FASTA index F:\biocbuild\ExperimentHub_cache/1114c3f1a132b_2551 line 1
[E::fai_load3_core] Failed to read FASTA index F:\biocbuild\ExperimentHub_cache/1114c3f1a132b_2551
[ FAIL 1 | WARN 2 | SKIP 8 | PASS 177 ]

══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• On Bioconductor (8): 'test-0SequenceDataFrame.R:23:3',
  'test-1SequenceDataSet.R:57:3', 'test-2Modifier.R:85:3',
  'test-3normalization.R:3:3', 'test-3subset.R:4:3', 'test-3zcomparison.R:4:3',
  'test-4roc.R:3:3', 'test-8visualization.R:158:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-0SequenceData.R:37:3'): SequenceData: ──────────────────────────
Error in `value[[3L]](cond)`: 'open' index failed
  file: F:\biocbuild\ExperimentHub_cache/1114c55a31869_2550
Backtrace:
     ▆
  1. └─RNAmodR::End5SequenceData(files, annotation = annotation, sequences = sequences) at test-0SequenceData.R:37:3
  2.   └─RNAmodR:::.new_SequenceData(...)
  3.     └─RNAmodR:::.load_sequences(sequences, grl, args)
  4.       ├─Biostrings::getSeq(sequences, unlist(grl))
  5.       └─Biostrings::getSeq(sequences, unlist(grl))
  6.         └─Rsamtools (local) .local(x, ...)
  7.           ├─Rsamtools::scanFa(x, param, ...)
  8.           └─Rsamtools::scanFa(x, param, ...)
  9.             ├─base::open(file)
 10.             └─Rsamtools::open.FaFile(file)
 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 1 | WARN 2 | SKIP 8 | PASS 177 ]
Error: Test failures
Execution halted