===============================
R CMD BUILD
===============================
* checking for file HumanRetinaLRSData/DESCRIPTION ... OK
* preparing HumanRetinaLRSData:
* checking DESCRIPTION meta-information ... 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 HumanRetinaLRSData_0.99.0.tar.gz
===============================
BiocCheckGitClone('HumanRetinaLRSData')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4017/HumanRetinaLRSData_20251202175057/HumanRetinaLRSData
BiocVersion: 3.23
Package: HumanRetinaLRSData
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4017/HumanRetinaLRSData_20251202175057/HumanRetinaLRSData.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4017/HumanRetinaLRSData_20251202175057/HumanRetinaLRSData
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
! WARNING: System files in '/inst' should not be Git tracked.
inst/.DS_Store
inst/extdata/.DS_Store
ERROR: System files found that should not be Git tracked.
HumanRetinaLRSData.Rproj
* 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 v1.47.1 results
1 ERRORS | 1 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/4017/HumanRetinaLRSData_20251202175057/HumanRetinaLRSData.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 HumanRetinaLRSData/DESCRIPTION ... OK
* checking extension type ... Package
* this is package HumanRetinaLRSData 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 HumanRetinaLRSData can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
* checking whether the package can be unloaded cleanly ... [1s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking whether startup messages can be suppressed ... [2s/2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
S4Vectors SummarizedExperiment utils
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [6s/8s] 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 files in vignettes ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
example_analysis.Rmd
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... NONE
* checking package vignettes ... NOTE
Package has vignettes subdirectory but apparently no vignettes.
Perhaps the VignetteBuilder information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/4017/HumanRetinaLRSData_20251202175057/HumanRetinaLRSData.Rcheck/00check.log
for details.
===============================
BiocCheck('HumanRetinaLRSData_0.99.0.tar.gz')
===============================
Installing HumanRetinaLRSData
Package installed successfully
HumanRetinaLRSData session metadata
sourceDir: /tmp/Rtmp17o1sI/file7e0e1725644fc/HumanRetinaLRSData
BiocVersion: 3.23
Package: HumanRetinaLRSData
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4017/HumanRetinaLRSData_20251202175057/HumanRetinaLRSData.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /tmp/Rtmp17o1sI/file7e0e1725644fc/HumanRetinaLRSData
installDir: /tmp/Rtmp17o1sI/file7e0e12c2521a8
isTarBall: TRUE
platform: unix
Running BiocCheck on HumanRetinaLRSData
* 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...
ExperimentData
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
i NOTE: Consider adding these automatically suggested biocViews: SequencingData
i Search 'biocViews' at https://contributions.bioconductor.org
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (60%).
* 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 NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Vignette(s) missing Vignette metadata. See
http://r-pkgs.had.co.nz/vignettes.html
Update the following files:
example_analysis.Rmd
ERROR: No 'VignetteEngine' specified in vignette.
Add 'VignetteEngine' to the following files:
vignettes/example_analysis.Rmd
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
Update the following files:
example_analysis.Rmd
* Checking whether vignette is built with 'R CMD build'...
ERROR: Vignette must be built by 'R CMD build'. Please see the `Vignette
Checks` section of the BiocCheck vignette.
* Checking package installation calls in R code...
* Checking for library/require of HumanRetinaLRSData...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid '<<-' if possible (found 3 times)
<<- in R/zzz.R (line 10, column 13)
<<- in R/zzz.R (line 20, column 15)
<<- in R/zzz.R (line 45, column 15)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
The longest 5 functions are:
load_object() (R/zzz.R): 51 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
man/clear_osf_cache.Rd
ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
ASEGeneCounts.Rd
...
ROIsoformLevelData.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 12 lines (4%) are > 80 characters long.
First few lines:
R/make-data.R#L17 #' Gene-level counts for flow through (F ...
...
vignettes/example_analysis.Rmd#L167 - **Gene vs. Isoform**: While samples ...
i NOTE: Consider multiples of 4 spaces for line indents; 116 lines (36%) are
not.
First few lines:
R/make-data.R#L6 load_object("ROGeneLevelData.rds") ...
...
vignettes/example_analysis.Rmd#L155 color_mapping = stage_colors ...
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...
ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
BiocCheck v1.47.1 results
5 ERRORS | 3 WARNINGS | i 10 NOTES
i See the HumanRetinaLRSData.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.