===============================
R CMD BUILD
===============================
* checking for file ‘visiumStitched/DESCRIPTION’ ... OK
* preparing ‘visiumStitched’:
* 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 ‘visiumStitched_0.99.8.tar.gz’
===============================
BiocCheckGitClone('visiumStitched')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3501/d2297f04b056eaa942ec9f004aa5b023cf3c2a61/visiumStitched
→ BiocVersion: 3.20
→ Package: visiumStitched
→ PackageVersion: 0.99.8
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3501/d2297f04b056eaa942ec9f004aa5b023cf3c2a61/visiumStitched.BiocCheck
→ BiocCheckVersion: 1.41.16
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3501/d2297f04b056eaa942ec9f004aa5b023cf3c2a61/visiumStitched
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.41.16 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3501/d2297f04b056eaa942ec9f004aa5b023cf3c2a61/visiumStitched.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘visiumStitched/DESCRIPTION’ ... OK
* this is package ‘visiumStitched’ version ‘0.99.8’
* 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 ‘visiumStitched’ 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 ... [16s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [16s/16s] OK
* checking whether the package can be unloaded cleanly ... [16s/16s] OK
* checking whether the namespace can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [16s/16s] OK
* checking loading without being on the library search path ... [16s/16s] 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 ... [51s/51s] NOTE
spe_to_seurat: no visible global function definition for ‘new’
Undefined global functions or variables:
new
Consider adding
importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... [148s/153s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
build_spe 60.416 3.009 63.187
add_array_coords 22.354 5.291 30.286
rescale_fiji_inputs 12.872 0.553 14.244
spe_to_seurat 11.726 0.167 13.771
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [131s/135s]
[131s/135s] 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/3501/d2297f04b056eaa942ec9f004aa5b023cf3c2a61/visiumStitched.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('visiumStitched_0.99.8.tar.gz')
===============================
── Installing visiumStitched ───────────────────────────────────────────────────
✔ Package installed successfully
── visiumStitched session metadata ─────────────────────────────────────────────
→ sourceDir: /tmp/RtmpGAfmkg/file2f074664a324be/visiumStitched
→ BiocVersion: 3.20
→ Package: visiumStitched
→ PackageVersion: 0.99.8
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3501/d2297f04b056eaa942ec9f004aa5b023cf3c2a61/visiumStitched.BiocCheck
→ BiocCheckVersion: 1.41.16
→ sourceDir: /tmp/RtmpGAfmkg/file2f074664a324be/visiumStitched
→ installDir: /tmp/RtmpGAfmkg/file2f0746572ae4d9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on visiumStitched ─────────────────────────────────────────
* 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 N: Consider adding these automatically suggested biocViews: Clustering,
SingleCell, ImmunoOncology
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...
i Bioconductor dependencies found in Imports & Depends (29%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i N: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/misc.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of visiumStitched...
* Checking coding practice...
i N: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/build_spe.R (line 183, column 17)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i N: The recommended function length is 50 lines or less. There are 8 functions
greater than 50 lines.
The longest 5 functions are:
• prep_fiji_coords() (R/prep_fiji_coords.R): 136 lines
• ...
• rescale_fiji_inputs() (R/rescale_fiji_inputs.R): 89 lines
* Checking man page documentation...
Registered S3 method overwritten by 'imager':
method from
plot.imlist
* 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 N: Consider shorter lines; 167 lines (8%) are > 80 characters long.
First few lines:
• R/add_array_coords.R#L3 #' Given a [SpatialExperiment-class][Spa ...
• ...
• vignettes/visiumStitched.Rmd#L503 ```{r vignetteBiblio, results = "asis", ...
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 v1.41.16 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 5 NOTES
i See the visiumStitched.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.