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R CMD BUILD
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* checking for file spatialFDA/DESCRIPTION ... OK
* preparing spatialFDA:
* 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 spatialFDA_0.99.2.tar.gz
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BiocCheckGitClone('spatialFDA')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3585/f31e11874d347fb5daac8de05229e231793c53c4/spatialFDA
BiocVersion: 3.21
Package: spatialFDA
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3585/f31e11874d347fb5daac8de05229e231793c53c4/spatialFDA.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3585/f31e11874d347fb5daac8de05229e231793c53c4/spatialFDA
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 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 v1.43.2 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
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R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3585/f31e11874d347fb5daac8de05229e231793c53c4/spatialFDA.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file spatialFDA/DESCRIPTION ... OK
* this is package spatialFDA version 0.99.2
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 spatialFDA 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 ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [23s/23s] 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 ... [187s/190s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calcCrossMetricPerFov 34.961 2.870 38.215
plotCrossMetricPerFov 26.972 0.616 27.848
plotMdl 13.512 1.005 14.746
functionalGam 12.679 0.908 13.820
print.fpca 7.939 0.346 8.516
plotFpca 7.303 0.436 8.042
functionalPCA 7.146 0.482 7.857
dot-speToDf 6.925 0.439 7.589
prepData 6.743 0.378 7.355
dot-dfToppp 6.336 0.445 7.008
plotMetricPerFov 6.173 0.323 6.758
calcMetricPerFov 5.918 0.477 6.630
dot-extractMetric 5.867 0.358 6.453
plotFbPlot 5.744 0.277 6.252
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [96s/97s]
[96s/97s] 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 ... [3s/3s] OK
* DONE
Status: OK
WARNING: R CMD check exceeded 10 min requirement
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BiocCheck('spatialFDA_0.99.2.tar.gz')
===============================
Installing spatialFDA
Package installed successfully
spatialFDA session metadata
sourceDir: /tmp/Rtmpc1f1qN/file3ca613165fd902/spatialFDA
BiocVersion: 3.21
Package: spatialFDA
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3585/f31e11874d347fb5daac8de05229e231793c53c4/spatialFDA.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/Rtmpc1f1qN/file3ca613165fd902/spatialFDA
installDir: /tmp/Rtmpc1f1qN/file3ca6131b86931d
isTarBall: TRUE
platform: unix
Running BiocCheck on spatialFDA
* 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:
PrincipalComponent
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 (13%).
* 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 spatialFDA...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/calcMetric.R (line 70, column 17)
...
print() in R/calcMetric.R (line 261, column 13)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/calcMetric.R (line 178, column 12)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
The longest 5 functions are:
.extractMetric() (R/calcMetric.R): 99 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
plotCrossFOV.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 NOTE: Consider shorter lines; 40 lines (3%) are > 80 characters long.
First few lines:
R/calcMetric.R#L56 # fov and more than one unique mark ...
...
vignettes/DiabetesIsletExample.Rmd#L376 We note that there is still some
structu ...
i NOTE: Consider multiples of 4 spaces for line indents; 60 lines (4%) are not.
First few lines:
R/calcMetric.R#L78 r = rSeq, ...
...
vignettes/DiabetesIsletExample.Rmd#L371 xlab("r [m]") ...
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 v1.43.2 results
0 ERRORS | 0 WARNINGS | i 7 NOTES
i See the spatialFDA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.