===============================
R CMD BUILD
===============================
* checking for file ‘superintervalsr/DESCRIPTION’ ... OK
* preparing ‘superintervalsr’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘superintervalsr_0.99.2.tar.gz’
===============================
BiocCheckGitClone('superintervalsr')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3870/2fc473079ee711da95557ead56908f86069ff0a9/superintervalsr
→ BiocVersion: 3.22
→ Package: superintervalsr
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3870/2fc473079ee711da95557ead56908f86069ff0a9/superintervalsr.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3870/2fc473079ee711da95557ead56908f86069ff0a9/superintervalsr
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3870/2fc473079ee711da95557ead56908f86069ff0a9/superintervalsr/.gitignore'
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.45.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3870/2fc473079ee711da95557ead56908f86069ff0a9/superintervalsr.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘superintervalsr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘superintervalsr’ version ‘0.99.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘superintervalsr’ can be installed ... WARNING
Found the following significant warnings:
intervalmap_r.cpp:34:48: warning: the address of ‘void cleanup_intervalmap(si::IntervalMap<int, SEXPREC*>*)’ will never be NULL [-Waddress]
intervalmap_r.cpp:67:48: warning: the address of ‘void cleanup_intervalmap(si::IntervalMap<int, SEXPREC*>*)’ will never be NULL [-Waddress]
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3870/2fc473079ee711da95557ead56908f86069ff0a9/superintervalsr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [2s/2s] 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 ... WARNING
Undocumented code objects:
‘as_granges’ ‘count.batch’ ‘search_idxs.batch’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [1s/1s]
[1s/1s] OK
* 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 ... [3s/3s] OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3870/2fc473079ee711da95557ead56908f86069ff0a9/superintervalsr.Rcheck/00check.log’
for details.
===============================
BiocCheck('superintervalsr_0.99.2.tar.gz')
===============================
── Installing superintervalsr ──────────────────────────────────────────────────
✔ Package installed successfully
── superintervalsr session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/RtmpP535gW/file2bd3d85e0bcbd/superintervalsr
→ BiocVersion: 3.22
→ Package: superintervalsr
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3870/2fc473079ee711da95557ead56908f86069ff0a9/superintervalsr.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /tmp/RtmpP535gW/file2bd3d85e0bcbd/superintervalsr
→ installDir: /tmp/RtmpP535gW/file2bd3d828c6a124
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on superintervalsr ────────────────────────────────────────
* 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...
i NOTE: Update R version dependency from 4.3.0 to 4.5.0
* 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 NOTE: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* 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 superintervalsr...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• superintervalsr.R (line 116, column 22)
• ...
• superintervalsr.R (line 243, column 15)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* 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; 35 lines (3%) are > 80 characters long.
First few lines:
• R/RcppExports.R#L9 .Call(`_superintervalsr_create_inter ...
• ...
• vignettes/workflows.Rmd#L353 cat("SuperIntervals count.batch:", round ...
i NOTE: Consider multiples of 4 spaces for line indents; 166 lines (14%) are
not.
First few lines:
• R/superintervalsr.R#L30 if (missing(x)) { ...
• ...
• vignettes/workflows.Rmd#L304 search_idxs(gene_imap, start(test_quer ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.45.12 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 6 NOTES
i See the superintervalsr.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.