Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/CatsCradle
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo2 Linux (Ubuntu 22.04.3 LTS)/x86_64   OK     ERROR     skipped     OK  
lconway macOS 12.7.1 Monterey/x86_64   OK     ERROR     WARNINGS     OK  

nebbiolo2 Summary

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Package: CatsCradle
Version: 0.99.1
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: 9 minutes 7.98 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/CatsCradle_20240701143253/CatsCradle.install-out.txt CatsCradle_0.99.1.tar.gz && BiocCheck('CatsCradle_0.99.1.tar.gz', `new-package`=TRUE)
CheckTime: 10 minutes 49.51 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 25665.61 KiB
BuildID:: CatsCradle_20240701143253
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

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===============================

 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_0.99.1.tar.gz’


nebbiolo2 CHECK output

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===============================

 BiocCheckGitClone('CatsCradle')

===============================

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: CatsCradle
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3452/CatsCradle_20240701143253/CatsCradle
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* 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/CatsCradle_20240701143253/CatsCradle.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 ‘0.99.1’
* 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/CatsCradle_20240701143253/CatsCradle.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data  13.0Mb
* 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 ... [35s/35s] NOTE
computeEdgeSeurat: warning in
  CreateSeuratObject(t(interactionsOnEdgesMat), meta =
  interactionsOnEdges[, 1:4]): 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’
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 as cellTypePair cellTypesPerCellTypeMatrix cutoff hist
  humanLRN mouseLRN
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 ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'edgeCutoffsByClustering.Rd'
  ‘annEdges’

Undocumented arguments in Rd file 'edgeCutoffsByPercentile.Rd'
  ‘percentileCutoff’
Documented arguments not in \usage in Rd file 'edgeCutoffsByPercentile.Rd':
  ‘percentileCutof’

Undocumented arguments in Rd file 'edgeCutoffsByZScore.Rd'
  ‘zCutoff’
Documented arguments not in \usage in Rd file 'edgeCutoffsByZScore.Rd':
  ‘zCutof’

Undocumented arguments in Rd file 'edgeLengthPlot.Rd'
  ‘xLim’
Documented arguments not in \usage in Rd file 'edgeLengthPlot.Rd':
  ‘xlim’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [15s/15s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [388s/387s] OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
computeNBHDVsCTSeurat         53.632  0.356  53.987
getAverageExpressionMatrix    45.807  0.268  46.075
predictAnnotation             41.168  0.164  41.332
getGeneClusterAveragesPerCell 40.734  0.180  40.914
predictAnnotationAllGenes     39.665  0.152  39.816
transposeSeuratObject         28.403  0.208  28.612
aggregateSeuratGeneExpression 26.213  1.044  27.257
runMoransI                     9.407  0.128   9.535
collapseExtendedNBHDs          7.056  0.096   7.152
* 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] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
* checking PDF version of manual without index ... ERROR
* DONE

Status: 1 ERROR, 3 WARNINGs, 4 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3452/CatsCradle_20240701143253/CatsCradle.Rcheck/00check.log’
for details.

 WARNING: R CMD check exceeded 10 min requirement






===============================

 BiocCheck('CatsCradle_0.99.1.tar.gz')

===============================

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: CatsCradle
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/RtmpjaLKdw/file36d45168fa0fc1/CatsCradle
─ installDir: /tmp/RtmpjaLKdw/file36d451496f9144
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3452/CatsCradle_20240701143253/CatsCradle.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* 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...
    * ERROR: Package tarball exceeds the Bioconductor size requirement.
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * NOTE: The Description field in the DESCRIPTION is made up of less
      than 3 sentences. Provide a more detailed description of the
      package.
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* 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 1:...; use seq_len() or seq_along()
    * 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
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking parsed R code in R directory, examples, vignettes...
    Found @ in vignettes/CatsCradleQuickStart.Rmd
    Found @ in vignettes/CatsCradleSpatial.Rmd
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 5 functions greater than 50 lines.
* Checking man page documentation...
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’
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
    * NOTE: 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...
    * NOTE: Consider shorter lines; 89 lines (2%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 566 lines
      (11%) are not.
    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...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package is in the Support Site Watched Tags.

─ BiocCheck results ──
1 ERRORS | 2 WARNINGS | 17 NOTES

See the CatsCradle.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

nebbiolo2 BUILD BIN output

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lconway Summary

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Package: CatsCradle
Version: 0.99.1
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 49.10 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/CatsCradle_20240701143253/CatsCradle.install-out.txt CatsCradle_0.99.1.tar.gz && BiocCheck('CatsCradle_0.99.1.tar.gz', `new-package`=TRUE)
CheckTime: 7 minutes 54.71 seconds
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh CatsCradle_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir
BuildBinTime: 1 minutes 12.44 seconds
PackageFileSize: 27875.36 KiB
BuildID:: CatsCradle_20240701143253
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

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===============================

 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_0.99.1.tar.gz’


lconway CHECK output

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===============================

 BiocCheckGitClone('CatsCradle')

===============================

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: CatsCradle
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3452/CatsCradle_20240701143253/CatsCradle
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* 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/CatsCradle_20240701143253/CatsCradle.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* 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 ‘0.99.1’
* 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/CatsCradle_20240701143253/CatsCradle.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data  13.1Mb
* 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 ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] 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/27s] NOTE
computeEdgeSeurat: warning in
  CreateSeuratObject(t(interactionsOnEdgesMat), meta =
  interactionsOnEdges[, 1:4]): 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’
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 as cellTypePair cellTypesPerCellTypeMatrix cutoff hist
  humanLRN mouseLRN
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 ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'edgeCutoffsByClustering.Rd'
  ‘annEdges’

Undocumented arguments in Rd file 'edgeCutoffsByPercentile.Rd'
  ‘percentileCutoff’
Documented arguments not in \usage in Rd file 'edgeCutoffsByPercentile.Rd':
  ‘percentileCutof’

Undocumented arguments in Rd file 'edgeCutoffsByZScore.Rd'
  ‘zCutoff’
Documented arguments not in \usage in Rd file 'edgeCutoffsByZScore.Rd':
  ‘zCutof’

Undocumented arguments in Rd file 'edgeLengthPlot.Rd'
  ‘xLim’
Documented arguments not in \usage in Rd file 'edgeLengthPlot.Rd':
  ‘xlim’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [11s/11s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [269s/269s] OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
computeNBHDVsCTSeurat         40.545  0.084  40.632
predictAnnotationAllGenes     26.886  1.073  27.959
getAverageExpressionMatrix    26.148  0.135  26.283
predictAnnotation             23.001  0.260  23.261
getGeneClusterAveragesPerCell 22.775  0.133  22.907
transposeSeuratObject         20.959  0.323  21.282
aggregateSeuratGeneExpression 17.994  2.115  20.109
runMoransI                     6.329  1.187   7.516
* 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 ... [6s/7s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
* checking PDF version of manual without index ... ERROR
* DONE

Status: 1 ERROR, 3 WARNINGs, 4 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3452/CatsCradle_20240701143253/CatsCradle.Rcheck/00check.log’
for details.





===============================

 BiocCheck('CatsCradle_0.99.1.tar.gz')

===============================

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: CatsCradle
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpI02Wb1/file167bb1bc6bf4f/CatsCradle
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpI02Wb1/file167bbd23545b
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3452/CatsCradle_20240701143253/CatsCradle.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* 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...
    * ERROR: Package tarball exceeds the Bioconductor size requirement.
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * NOTE: The Description field in the DESCRIPTION is made up of less
      than 3 sentences. Provide a more detailed description of the
      package.
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* 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 1:...; use seq_len() or seq_along()
    * 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
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking parsed R code in R directory, examples, vignettes...
    Found @ in vignettes/CatsCradleQuickStart.Rmd
    Found @ in vignettes/CatsCradleSpatial.Rmd
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 5 functions greater than 50 lines.
* Checking man page documentation...
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’
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
    * NOTE: 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...
    * NOTE: Consider shorter lines; 89 lines (2%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 566 lines
      (11%) are not.
    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...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package is in the Support Site Watched Tags.

─ BiocCheck results ──
1 ERRORS | 2 WARNINGS | 17 NOTES

See the CatsCradle.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

lconway BUILD BIN output

[top]

===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir CatsCradle_0.99.1.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)