===============================
R CMD BUILD
===============================
* checking for file ‘panoramic/DESCRIPTION’ ... OK
* preparing ‘panoramic’:
* 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 ‘panoramic_0.99.3.tar.gz’
===============================
BiocCheckGitClone('panoramic')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4039/ca3f3cacb6ccdaca6b0052bea79e83f47773b813/panoramic
→ BiocVersion: 3.23
→ Package: panoramic
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4039/ca3f3cacb6ccdaca6b0052bea79e83f47773b813/panoramic.BiocCheck
→ BiocCheckVersion: 1.47.25
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4039/ca3f3cacb6ccdaca6b0052bea79e83f47773b813/panoramic
→ 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...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.47.25 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4039/ca3f3cacb6ccdaca6b0052bea79e83f47773b813/panoramic.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-21 06:32:00 UTC
* using option ‘--no-vignettes’
* checking for file ‘panoramic/DESCRIPTION’ ... OK
* this is package ‘panoramic’ version ‘0.99.3’
* 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 ‘panoramic’ 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 ... [7s/7s] 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’ ... OK
* checking examples ... [26s/26s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
create_spatial_network 6.995 0.273 7.27
* 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 ... [4s/4s] OK
* DONE
Status: OK
===============================
BiocCheck('panoramic_0.99.3.tar.gz')
===============================
── Installing panoramic ────────────────────────────────────────────────────────
✔ Package installed successfully
── panoramic session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4Z2bWg/file33506578b241f1/panoramic
→ BiocVersion: 3.23
→ Package: panoramic
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4039/ca3f3cacb6ccdaca6b0052bea79e83f47773b813/panoramic.BiocCheck
→ BiocCheckVersion: 1.47.25
→ sourceDir: /tmp/Rtmp4Z2bWg/file33506578b241f1/panoramic
→ installDir: /tmp/Rtmp4Z2bWg/file3350657249399
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on panoramic ──────────────────────────────────────────────
* 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:
CellBasedAssays, Network, Clustering, GraphAndNetwork
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 (22%).
* 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 panoramic...
* Checking coding practice...
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/panoramic-spatialstats.R (line 191, column 11)
• ...
• R/panoramic-spatialstats.R (line 695, column 7)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
• suppressWarnings() in R/panoramic-spatialstats.R (line 205, column 9)
• suppressWarnings() in R/panoramic-spatialstats.R (line 785, column 3)
• suppressWarnings() in R/panoramic-visualization.R (line 101, column 20)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 20
functions greater than 50 lines.
The longest 5 functions are:
• panoramic_meta_mv() (R/panoramic-meta-mv.R): 364 lines
• ...
• fit_one() (R/panoramic-meta-mv.R): 196 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...
i NOTE: Consider shorter lines; 141 lines (3%) are > 80 characters long.
First few lines:
• R/panoramic_prepare.R#L3 #' Mainly used for convex spatial window ...
• ...
• vignettes/tutorial.Rmd#L153 # In real data, patient_col can differ f ...
i NOTE: Consider multiples of 4 spaces for line indents; 1539 lines (37%) are
not.
First few lines:
• R/panoramic_prepare.R#L9 if (!is.matrix(coords)) coords <- as.m ...
• ...
• vignettes/tutorial.Rmd#L238 node_size_by = "degree" ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 504 Gateway
Timeout.
── BiocCheck v1.47.25 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 6 NOTES
i See the panoramic.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.