===============================
BiocCheckGitClone('SETA')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3896/SETA_20250819184800/SETA
BiocVersion: 3.22
Package: SETA
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3896/SETA_20250819184800/SETA.BiocCheck
BiocCheckVersion: 1.45.12
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3896/SETA_20250819184800/SETA
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 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/3896/SETA_20250819184800/SETA.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 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file SETA/DESCRIPTION ... OK
* this is package SETA 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section Package
structure in the Writing R Extensions manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package SETA 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 ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] 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 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 ... [7s/7s] NOTE
taxonomy_to_tbl_graph: no visible binding for global variable .data
Undefined global functions or variables:
.data
* 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 ... [15s/15s] ERROR
Running examples in SETA-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: setaTaxonomyDF
> ### Title: Build a taxonomy data frame at multiple resolutions
> ### Aliases: setaTaxonomyDF
>
> ### ** Examples
>
> meta <- data.frame(
+ bc = paste0("cell", 1:6),
+ broad_type = c("AT1","AT2","AT1","Fib1","Fib1","AT2"),
+ mid_type = c("Alv","Alv","Alv","Fib","Fib","Alv"),
+ fine_type = c("Epi","Epi","Epi","Stroma","Stroma","Epi")
+ )
> setaTaxonomyDF(meta,
+ resolution_cols = c("broad_type","mid_type","fine_type"))
Error in setaTaxonomyDF(meta, resolution_cols = c("broad_type", "mid_type", :
Finest labels mapping to >1 coarser combo: Epi
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
data 6.596 0.334 6.93
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [16s/16s]
[16s/16s] 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 ... [5s/5s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character (U+202F)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
! LaTeX Error: Unicode character (U+202F)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
! LaTeX Error: Unicode character (U+202F)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
! LaTeX Error: Unicode character (U+202F)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
! Missing $ inserted.
<inserted text>
$
l.214 and \eqn{(\text{n_taxa} - 1)}{}
columns.
! Extra }, or forgotten $.
\textdef@ ...th {#1}\let \f@size #2\selectfont #3}
}
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columns.
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\textdef@ ...h {#1}\let \f@size #2\selectfont #3}}
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{\textdef@ \textstyle \f@s...
l.214 and \eqn{(\text{n_taxa} - 1)}{}
columns.
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\textdef@ ...th {#1}\let \f@size #2\selectfont #3}
}
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\textdef@ ...h {#1}\let \f@size #2\selectfont #3}}
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! Extra }, or forgotten $.
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! LaTeX Error: Unicode character (U+222A)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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* checking PDF version of manual without index ... ERROR
* DONE
Status: 2 ERRORs, 1 WARNING, 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3896/SETA_20250819184800/SETA.Rcheck/00check.log
for details.
===============================
BiocCheck('SETA_0.99.0.tar.gz')
===============================
Installing SETA
Package installed successfully
SETA session metadata
sourceDir: /tmp/RtmpE5GAHu/file1da0861d4af052/SETA
BiocVersion: 3.22
Package: SETA
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3896/SETA_20250819184800/SETA.BiocCheck
BiocCheckVersion: 1.45.12
sourceDir: /tmp/RtmpE5GAHu/file1da0861d4af052/SETA
installDir: /tmp/RtmpE5GAHu/file1da0864a6fdce1
isTarBall: TRUE
platform: unix
Running BiocCheck on SETA
* 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...
i NOTE: Consider adding these automatically suggested biocViews: ATACSeq
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
! WARNING: 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
comparing_samples.Rmd
introductory_vignette.Rmd
reference_frames.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of SETA...
* 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 4
functions greater than 50 lines.
The longest 5 functions are:
setaTransform() (R/transforms.R): 97 lines
...
setaTaxonomyDF() (R/utils.R): 55 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
setaMetadata.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 7% of man
pages use at least one of these tags.
Found in files:
setaMetadata.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...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 51 lines (2%) are > 80 characters long.
First few lines:
R/data.R#L70 fine_type <- rep(type_levels, each = ...
...
vignettes/reference_frames.Rmd#L308 We color points by age to see if the sub
...
i NOTE: Consider multiples of 4 spaces for line indents; 89 lines (4%) are not.
First few lines:
R/data.R#L139 dimnames = list(paste0 ...
...
vignettes/reference_frames.Rmd#L351 signif(latent_lineage$v ...
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...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.45.12 results
1 ERRORS | 1 WARNINGS | i 9 NOTES
i See the SETA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.