===============================
R CMD BUILD
===============================
* checking for file splicelogic/DESCRIPTION ... OK
* preparing splicelogic:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building splicelogic_0.99.0.tar.gz
===============================
BiocCheckGitClone('splicelogic')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4212/splicelogic_20260324155139/splicelogic
BiocVersion: 3.23
Package: splicelogic
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4212/splicelogic_20260324155139/splicelogic.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4212/splicelogic_20260324155139/splicelogic
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...
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 v1.47.20 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/4212/splicelogic_20260324155139/splicelogic.Rcheck
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-24 15:53:25 UTC
* using option --no-vignettes
* checking for file splicelogic/DESCRIPTION ... OK
* this is package splicelogic version 0.99.0
* 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 for sufficient/correct file permissions ... OK
* checking whether package splicelogic can be installed ... OK
* 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 ... [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 ... [3s/3s] NOTE
candidates_by_non_overlap_directed: no visible binding for global
variable internal
candidates_by_non_overlap_directed: no visible binding for global
variable key
candidates_by_presence: no visible binding for global variable
gene_id
candidates_by_presence: no visible binding for global variable tx_id
candidates_by_presence: no visible binding for global variable
internal
candidates_by_presence: no visible binding for global variable
overlap_count
candidates_by_presence: no visible binding for global variable
n_txp_pos
candidates_by_presence: no visible binding for global variable key
compute_matches: no visible binding for global variable .
create_mock_data: no visible binding for global variable gene_id
create_mock_data: no visible binding for global variable tx_id
create_mock_data: no visible binding for global variable exon_rank
create_mock_data: no visible binding for global variable strand
create_mock_data: no visible binding for global variable tx_order
create_mock_data: no visible binding for global variable estimate
find_alt_ss: no visible binding for global variable estimate
find_alt_ss: no visible binding for global variable cand_idx
find_alt_ss: no visible binding for global variable neg_idx
find_alt_ss: no visible binding for global variable gene_id_cand
find_alt_ss: no visible binding for global variable gene_id_neg
find_alt_ss: no visible binding for global variable tx_id_neg
find_alt_ss: no visible binding for global variable n
find_alt_ss: no visible binding for global variable match_start
find_alt_ss: no visible binding for global variable match_end
find_alt_ss: no visible binding for global variable event
find_alt_ss: no visible binding for global variable tx_event
find_candidates_and_flanks: no visible binding for global variable
estimate
find_candidates_and_flanks: no visible binding for global variable
pos_idx
find_candidates_and_flanks: no visible binding for global variable
gene_id_pos
find_candidates_and_flanks: no visible binding for global variable
cand_idx
find_introns: no visible binding for global variable tx_id
find_introns: no visible binding for global variable start
find_introns: no visible binding for global variable gene_id
find_introns: no visible binding for global variable end
find_introns: no visible binding for global variable intron_start
find_introns: no visible binding for global variable intron_end
find_matches_batch: no visible binding for global variable queryHits
find_matches_batch: no visible binding for global variable
subjectHits
find_mxe: no visible binding for global variable cand_idx
find_mxe: no visible binding for global variable tx_id
find_mxe: no visible binding for global variable l
find_mxe: no visible binding for global variable r
find_mxe: no visible binding for global variable exon_rank
find_mxe: no visible binding for global variable pos_row
find_mxe: no visible binding for global variable .pair_order
find_mxe: no visible binding for global variable event
find_mxe: no visible binding for global variable tx_event
find_ri: no visible binding for global variable estimate
find_ri: no visible binding for global variable intron_idx
find_ri: no visible binding for global variable pos_idx
find_ri: no visible binding for global variable gene_id_intron
find_ri: no visible binding for global variable gene_id_pos
find_ri: no visible binding for global variable tx_id_intron
find_ri: no visible binding for global variable event
find_ri: no visible binding for global variable tx_event
find_se: no visible binding for global variable cand_idx
find_se: no visible binding for global variable tx_id
find_se: no visible binding for global variable l
find_se: no visible binding for global variable r
find_se: no visible binding for global variable event
find_se: no visible binding for global variable tx_event
generate_a3ss: no visible binding for global variable estimate
generate_a3ss: no visible binding for global variable internal
generate_a3ss: no visible binding for global variable key
generate_a3ss: no visible binding for global variable start
generate_a5ss: no visible binding for global variable estimate
generate_a5ss: no visible binding for global variable internal
generate_a5ss: no visible binding for global variable key
generate_a5ss: no visible binding for global variable end
generate_mxe: no visible binding for global variable estimate
generate_mxe: no visible binding for global variable internal
generate_mxe: no visible binding for global variable tx_id
generate_mxe: no visible binding for global variable exon_rank
generate_mxe: no visible binding for global variable next_key
generate_mxe: no visible binding for global variable gene_id
generate_mxe: no visible binding for global variable neg_tx_id
generate_mxe: no visible binding for global variable key
generate_ri: no visible binding for global variable estimate
generate_ri: no visible binding for global variable tx_id
generate_ri: no visible binding for global variable exon_rank
generate_ri: no visible binding for global variable end
generate_se: no visible binding for global variable estimate
generate_se: no visible binding for global variable internal
generate_se: no visible binding for global variable key
match_left_right: no visible binding for global variable match_left
match_left_right: no visible binding for global variable tx_id
match_left_right: no visible binding for global variable exon_rank
match_left_right: no visible binding for global variable match_right
preprocess: no visible binding for global variable tx_id
preprocess: no visible binding for global variable exon_rank
preprocess: no visible binding for global variable nexons
rerank_exons: no visible binding for global variable tx_id
rerank_exons: no visible binding for global variable strand
rerank_exons: no visible binding for global variable exon_rank
Undefined global functions or variables:
. .pair_order cand_idx end estimate event exon_rank gene_id
gene_id_cand gene_id_intron gene_id_neg gene_id_pos internal
intron_end intron_idx intron_start key l match_end match_left
match_right match_start n n_txp_pos neg_idx neg_tx_id nexons next_key
overlap_count pos_idx pos_row queryHits r start strand subjectHits
tx_event tx_id tx_id_intron tx_id_neg tx_order
Consider adding
importFrom("stats", "end", "start")
to your NAMESPACE file.
* 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 files in vignettes ... OK
* checking examples ... [18s/18s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
create_mock_data 8.262 0.389 8.651
find_events 5.002 0.134 5.137
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [20s/20s]
[20s/20s] 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: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/4212/splicelogic_20260324155139/splicelogic.Rcheck/00check.log
for details.
===============================
BiocCheck('splicelogic_0.99.0.tar.gz')
===============================
Installing splicelogic
Package installed successfully
splicelogic session metadata
sourceDir: /tmp/RtmpC3aW3y/file17fab97138565c/splicelogic
BiocVersion: 3.23
Package: splicelogic
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4212/splicelogic_20260324155139/splicelogic.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /tmp/RtmpC3aW3y/file17fab97138565c/splicelogic
installDir: /tmp/RtmpC3aW3y/file17fab9661b6342
isTarBall: TRUE
platform: unix
Running BiocCheck on splicelogic
* 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 4.1.0 to 4.6.0
* 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 Bioconductor dependencies found in Imports & Depends (40%).
* 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 splicelogic...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
suppressMessages() in R/input_formatting.R (line 166, column 13)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
The longest 5 functions are:
prepare_exons() (R/input_formatting.R): 103 lines
...
find_candidates_and_flanks() (R/aux_logic.R): 66 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
prepare_exons.Rd
* 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; 49 lines (3%) are > 80 characters long.
First few lines:
R/aux_logic.R#L366 #' @return Character vector of column na ...
...
vignettes/splicelogic.Rmd#L307 Next flattening the exons (here using a ...
i NOTE: Consider multiples of 4 spaces for line indents; 593 lines (32%) are
not.
First few lines:
R/aux_logic.R#L17 gr, ...
...
vignettes/splicelogic.Rmd#L301 ) ...
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 v1.47.20 results
0 ERRORS | 0 WARNINGS | i 6 NOTES
i See the splicelogic.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.