===============================
R CMD BUILD
===============================
* checking for file ‘SpatialExperimentIO/DESCRIPTION’ ... OK
* preparing ‘SpatialExperimentIO’:
* 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
* building ‘SpatialExperimentIO_0.99.3.tar.gz’
===============================
BiocCheckGitClone('SpatialExperimentIO')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3370/2a7b2fea0536bca12e98ddbd5dcc0f94da1b1e82/SpatialExperimentIO
→ BiocVersion: 3.20
→ Package: SpatialExperimentIO
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3370/2a7b2fea0536bca12e98ddbd5dcc0f94da1b1e82/SpatialExperimentIO.BiocCheck
→ BiocCheckVersion: 1.41.16
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3370/2a7b2fea0536bca12e98ddbd5dcc0f94da1b1e82/SpatialExperimentIO
→ 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...
i N: (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 v1.41.16 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3370/2a7b2fea0536bca12e98ddbd5dcc0f94da1b1e82/SpatialExperimentIO.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 ‘SpatialExperimentIO/DESCRIPTION’ ... OK
* this is package ‘SpatialExperimentIO’ 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 serialization versions ... OK
* checking whether package ‘SpatialExperimentIO’ 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [24s/24s] NOTE
readCosmxSXE: no visible binding for global variable ‘fov’
readCosmxSXE: no visible binding for global variable ‘cell_ID’
readMerscopeSXE: no visible binding for global variable ‘cell’
readSeqfishSXE: no visible binding for global variable ‘cell’
readStarmapplusSXE: no visible binding for global variable ‘GENE’
Undefined global functions or variables:
GENE cell cell_ID fov
* 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 ... [12s/12s] 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/3370/2a7b2fea0536bca12e98ddbd5dcc0f94da1b1e82/SpatialExperimentIO.Rcheck/00check.log’
for details.
===============================
BiocCheck('SpatialExperimentIO_0.99.3.tar.gz')
===============================
── Installing SpatialExperimentIO ──────────────────────────────────────────────
✔ Package installed successfully
── SpatialExperimentIO session metadata ────────────────────────────────────────
→ sourceDir: /tmp/RtmpD6XbK1/file34048e2543db4e/SpatialExperimentIO
→ BiocVersion: 3.20
→ Package: SpatialExperimentIO
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3370/2a7b2fea0536bca12e98ddbd5dcc0f94da1b1e82/SpatialExperimentIO.BiocCheck
→ BiocCheckVersion: 1.41.16
→ sourceDir: /tmp/RtmpD6XbK1/file34048e2543db4e/SpatialExperimentIO
→ installDir: /tmp/RtmpD6XbK1/file34048e2addb918
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SpatialExperimentIO ────────────────────────────────────
* 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 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 (60%).
* Checking for pinned package versions in DESCRIPTION...
* 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 SpatialExperimentIO...
* Checking coding practice...
* 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 5 functions
greater than 50 lines.
The longest 5 functions are:
• readXeniumSXE() (R/readXeniumSXE.R): 77 lines
• ...
• readCosmxSXE() (R/readCosmxSXE.R): 64 lines
* Checking man page documentation...
i N: Usage of dontrun / donttest tags found in man page examples. 20% of man
pages use at least one of these tags.
Found in files:
• readXeniumSXE.Rd
i N: Use donttest instead of dontrun.
Found in files:
• readXeniumSXE.Rd
* 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; 106 lines (11%) are > 80 characters long.
First few lines:
• R/readCosmxSXE.R#L6 #' Creates a \code{\link{SpatialExperime ...
• ...
• vignettes/SpatialExperimentIO.Rmd#L338 So far, publicly available seqFISH
data ...
i N: Consider multiples of 4 spaces for line indents; 271 lines (27%) are not.
First few lines:
• R/readCosmxSXE.R#L58 returnType = "S ...
• ...
• vignettes/SpatialExperimentIO.Rmd#L309 package = "SpatialExperimentIO") ...
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 SpatialExperimentIO.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.