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This page was generated on 2024-12-04 09:55 -0500 (Wed, 04 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences" 861
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Package 60/216HostnameOS / ArchINSTALLBUILDCHECK
DelayedMatrixStats 1.29.0  (landing page)
Peter Hickey
Snapshot Date: 2024-12-04 06:00 -0500 (Wed, 04 Dec 2024)
git_url: https://git.bioconductor.org/packages/DelayedMatrixStats
git_branch: devel
git_last_commit: bfe5e8b
git_last_commit_date: 2024-10-29 10:23:18 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  


CHECK results for DelayedMatrixStats on teran2

To the developers/maintainers of the DelayedMatrixStats package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: DelayedMatrixStats
Version: 1.29.0
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:DelayedMatrixStats.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings DelayedMatrixStats_1.29.0.tar.gz
StartedAt: 2024-12-04 08:19:30 -0500 (Wed, 04 Dec 2024)
EndedAt: 2024-12-04 08:26:06 -0500 (Wed, 04 Dec 2024)
EllapsedTime: 396.5 seconds
RetCode: 0
Status:   OK  
CheckDir: DelayedMatrixStats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:DelayedMatrixStats.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings DelayedMatrixStats_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/DelayedMatrixStats.Rcheck’
* using R Under development (unstable) (2024-11-14 r87333)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘DelayedMatrixStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DelayedMatrixStats’ version ‘1.29.0’
* 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 ‘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 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/DelayedMatrixStats.Rcheck/00check.log’
for details.


Installation output

DelayedMatrixStats.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL DelayedMatrixStats
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘DelayedMatrixStats’ ...
** 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)

Tests output

DelayedMatrixStats.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(DelayedMatrixStats)
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

The following object is masked from 'package:abind':

    abind

The following object is masked from 'package:base':

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    apply, scale, sweep

> 
> test_check("DelayedMatrixStats")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14108 ]
> 
> proc.time()
   user  system elapsed 
108.657   9.358 118.061 

Example timings

DelayedMatrixStats.Rcheck/DelayedMatrixStats-Ex.timings

nameusersystemelapsed
colAlls0.0650.0000.065
colAnyNAs0.7710.0240.794
colAvgsPerRowSet0.1500.0370.187
colCollapse0.0610.0250.085
colCounts0.0660.0190.085
colCummaxs0.0690.0020.072
colDiffs0.0630.0010.064
colIQRDiffs0.0590.0000.059
colIQRs0.0040.0000.004
colLogSumExps0.0120.0000.011
colMads0.0520.0010.053
colMeans20.0120.0000.012
colMedians0.0090.0010.011
colOrderStats0.0380.0000.039
colProds0.0400.0020.043
colQuantiles0.0130.0000.013
colRanks0.0100.0000.011
colSums20.0070.0000.007
colTabulates0.0760.0140.089
colVars0.0420.0130.054
colWeightedMads0.0020.0010.003
colWeightedMeans0.0220.0090.030
colWeightedMedians0.0100.0060.016
colWeightedVars0.0500.0150.065