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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:velociraptor.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings velociraptor_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/velociraptor.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘velociraptor/DESCRIPTION’ ... OK
* this is package ‘velociraptor’ version ‘1.17.0’
* 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 ‘velociraptor’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/velociraptor.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘basilisk.utils’
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.make_np_friendly’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  embedVelocity.Rd: SingleCellExperiment-class, reducedDims
  gridVectors.Rd: SingleCellExperiment-class, reducedDims
  plotVelocity.Rd: SingleCellExperiment-class, reducedDims
  plotVelocityStream.Rd: SingleCellExperiment-class, reducedDims
  scvelo.Rd: SummarizedExperiment-class, librarySizeFactors,
    BiocParallelParam-class, BiocSingularParam-class, reducedDims,
    normalizeCounts, SingleCellExperiment-class, colData, assays
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... WARNING
'::' or ':::' import not declared from: ‘basilisk.utils’
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
embedVelocity      24.638  5.394  34.223
plotVelocity        8.429  1.131   7.567
scvelo              4.365  1.124   4.691
plotVelocityStream  4.375  0.706   3.405
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/velociraptor.Rcheck/00check.log’
for details.