===============================
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_0.99.0.tar.gz’
===============================
BiocCheckGitClone('visiumStitched')
===============================
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3501/visiumStitched_20240812172455/visiumStitched
─ BiocVersion: 3.20
─ Package: visiumStitched
─ PackageVersion: 0.99.0
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3501/visiumStitched_20240812172455/visiumStitched.BiocCheck
─ BiocCheckVersion: 1.41.10
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3501/visiumStitched_20240812172455/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 results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3501/visiumStitched_20240812172455/visiumStitched.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘visiumStitched/DESCRIPTION’ ... OK
* this is package ‘visiumStitched’ 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 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘Seurat:::VisiumV1’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [38s/38s] 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 ... [137s/156s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
build_spe 49.547 2.119 51.641
add_array_coords 16.177 2.460 25.278
spe_to_seurat 14.937 0.619 26.622
prep_fiji_image 9.460 1.296 10.945
prep_fiji_coords 8.639 1.270 9.883
rescale_fiji_inputs 7.659 0.874 8.734
* checking for unstated dependencies in ‘tests’ ... WARNING
'::' or ':::' import not declared from: ‘SingleCellExperiment’
* checking tests ...
Running ‘testthat.R’ [128s/129s]
[128s/129s] 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: 1 WARNING, 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3501/visiumStitched_20240812172455/visiumStitched.Rcheck/00check.log’
for details.
===============================
BiocCheck('visiumStitched_0.99.0.tar.gz')
===============================
* Installing package...
─ sourceDir: /tmp/RtmpNAdvQG/fileea6e7c39e521/visiumStitched
─ BiocVersion: 3.20
─ Package: visiumStitched
─ PackageVersion: 0.99.0
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3501/visiumStitched_20240812172455/visiumStitched.BiocCheck
─ BiocCheckVersion: 1.41.10
─ sourceDir: /tmp/RtmpNAdvQG/fileea6e7c39e521/visiumStitched
─ installDir: /tmp/RtmpNAdvQG/fileea6e3cf2193e
─ isTarBall: TRUE
─ platform: unix
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
Clustering, SingleCell, ImmunoOncology
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...
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...
* NOTE: 'sessionInfo' not found in vignette(s)
* 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...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 8 functions greater than 50 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...
* NOTE: Consider shorter lines; 159 lines (8%) are > 80 characters
long.
See https://contributions.bioconductor.org/r-code.html
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...
Maintainer is registered at support site.
* ERROR: Add package to Watched Tags in your Support Site profile;
visit https://support.bioconductor.org/accounts/edit/profile
─ BiocCheck results ──
2 ERRORS | 0 WARNINGS | 4 NOTES
See the visiumStitched.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir visiumStitched_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘visiumStitched’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (visiumStitched)