lconway Summary
[top]
| Package: CatsCradle |
| Version: 0.99.8 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CatsCradle |
| BuildTime: 6 minutes 30.57 seconds |
| CheckCommand: BiocCheckGitClone('CatsCradle') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3452/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/CatsCradle.install-out.txt CatsCradle_0.99.8.tar.gz && BiocCheck('CatsCradle_0.99.8.tar.gz', `new-package`=TRUE) |
| CheckTime: 9 minutes 8.58 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh CatsCradle_0.99.8.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 29.87 seconds |
| PackageFileSize: 6865.76 KiB |
| BuildID:: CatsCradle_20240724100849 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: CatsCradle. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* 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
* building ‘CatsCradle_0.99.8.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('CatsCradle')
===============================
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/CatsCradle
─ BiocVersion: 3.20
─ Package: CatsCradle
─ PackageVersion: 0.99.8
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/CatsCradle.BiocCheck
─ BiocCheckVersion: 1.41.7
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/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...
* WARNING: 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 results ──
0 ERRORS | 1 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/CatsCradle.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 ‘CatsCradle/DESCRIPTION’ ... OK
* this is package ‘CatsCradle’ version ‘0.99.8’
* 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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘Rfast::transpose’ by ‘data.table::transpose’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::nth’ by ‘dplyr::nth’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Seurat::components’ by ‘igraph::components’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::knn’ by ‘igraph::knn’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘CatsCradle’
Warning: replacing previous import ‘SeuratObject::JS’ by ‘networkD3::JS’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::squareform’ by ‘pracma::squareform’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::Rank’ by ‘pracma::Rank’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::sph2cart’ by ‘pracma::sph2cart’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::cart2pol’ by ‘pracma::cart2pol’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::cart2sph’ by ‘pracma::cart2sph’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::polyarea’ by ‘pracma::polyarea’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::Norm’ by ‘pracma::Norm’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::pol2cart’ by ‘pracma::pol2cart’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::dot’ by ‘pracma::dot’ when loading ‘CatsCradle’
Warning: replacing previous import ‘pracma::pdist’ by ‘rdist::pdist’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::melt’ by ‘reshape2::melt’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::dcast’ by ‘reshape2::dcast’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘CatsCradle’
Warning: replacing previous import ‘SingleCellExperiment::weights’ by ‘stats::weights’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘CatsCradle’
Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘CatsCradle’
Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘CatsCradle’
See ‘/Users/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/CatsCradle.Rcheck/00install.out’ for details.
* 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 ... [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 ... [7s/7s] 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 ... NOTE
Namespaces in Imports field not imported from:
‘fossil’ ‘interp’ ‘knitr’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [26s/26s] NOTE
computeEdgeSeurat: warning in
CreateSeuratObject(t(interactionsOnEdgesMat), meta =
interactionsOnEdges[, seq_len(4)]): partial argument match of 'meta'
to 'meta.data'
cellTypesPerCellTypeGraphFromNbhdMatrix: no visible global function
definition for ‘cellTypesPerCellTypeMatrix’
edgeCutoffsByWatershed: no visible global function definition for
‘hist’
edgeLengthPlot: no visible binding for global variable ‘cellTypePair’
edgeLengthPlot: no visible binding for global variable ‘cutoff’
getLigandReceptorNetwork: no visible binding for global variable
‘humanLRN’
getLigandReceptorNetwork: no visible binding for global variable
‘mouseLRN’
getNearestNeighborListsSeurat: no visible global function definition
for ‘as’
make.getExample: no visible binding for global variable ‘S’
make.getExample: no visible binding for global variable ‘smallXenium’
make.getExample: no visible binding for global variable
‘ligandReceptorResults’
make.getExample: no visible binding for global variable ‘moransI’
make.getExample: no visible binding for global variable
‘moransILigandReceptor’
make.getExample: no visible binding for global variable ‘hallmark’
make.getExample: no visible binding for global variable ‘humanLRN’
make.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:
S UMAP_1 UMAP_2 as cellTypePair cellTypesPerCellTypeMatrix cutoff
hallmark hist humanLRN ligandReceptorResults moransI
moransILigandReceptor mouseLRN smallXenium
Consider adding
importFrom("graphics", "hist")
importFrom("methods", "as")
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 ... WARNING
Codoc mismatches from Rd file 'transposeSeuratObject.Rd':
transposeSeuratObject
Code: function(f, active.assay = "RNA", npcs = 30, dims =
seq_len(20), res = 1, returnType = "Seurat")
Docs: function(f, active.assay = "RNA", npcs = 30, dims = 1:20, res =
1, returnType = "Seurat")
Mismatches in argument default values:
Name: 'dims' Code: seq_len(20) Docs: 1:20
* 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 ... [2s/2s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [366s/366s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
computeNBHDVsCTSeurat 40.950 0.194 41.144
predictAnnotationAllGenes 32.381 0.846 33.227
predictAnnotation 29.715 0.404 30.120
aggregateSeuratGeneExpression 21.724 1.340 23.066
computeGraphEmbedding 22.210 0.061 22.271
transposeSeuratObject 11.559 0.099 11.658
randomiseNodeIndices 8.946 0.066 9.013
getSeuratSubsetClusteringStatistics 7.753 0.408 8.160
medianComplementPValue 7.307 0.374 7.681
runGeometricClusteringTrials 7.219 0.376 7.596
getSeuratSubsetClusteringPValue 7.228 0.347 7.574
desymmetriseNN 7.436 0.031 7.468
runMoransI 6.020 1.318 7.338
predictGeneAnnotationImpl 6.235 0.181 6.417
getAverageExpressionMatrix 6.286 0.060 6.347
getAverageExpressionDF 6.290 0.054 6.345
tagRowAndColNames 6.263 0.041 6.304
getNearbyGenes 6.145 0.032 6.178
combinatorialSpheres 6.108 0.063 6.171
getGeneNeighbors 6.123 0.028 6.152
geneSetsVsGeneClustersPValueMatrix 5.896 0.049 5.946
symmetryCheckNN 5.897 0.030 5.927
symmetriseNN 5.867 0.053 5.921
getGeneClusterAveragesPerCell 5.859 0.059 5.918
meanGeneClusterOnCellUMAP 5.688 0.029 5.718
getNearestNeighborListsSeurat 5.628 0.036 5.664
getClusterOrder 5.615 0.040 5.655
collapseExtendedNBHDs 5.348 0.082 5.431
* 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 ... [5s/5s] OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/CatsCradle.Rcheck/00check.log’
for details.
===============================
BiocCheck('CatsCradle_0.99.8.tar.gz')
===============================
* Installing package...
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp5JmTYw/file1491b396261d5/CatsCradle
─ BiocVersion: 3.20
─ Package: CatsCradle
─ PackageVersion: 0.99.8
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/CatsCradle.BiocCheck
─ BiocCheckVersion: 1.41.7
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp5JmTYw/file1491b396261d5/CatsCradle
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp5JmTYw/file1491b6a050461
─ isTarBall: TRUE
─ platform: unix
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.0 to 4.4.0.
* 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...
* 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...
* NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (18%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* 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 CatsCradle...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
Error in seq.default(which(cond) - length(notLookback), which(cond)) :
'from' must be of length 1
Calls: BiocCheck ... Map -> mapply -> <Anonymous> -> FUN -> seq -> seq.default
Execution halted
lconway BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir CatsCradle_0.99.8.tar.gz'
>>>>>>>
* installing *source* package ‘CatsCradle’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Rfast::transpose’ by ‘data.table::transpose’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::nth’ by ‘dplyr::nth’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Seurat::components’ by ‘igraph::components’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::knn’ by ‘igraph::knn’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘CatsCradle’
Warning: replacing previous import ‘SeuratObject::JS’ by ‘networkD3::JS’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::squareform’ by ‘pracma::squareform’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::Rank’ by ‘pracma::Rank’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::sph2cart’ by ‘pracma::sph2cart’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::cart2pol’ by ‘pracma::cart2pol’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::cart2sph’ by ‘pracma::cart2sph’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::polyarea’ by ‘pracma::polyarea’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::Norm’ by ‘pracma::Norm’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::pol2cart’ by ‘pracma::pol2cart’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::dot’ by ‘pracma::dot’ when loading ‘CatsCradle’
Warning: replacing previous import ‘pracma::pdist’ by ‘rdist::pdist’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::melt’ by ‘reshape2::melt’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::dcast’ by ‘reshape2::dcast’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘CatsCradle’
Warning: replacing previous import ‘SingleCellExperiment::weights’ by ‘stats::weights’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘CatsCradle’
Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘CatsCradle’
Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘CatsCradle’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Rfast::transpose’ by ‘data.table::transpose’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::nth’ by ‘dplyr::nth’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Seurat::components’ by ‘igraph::components’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::knn’ by ‘igraph::knn’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘CatsCradle’
Warning: replacing previous import ‘SeuratObject::JS’ by ‘networkD3::JS’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::squareform’ by ‘pracma::squareform’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::Rank’ by ‘pracma::Rank’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::sph2cart’ by ‘pracma::sph2cart’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::cart2pol’ by ‘pracma::cart2pol’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::cart2sph’ by ‘pracma::cart2sph’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::polyarea’ by ‘pracma::polyarea’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::Norm’ by ‘pracma::Norm’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::pol2cart’ by ‘pracma::pol2cart’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::dot’ by ‘pracma::dot’ when loading ‘CatsCradle’
Warning: replacing previous import ‘pracma::pdist’ by ‘rdist::pdist’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::melt’ by ‘reshape2::melt’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::dcast’ by ‘reshape2::dcast’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘CatsCradle’
Warning: replacing previous import ‘SingleCellExperiment::weights’ by ‘stats::weights’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘CatsCradle’
Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘CatsCradle’
Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘CatsCradle’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Rfast::transpose’ by ‘data.table::transpose’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::nth’ by ‘dplyr::nth’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Seurat::components’ by ‘igraph::components’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::knn’ by ‘igraph::knn’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘CatsCradle’
Warning: replacing previous import ‘SeuratObject::JS’ by ‘networkD3::JS’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::squareform’ by ‘pracma::squareform’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::Rank’ by ‘pracma::Rank’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::sph2cart’ by ‘pracma::sph2cart’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::cart2pol’ by ‘pracma::cart2pol’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::cart2sph’ by ‘pracma::cart2sph’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::polyarea’ by ‘pracma::polyarea’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::Norm’ by ‘pracma::Norm’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::pol2cart’ by ‘pracma::pol2cart’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::dot’ by ‘pracma::dot’ when loading ‘CatsCradle’
Warning: replacing previous import ‘pracma::pdist’ by ‘rdist::pdist’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::melt’ by ‘reshape2::melt’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::dcast’ by ‘reshape2::dcast’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘CatsCradle’
Warning: replacing previous import ‘SingleCellExperiment::weights’ by ‘stats::weights’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘CatsCradle’
Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘CatsCradle’
Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘CatsCradle’
** testing if installed package keeps a record of temporary installation path
* DONE (CatsCradle)
nebbiolo2 Summary
[top]
| Package: CatsCradle |
| Version: 0.99.8 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CatsCradle |
| BuildTime: 8 minutes 37.55 seconds |
| CheckCommand: BiocCheckGitClone('CatsCradle') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3452/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/CatsCradle.install-out.txt CatsCradle_0.99.8.tar.gz && BiocCheck('CatsCradle_0.99.8.tar.gz', `new-package`=TRUE) |
| CheckTime: 12 minutes 6.26 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4459.78 KiB |
| BuildID:: CatsCradle_20240724100849 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: CatsCradle. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* 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
* building ‘CatsCradle_0.99.8.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('CatsCradle')
===============================
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/CatsCradle
─ BiocVersion: 3.20
─ Package: CatsCradle
─ PackageVersion: 0.99.8
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/CatsCradle.BiocCheck
─ BiocCheckVersion: 1.41.7
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/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...
* WARNING: 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 results ──
0 ERRORS | 1 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/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 ‘0.99.8’
* 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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘Rfast::transpose’ by ‘data.table::transpose’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::nth’ by ‘dplyr::nth’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Seurat::components’ by ‘igraph::components’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::knn’ by ‘igraph::knn’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘CatsCradle’
Warning: replacing previous import ‘SeuratObject::JS’ by ‘networkD3::JS’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::squareform’ by ‘pracma::squareform’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::Rank’ by ‘pracma::Rank’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::sph2cart’ by ‘pracma::sph2cart’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::cart2pol’ by ‘pracma::cart2pol’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::cart2sph’ by ‘pracma::cart2sph’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::polyarea’ by ‘pracma::polyarea’ when loading ‘CatsCradle’
Warning: replacing previous import ‘Rfast::Norm’ by ‘pracma::Norm’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::pol2cart’ by ‘pracma::pol2cart’ when loading ‘CatsCradle’
Warning: replacing previous import ‘geometry::dot’ by ‘pracma::dot’ when loading ‘CatsCradle’
Warning: replacing previous import ‘pracma::pdist’ by ‘rdist::pdist’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::melt’ by ‘reshape2::melt’ when loading ‘CatsCradle’
Warning: replacing previous import ‘data.table::dcast’ by ‘reshape2::dcast’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘CatsCradle’
Warning: replacing previous import ‘SingleCellExperiment::weights’ by ‘stats::weights’ when loading ‘CatsCradle’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘CatsCradle’
Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘CatsCradle’
Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘CatsCradle’
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/CatsCradle.Rcheck/00install.out’ for details.
* 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 ... [11s/11s] 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/10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘fossil’ ‘interp’ ‘knitr’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [36s/36s] NOTE
computeEdgeSeurat: warning in
CreateSeuratObject(t(interactionsOnEdgesMat), meta =
interactionsOnEdges[, seq_len(4)]): partial argument match of 'meta'
to 'meta.data'
cellTypesPerCellTypeGraphFromNbhdMatrix: no visible global function
definition for ‘cellTypesPerCellTypeMatrix’
edgeCutoffsByWatershed: no visible global function definition for
‘hist’
edgeLengthPlot: no visible binding for global variable ‘cellTypePair’
edgeLengthPlot: no visible binding for global variable ‘cutoff’
getLigandReceptorNetwork: no visible binding for global variable
‘humanLRN’
getLigandReceptorNetwork: no visible binding for global variable
‘mouseLRN’
getNearestNeighborListsSeurat: no visible global function definition
for ‘as’
make.getExample: no visible binding for global variable ‘S’
make.getExample: no visible binding for global variable ‘smallXenium’
make.getExample: no visible binding for global variable
‘ligandReceptorResults’
make.getExample: no visible binding for global variable ‘moransI’
make.getExample: no visible binding for global variable
‘moransILigandReceptor’
make.getExample: no visible binding for global variable ‘hallmark’
make.getExample: no visible binding for global variable ‘humanLRN’
make.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:
S UMAP_1 UMAP_2 as cellTypePair cellTypesPerCellTypeMatrix cutoff
hallmark hist humanLRN ligandReceptorResults moransI
moransILigandReceptor mouseLRN smallXenium
Consider adding
importFrom("graphics", "hist")
importFrom("methods", "as")
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 ... WARNING
Codoc mismatches from Rd file 'transposeSeuratObject.Rd':
transposeSeuratObject
Code: function(f, active.assay = "RNA", npcs = 30, dims =
seq_len(20), res = 1, returnType = "Seurat")
Docs: function(f, active.assay = "RNA", npcs = 30, dims = 1:20, res =
1, returnType = "Seurat")
Mismatches in argument default values:
Name: 'dims' Code: seq_len(20) Docs: 1:20
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [495s/494s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
computeNBHDVsCTSeurat 53.224 0.308 53.533
predictAnnotation 49.841 0.220 50.061
predictAnnotationAllGenes 46.669 0.220 46.889
aggregateSeuratGeneExpression 29.629 0.780 30.263
computeGraphEmbedding 29.070 0.236 29.307
transposeSeuratObject 16.087 0.028 16.116
randomiseNodeIndices 12.252 0.052 12.304
getSeuratSubsetClusteringStatistics 10.247 0.108 10.354
desymmetriseNN 10.157 0.044 10.201
medianComplementPValue 9.716 0.088 9.804
runMoransI 9.568 0.172 9.739
getSeuratSubsetClusteringPValue 9.643 0.096 9.740
runGeometricClusteringTrials 9.618 0.084 9.702
tagRowAndColNames 8.936 0.052 8.988
getAverageExpressionDF 8.578 0.016 8.595
getAverageExpressionMatrix 8.561 0.024 8.585
predictGeneAnnotationImpl 8.341 0.112 8.453
symmetryCheckNN 8.442 0.004 8.447
getNearbyGenes 8.271 0.080 8.351
getGeneNeighbors 8.252 0.024 8.276
combinatorialSpheres 8.196 0.076 8.271
symmetriseNN 8.118 0.004 8.122
geneSetsVsGeneClustersPValueMatrix 7.948 0.052 8.000
collapseExtendedNBHDs 7.936 0.056 7.838
getGeneClusterAveragesPerCell 7.883 0.072 7.955
meanGeneClusterOnCellUMAP 7.589 0.056 7.646
getNearestNeighborListsSeurat 7.543 0.008 7.551
getClusterOrder 7.494 0.024 7.519
* 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: 2 WARNINGs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/CatsCradle.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('CatsCradle_0.99.8.tar.gz')
===============================
* Installing package...
─ sourceDir: /tmp/RtmpWGX527/fileecc367a6261ea/CatsCradle
─ BiocVersion: 3.20
─ Package: CatsCradle
─ PackageVersion: 0.99.8
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3452/5f76e3602ec1042f06597fd5bf248a522200ba9c/CatsCradle.BiocCheck
─ BiocCheckVersion: 1.41.7
─ sourceDir: /tmp/RtmpWGX527/fileecc367a6261ea/CatsCradle
─ installDir: /tmp/RtmpWGX527/fileecc363399ff9f
─ isTarBall: TRUE
─ platform: unix
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.0 to 4.4.0.
* 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...
* 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...
* NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (18%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* 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 CatsCradle...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
Error in seq.default(which(cond) - length(notLookback), which(cond)) :
'from' must be of length 1
Calls: BiocCheck ... Map -> mapply -> <Anonymous> -> FUN -> seq -> seq.default
Execution halted
nebbiolo2 BUILD BIN output
[top]