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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:circRNAprofiler.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings circRNAprofiler_1.13.2.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/circRNAprofiler.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'circRNAprofiler/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'circRNAprofiler' version '1.13.2'
* 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 'circRNAprofiler' 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 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 'circRNAprofiler-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getMotifs
> ### Title: Screen target sequences for recurrent motifs
> ### Aliases: getMotifs
>
> ### ** Examples
>
> # Load data frame containing detected back-spliced junctions
> data("mergedBSJunctions")
>
> # Load short version of the gencode v19 annotation file
> data("gtf")
>
> # Example with the first back-spliced junction
> # Multiple back-spliced junctions can also be analyzed at the same time
>
> # Annotate the first back-spliced junction
> annotatedBSJs <- annotateBSJs(mergedBSJunctions[1, ], gtf)
transcripts.txt is empty or absent. The longest
transcripts for all circRNAs will be analyzed>
> # Get genome
> if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)){
+
+ genome <- BSgenome::getBSgenome("BSgenome.Hsapiens.UCSC.hg19")
+
+ # Retrieve target sequences
+ targets <- getSeqsFromGRs(
+ annotatedBSJs,
+ genome,
+ lIntron = 200,
+ lExon = 10,
+ type = "ie"
+ )
+
+ # Get motifs
+ motifs <- getMotifs(
+ targets,
+ width = 6,
+ database = 'ATtRACT',
+ species = "Hsapiens",
+ rbp = TRUE,
+ reverse = FALSE)
+
+ }
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, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB
New names:
• `Experiment_description` -> `Experiment_description...7`
• `Experiment_description` -> `Experiment_description...10`
motifs.txt is empty or absent. Only ATtRACT motifs will be analyzed if availableError in `stringr::str_count()`:
! `string` must be a vector, not a <RNAStringSet> object.
Backtrace:
▆
1. ├─circRNAprofiler::getMotifs(...)
2. │ └─stringr::str_count(rnaSS, paste("(?=", stringMotif, ")", sep = ""))
3. │ └─stringr:::check_lengths(string, pattern)
4. │ └─vctrs::vec_size_common(...)
5. └─vctrs:::stop_scalar_type(`<fn>`(`<RNAStrnS>`), "string", `<env>`)
6. └─vctrs:::stop_vctrs(...)
7. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* 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: 1 ERROR
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/circRNAprofiler.Rcheck/00check.log'
for details.