===============================
R CMD BUILD
===============================
* checking for file ‘BREW3R.r/DESCRIPTION’ ... OK
* preparing ‘BREW3R.r’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘BREW3R.r_0.99.0.tar.gz’
===============================
BiocCheckGitClone('BREW3R.r')
===============================
─ BiocCheckVersion: 1.39.26
─ BiocVersion: 3.19
─ Package: BREW3R.r
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3313/BREW3R.r_20240226162603/BREW3R.r
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* 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 results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3313/BREW3R.r_20240226162603/BREW3R.r.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BREW3R.r/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BREW3R.r’ 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 serialization versions ... OK
* checking whether package ‘BREW3R.r’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] 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 ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [4s/4s] NOTE
add_new_exons: no visible binding for global variable ‘query_extremity’
add_new_exons: no visible binding for global variable
‘subject_extremity’
add_new_exons: no visible binding for global variable ‘transcript_id’
add_new_exons: no visible binding for global variable
‘subject_transcript_extremity’
add_new_exons: no visible binding for global variable ‘strand’
add_new_exons: no visible binding for global variable ‘start’
add_new_exons: no visible binding for global variable ‘query_end’
add_new_exons: no visible binding for global variable ‘end’
add_new_exons: no visible binding for global variable ‘query_start’
add_new_exons: no visible binding for global variable
‘transcript_id_to_extend’
add_new_exons: no visible binding for global variable ‘transcript_pair’
add_new_exons: no visible binding for global variable ‘to_extend_5p’
add_new_exons: no visible binding for global variable
‘first_colliding_base’
add_new_exons: no visible binding for global variable ‘exon_number’
adjust_for_collision: no visible binding for global variable
‘old_start’
adjust_for_collision: no visible binding for global variable ‘start’
adjust_for_collision: no visible binding for global variable ‘old_end’
adjust_for_collision: no visible binding for global variable ‘end’
adjust_for_collision: no visible binding for global variable
‘queryHits’
adjust_for_collision: no visible binding for global variable
‘subject_start’
adjust_for_collision: no visible binding for global variable
‘query_old_end’
adjust_for_collision: no visible binding for global variable
‘subject_end’
adjust_for_collision: no visible binding for global variable
‘query_old_start’
adjust_for_collision: no visible binding for global variable ‘strand’
adjust_for_collision: no visible binding for global variable
‘max_subject_end_collision’
adjust_for_collision: no visible binding for global variable
‘min_subject_start_collision’
adjust_for_collision: no visible binding for global variable ‘id’
adjust_for_collision: no visible binding for global variable
‘subject_id’
adjust_for_collision: no visible binding for global variable
‘query_extension_limit’
adjust_for_collision: no visible binding for global variable
‘extension_width’
adjust_for_collision: no visible binding for global variable
‘query_gene_id’
adjust_for_collision: no visible binding for global variable
‘min_extension’
adjust_for_collision: no visible binding for global variable ‘keep’
adjust_for_collision: no visible binding for global variable
‘fixed_start_same_extension’
adjust_for_collision: no visible binding for global variable
‘fixed_end_same_extension’
extend_granges: no visible binding for global variable ‘type’
extend_granges: no visible binding for global variable ‘id’
extract_last_exon: no visible binding for global variable ‘type’
extract_last_exon: no visible binding for global variable ‘strand’
extract_last_exon: no visible binding for global variable ‘end’
extract_last_exon: no visible binding for global variable ‘start’
extract_last_exon: no visible binding for global variable ‘is_last’
extract_last_exon: no visible binding for global variable ‘row_number’
get_extending_overlap: no visible binding for global variable ‘type’
get_extending_overlap: no visible binding for global variable
‘new_start’
get_extending_overlap: no visible binding for global variable ‘start’
get_extending_overlap: no visible binding for global variable ‘new_end’
get_extending_overlap: no visible binding for global variable ‘end’
overlap_different_genes: no visible binding for global variable
‘query_gene_id’
overlap_different_genes: no visible binding for global variable
‘subject_gene_id’
Undefined global functions or variables:
end exon_number extension_width first_colliding_base
fixed_end_same_extension fixed_start_same_extension id is_last keep
max_subject_end_collision min_extension min_subject_start_collision
new_end new_start old_end old_start queryHits query_end
query_extension_limit query_extremity query_gene_id query_old_end
query_old_start query_start row_number start strand subject_end
subject_extremity subject_gene_id subject_id subject_start
subject_transcript_extremity to_extend_5p transcript_id
transcript_id_to_extend transcript_pair type
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 ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [11s/11s]
[11s/11s] 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 ... [2s/2s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3313/BREW3R.r_20240226162603/BREW3R.r.Rcheck/00check.log’
for details.
===============================
BiocCheck('BREW3R.r_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.39.26
─ BiocVersion: 3.19
─ Package: BREW3R.r
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/Rtmp6TzeG7/file1600984885a719/BREW3R.r
─ installDir: /tmp/Rtmp6TzeG7/file16009857c5fb3d
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3313/BREW3R.r_20240226162603/BREW3R.r.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (33%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 BREW3R.r...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 4 functions greater than 50 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...
* NOTE: Consider shorter lines; 29 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 77 lines
(7%) are not.
See https://contributions.bioconductor.org/r-code.html
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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 4 NOTES
See the BREW3R.r.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.