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R CMD BUILD
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* checking for file spammR/DESCRIPTION ... OK
* preparing spammR:
* 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
* looking to see if a data/datalist file should be added
* building spammR_0.99.13.tar.gz
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BiocCheckGitClone('spammR')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3879/4f1f9615fc250eb998de1d590e369484d16dae79/spammR
BiocVersion: 3.23
Package: spammR
PackageVersion: 0.99.13
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3879/4f1f9615fc250eb998de1d590e369484d16dae79/spammR.BiocCheck
BiocCheckVersion: 1.47.12
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3879/4f1f9615fc250eb998de1d590e369484d16dae79/spammR
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...
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 v1.47.12 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3879/4f1f9615fc250eb998de1d590e369484d16dae79/spammR.Rcheck
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file spammR/DESCRIPTION ... OK
* this is package spammR version 0.99.13
* 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 spammR 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 ... NOTE
License stub is invalid DCF.
* 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] OK
* checking whether startup messages can be suppressed ... [11s/10s] 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 ... [33s/32s] NOTE
calc_missingness: no visible global function definition for DataFrame
calc_spatial_diff_ex: no visible binding for global variable
adj.P.Val
calc_spatial_diff_ex: no visible binding for global variable logFC
distance_based_analysis: no visible global function definition for
exit
distance_based_analysis: no visible global function definition for
cor
spat_reduce: no visible global function definition for altExp<-
spatial_heatmap: no visible global function definition for is
spatial_heatmap: no visible binding for global variable .
spatial_network: no visible global function definition for is
spatial_network: no visible binding for global variable name
spatial_network: no visible global function definition for cor
spatial_network: no visible binding for global variable feature1
spatial_network: no visible binding for global variable feature2
spatial_network: no visible binding for global variable corval
spatial_network: no visible binding for global variable edges
spatial_network: no visible binding for global variable nodes
Undefined global functions or variables:
. DataFrame adj.P.Val altExp<- cor corval edges exit feature1
feature2 is logFC name nodes
Consider adding
importFrom("methods", "is")
importFrom("stats", "cor")
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 contents of data directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
protMeta.rda 428Kb 303Kb xz
smallPancData.rda 637Kb 527Kb xz
* checking files in vignettes ... OK
* checking examples ... [129s/347s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
retrieve_metaspace_data 73.823 4.733 296.954
enrich_gradient 19.883 0.141 20.013
enrich_ora 6.067 0.008 6.076
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [43s/43s]
[43s/43s] 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: 1 WARNING, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3879/4f1f9615fc250eb998de1d590e369484d16dae79/spammR.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('spammR_0.99.13.tar.gz')
===============================
Installing spammR
Package installed successfully
spammR session metadata
sourceDir: /tmp/RtmpVlbpGK/file2bff69595f3f60/spammR
BiocVersion: 3.23
Package: spammR
PackageVersion: 0.99.13
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3879/4f1f9615fc250eb998de1d590e369484d16dae79/spammR.BiocCheck
BiocCheckVersion: 1.47.12
sourceDir: /tmp/RtmpVlbpGK/file2bff69595f3f60/spammR
installDir: /tmp/RtmpVlbpGK/file2bff696857727
isTarBall: TRUE
platform: unix
Running BiocCheck on spammR
* 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...
i NOTE: Update R version dependency from 4.5.0 to 4.6.0
* 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: Sequencing,
Transcriptomics, Coverage, SingleCell, ImmunoOncology, DataImport
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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (27%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
spatMicrobiome.Rmd
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/lipidProt.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of spammR...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
convert_to_spe.R (line 168, column 27)
...
impute_spe.R (line 199, column 42)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/spat_reduce.R (line 43, column 13)
...
R/spatial_heatmap.R (line 156, column 11)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/spatial_network.R (line 84, column 15)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/convert_to_spe.R (line 94, column 12)
R/distance_based_analysis.R (line 109, column 19)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
The longest 5 functions are:
spatial_heatmap() (R/spatial_heatmap.R): 200 lines
...
calc_spatial_diff_ex() (R/calc_spatial_diff_ex.R): 79 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
spat_reduce.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; 4 lines (0%) are > 80 characters long.
First few lines:
vignettes/lipidProt.Rmd#L290 lvs <- sort(apply(assay(mspe,'lipids'),1 ...
...
vignettes/spatProt.Rmd#L458 ##correlation analysis can be slow, so l ...
i NOTE: Consider multiples of 4 spaces for line indents; 667 lines (21%) are
not.
First few lines:
R/calc_centers.R#L33 spatial_coo ...
...
vignettes/spatProt.Rmd#L478 geom_node_label(aes(label = name)) ...
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 v1.47.12 results
0 ERRORS | 0 WARNINGS | i 14 NOTES
i See the spammR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.