##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no DelayedMatrixStats_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/DelayedMatrixStats.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘DelayedMatrixStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DelayedMatrixStats’ version ‘1.30.0’
* 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 ‘DelayedMatrixStats’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Missing object imported by a ':::' call: ‘DelayedArray:::.reduce_array_dimensions’
Unexported objects imported by ':::' calls:
  ‘DelayedArray:::.get_ans_type’ ‘DelayedArray:::BLOCK_colVars’
  ‘DelayedArray:::BLOCK_rowVars’ ‘DelayedArray:::RleArraySeed’
  ‘DelayedArray:::get_Nindex_lengths’ ‘DelayedArray:::set_dim’
  ‘DelayedArray:::set_dimnames’ ‘DelayedArray:::subset_by_Nindex’
  ‘DelayedArray:::to_linear_index’
  See the note in ?`:::` about the use of this operator.
* 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:
  colAlls.Rd: DelayedMatrix-class
  colAnyNAs.Rd: DelayedMatrix-class
  colAvgsPerRowSet.Rd: DelayedMatrix-class
  colCollapse.Rd: DelayedMatrix-class
  colCounts.Rd: DelayedMatrix-class
  colCummaxs.Rd: DelayedMatrix-class
  colDiffs.Rd: DelayedMatrix-class
  colIQRDiffs.Rd: DelayedMatrix-class
  colIQRs.Rd: DelayedMatrix-class
  colLogSumExps.Rd: DelayedMatrix-class
  colMads.Rd: DelayedMatrix-class
  colMeans2.Rd: DelayedMatrix-class
  colMedians.Rd: DelayedMatrix-class
  colOrderStats.Rd: DelayedMatrix-class
  colProds.Rd: DelayedMatrix-class
  colQuantiles.Rd: DelayedMatrix-class
  colRanks.Rd: DelayedMatrix-class
  colSums2.Rd: DelayedMatrix-class
  colTabulates.Rd: DelayedMatrix-class
  colVars.Rd: DelayedMatrix-class
  colWeightedMads.Rd: DelayedMatrix-class
  colWeightedMeans.Rd: DelayedMatrix-class
  colWeightedMedians.Rd: DelayedMatrix-class
  colWeightedVars.Rd: DelayedMatrix-class
  from_DelayedArray_to_simple_seed_class.Rd: DelayedArray-class
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 ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/DelayedMatrixStats.Rcheck/00check.log’
for details.

* installing *source* package ‘DelayedMatrixStats’ ...
** this is package ‘DelayedMatrixStats’ version ‘1.30.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DelayedMatrixStats)