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R CMD BUILD
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* checking for file ‘CatsCradle/DESCRIPTION’ ... OK
* preparing ‘CatsCradle’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘CatsCradle_0.99.13.tar.gz’
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BiocCheckGitClone('CatsCradle')
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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3452/b87f7f45fbd61e93621a8abfc0615eb17f81d26d/CatsCradle
→ BiocVersion: 3.20
→ Package: CatsCradle
→ PackageVersion: 0.99.13
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3452/b87f7f45fbd61e93621a8abfc0615eb17f81d26d/CatsCradle.BiocCheck
→ BiocCheckVersion: 1.41.16
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3452/b87f7f45fbd61e93621a8abfc0615eb17f81d26d/CatsCradle
→ 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...
! W: The 'doi' argument is missing or empty in the CITATION's 'bibentry()'.
Only include a CITATION file if there is a preprint or publication associated
with this Bioconductor package.
── BiocCheck v1.41.16 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | • 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3452/b87f7f45fbd61e93621a8abfc0615eb17f81d26d/CatsCradle.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 ‘CatsCradle/DESCRIPTION’ ... OK
* this is package ‘CatsCradle’ 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 ‘CatsCradle’ 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 ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [40s/40s] NOTE
edgeLengthPlot: no visible binding for global variable ‘cellTypePair’
edgeLengthPlot: no visible binding for global variable ‘cutoff’
make.getExample : getExample: no visible binding for global variable
‘moransI’
make.getExample : getExample: no visible binding for global variable
‘moransILigandReceptor’
make.getExample : getExample: no visible binding for global variable
‘humanLRN’
make.getExample : getExample: no visible binding for global variable
‘mouseLRN’
meanGeneClusterOnCellUMAP: no visible binding for global variable
‘UMAP_1’
meanGeneClusterOnCellUMAP: no visible binding for global variable
‘UMAP_2’
Undefined global functions or variables:
UMAP_1 UMAP_2 cellTypePair cutoff humanLRN moransI
moransILigandReceptor mouseLRN
* 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 ... [3s/3s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [523s/522s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
computeNBHDVsCTObject 66.824 0.388 67.217
predictAnnotationAllGenes 51.652 0.136 51.789
aggregateGeneExpression 32.531 0.856 33.239
computeGraphEmbedding 30.409 0.156 30.566
transposeObject 17.197 0.124 17.321
randomiseNodeIndices 12.860 0.096 12.957
runMoransI 12.691 0.116 12.808
getObjectSubsetClusteringPValue 11.574 0.052 11.625
predictAnnotation 11.468 0.056 11.524
desymmetriseNN 11.420 0.084 11.504
runGeometricClusteringTrials 11.190 0.160 11.350
medianComplementPValue 11.081 0.112 11.193
getObjectSubsetClusteringStatistics 10.835 0.044 10.879
getAverageExpressionDF 9.656 0.064 9.720
getNearbyGenes 9.643 0.012 9.655
getGeneNeighbors 9.554 0.048 9.603
getAverageExpressionMatrix 9.527 0.064 9.592
tagRowAndColNames 9.380 0.108 9.488
combinatorialSpheres 9.255 0.048 9.303
predictGeneAnnotationImpl 9.162 0.048 9.210
symmetriseNN 9.068 0.060 9.128
getGeneClusterAveragesPerCell 8.927 0.012 8.939
symmetryCheckNN 8.768 0.076 8.844
geneSetsVsGeneClustersPValueMatrix 8.786 0.024 8.810
meanGeneClusterOnCellUMAP 8.668 0.084 8.752
collapseExtendedNBHDs 8.572 0.136 8.536
getNearestNeighbourLists 8.552 0.060 8.612
getClusterOrder 8.534 0.000 8.534
* 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 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3452/b87f7f45fbd61e93621a8abfc0615eb17f81d26d/CatsCradle.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('CatsCradle_0.99.13.tar.gz')
===============================
── Installing CatsCradle ───────────────────────────────────────────────────────
✔ Package installed successfully
── CatsCradle session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpKwwLZw/file1baae11570bc0/CatsCradle
→ BiocVersion: 3.20
→ Package: CatsCradle
→ PackageVersion: 0.99.13
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3452/b87f7f45fbd61e93621a8abfc0615eb17f81d26d/CatsCradle.BiocCheck
→ BiocCheckVersion: 1.41.16
→ sourceDir: /tmp/RtmpKwwLZw/file1baae11570bc0/CatsCradle
→ installDir: /tmp/RtmpKwwLZw/file1baae110706e51
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CatsCradle ─────────────────────────────────────────────
* 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 (24%).
* 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 CatsCradle...
* Checking coding practice...
i N: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/CatsCradleNNGraphs.R (line 213, column 5)
i N: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/CatsCradleEdgeQualityControl.R (line 23, column 29)
• ...
• R/CatsCradleNNGraphs.R (line 211, column 9)
i N: Avoid the use of 'paste' in condition signals
Found in files:
• R/CatsCradleExampleServer.R (line 99, column 18)
• R/CatsCradleNNGraphs.R (line 93, column 14)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/CatsCradleQuickStart.Rmd
i Found @ in vignettes/CatsCradleSpatial.Rmd
i N: Use accessors; don't access S4 class slots via '@' in examples/vignettes.
i N: Avoid '<<-' if possible (found 1 times)
• <<- in R/CatsCradleExampleServer.R (line 302, column 34)
* Checking function lengths...
i N: The recommended function length is 50 lines or less. There are 7 functions
greater than 50 lines.
The longest 5 functions are:
• make.getExample() (R/CatsCradleExampleServer.R): 291 lines
• ...
• sankeyFromMatrix() (R/CatsCradleGenesVsCells.R): 60 lines
* Checking man page documentation...
i N: Consider adding runnable examples to man pages that document exported
objects.
• aggregateFeatureMatrix.Rd
• ...
• stripGeneSet.Rd
* Checking package NEWS...
* Checking unit tests...
i N: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i N: Consider shorter lines; 88 lines (1%) are > 80 characters long.
First few lines:
• R/CatsCradleExampleServer.R#L270 answer = computeCellTypesPer ...
• ...
• vignettes/CatsCradleSpatial.Rmd#L661 View ligand-receptor interaction with th
...
i N: Consider 4 spaces instead of tabs; 10 lines (0%) contain tabs.
First few lines:
• vignettes/CatsCradle.Rmd#L186 ``` ...
• ...
• vignettes/CatsCradleSpatial.Rmd#L458 clusteringName='neighbourhood_clu ...
i N: Consider multiples of 4 spaces for line indents; 530 lines (9%) are not.
First few lines:
• R/CatsCradleEdgeQualityControl.R#L117 perce ...
• ...
• vignettes/CatsCradleSpatial.Rmd#L641 layer = "counts", n ...
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...
✖ E: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.41.16 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | • 11 NOTES
i See the CatsCradle.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.