===============================
BiocCheckGitClone('DOTSeq')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3989/d5e8832c3731a877cd15e2e6a444db241aad1448/DOTSeq
→ BiocVersion: 3.23
→ Package: DOTSeq
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3989/d5e8832c3731a877cd15e2e6a444db241aad1448/DOTSeq.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3989/d5e8832c3731a877cd15e2e6a444db241aad1448/DOTSeq
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.47.1 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3989/d5e8832c3731a877cd15e2e6a444db241aad1448/DOTSeq.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DOTSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DOTSeq’ version ‘0.99.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘DOTSeq’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking use of S3 registration ... 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 ... [44s/44s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-Werror=format-security’
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [58s/57s] ERROR
Running examples in ‘DOTSeq-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getExonicReads
> ### Title: Filter BAM files to retain only reads overlapping exonic regions
> ### Aliases: getExonicReads
>
> ### ** Examples
>
> ## Don't show:
> if (requireNamespace("TxDb.Dmelanogaster.UCSC.dm3.ensGene", quietly = TRUE) && requireNamespace("pasillaBamSubset", quietly = TRUE)) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
+ library(pasillaBamSubset)
+ library(AnnotationDbi)
+ library(GenomeInfoDb)
+
+ # Save a subset of TxDb as an sqlite file
+ txdb_chr4 <- keepSeqlevels(
+ TxDb.Dmelanogaster.UCSC.dm3.ensGene,
+ "chr4",
+ pruning.mode = "coarse"
+ )
+ txdb_path <- file.path(getwd(), "dm3_chr4.sqlite")
+ saveDb(txdb_chr4, file = txdb_path)
+
+ # Create a GRanges object with a link to the TxDb sqlite file,
+ # which is required for getExonicReads()
+ gr <- GRanges(seqnames = "chr4", ranges = IRanges(start = 233, end = 2300))
+ metadata(gr)$txdb <- txdb_path
+
+ getExonicReads(gr, bam_files = c(untreated1_chr4()))
+
+ # Get the directory of the BAM file and clean up output files
+ bam_dir <- dirname(untreated1_chr4())
+ output_files <- list.files(
+ path = bam_dir,
+ pattern = "*exonic.*",
+ full.names = TRUE
+ )
+ file.remove(c(txdb_path, output_files))
+ ## Don't show:
+ }) # examplesIf
> library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
Loading required package: GenomicFeatures
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
Loading required package: S4Vectors
Loading required package: stats4
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
Loading required package: Seqinfo
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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")'.
> library(pasillaBamSubset)
> library(AnnotationDbi)
> library(GenomeInfoDb)
> txdb_chr4 <- keepSeqlevels(TxDb.Dmelanogaster.UCSC.dm3.ensGene, "chr4",
+ pruning.mode = "coarse")
> txdb_path <- file.path(getwd(), "dm3_chr4.sqlite")
> saveDb(txdb_chr4, file = txdb_path)
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: UCSC
# Genome: dm3
# Organism: Drosophila melanogaster
# Taxonomy ID: 7227
# UCSC Table: ensGene
# Resource URL: http://genome.ucsc.edu/
# Type of Gene ID: Ensembl gene ID
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 29173
# exon_nrow: 76920
# cds_nrow: 62135
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-10-07 18:15:53 +0000 (Wed, 07 Oct 2015)
# GenomicFeatures version at creation time: 1.21.30
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
> gr <- GRanges(seqnames = "chr4", ranges = IRanges(start = 233, end = 2300))
> metadata(gr)$txdb <- txdb_path
> getExonicReads(gr, bam_files = c(untreated1_chr4()))
starting filtering /home/biocbuild/bbs-3.23-bioc/R/site-library/pasillaBamSubset/extdata/untreated1_chr4.bam
[E::hts_open_format] Failed to open file "/home/biocbuild/bbs-3.23-bioc/R/site-library/pasillaBamSubset/extdata/untreated1_chr4.exonic.bam" : Permission denied
Error in value[[3L]](cond) : failed to open SAM/BAM file
file: '/home/biocbuild/bbs-3.23-bioc/R/site-library/pasillaBamSubset/extdata/untreated1_chr4.exonic.bam'
file: /home/biocbuild/bbs-3.23-bioc/R/site-library/pasillaBamSubset/extdata/untreated1_chr4.bam
index: /home/biocbuild/bbs-3.23-bioc/R/site-library/pasillaBamSubset/extdata/untreated1_chr4.bam
Calls: withAutoprint ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DOTSeq 15.887 0.221 16.038
* checking for unstated dependencies in ‘tests’ ... WARNING
'::' or ':::' import not declared from: ‘withr’
'library' or 'require' call not declared from: ‘withr’
* checking tests ...
Running ‘testthat.R’ [171s/154s]
[171s/155s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
file: '/home/biocbuild/bbs-3.23-bioc/R/site-library/pasillaBamSubset/extdata/untreated1_chr4.exonic.bam'
file: /home/biocbuild/bbs-3.23-bioc/R/site-library/pasillaBamSubset/extdata/untreated1_chr4.bam
index: /home/biocbuild/bbs-3.23-bioc/R/site-library/pasillaBamSubset/extdata/untreated1_chr4.bam
Backtrace:
▆
1. └─DOTSeq::getExonicReads(gr = gr, bam_files = bam_list, coding_genes_only = TRUE) at test_DOTSeqDataSets.R:255:5
2. ├─Rsamtools::filterBam(...)
3. └─Rsamtools::filterBam(...)
4. └─Rsamtools (local) .local(file, destination, index, ...)
5. ├─Rsamtools::filterBam(...)
6. └─Rsamtools::filterBam(...)
7. └─Rsamtools (local) .local(file, destination, index, ...)
8. └─Rsamtools:::.io_bam(...)
9. └─base::tryCatch(...)
10. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
11. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. └─value[[3L]](cond)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 208 ]
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 ... [5s/5s] OK
* DONE
Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3989/d5e8832c3731a877cd15e2e6a444db241aad1448/DOTSeq.Rcheck/00check.log’
for details.
===============================
BiocCheck('DOTSeq_0.99.3.tar.gz')
===============================
── Installing DOTSeq ───────────────────────────────────────────────────────────
✔ Package installed successfully
── DOTSeq session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNpjJN3/file1ad5e28479bf4/DOTSeq
→ BiocVersion: 3.23
→ Package: DOTSeq
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3989/d5e8832c3731a877cd15e2e6a444db241aad1448/DOTSeq.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /tmp/RtmpNpjJN3/file1ad5e28479bf4/DOTSeq
→ installDir: /tmp/RtmpNpjJN3/file1ad5e388fe806
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DOTSeq ─────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (54%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of DOTSeq...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 30
functions greater than 50 lines.
The longest 5 functions are:
• fit_beta_binomial() (R/fit.R): 495 lines
• ...
• plotDOT() (R/plot.R): 365 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 287 lines (3%) are > 80 characters long.
First few lines:
• R/annotation.R#L51 message("selected ", length(gtf) ...
• ...
• vignettes/DOTSeq.Rmd#L486 ribo_control_reps <- do.call(cbind, repl ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.47.1 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 2 NOTES
i See the DOTSeq.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.