Package: DelayedMatrixStats

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DelayedMatrixStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DelayedMatrixStats_1.9.0.tar.gz

StartedAt: 2020-01-16 03:37:29 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 04:00:38 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 1389.1 seconds

RetCode: 0

Status:  OK

CheckDir: DelayedMatrixStats.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DelayedMatrixStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DelayedMatrixStats_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/DelayedMatrixStats.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DelayedMatrixStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DelayedMatrixStats’ version ‘1.9.0’
* 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 R 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocParallel’ ‘HDF5Array’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘DelayedArray:::.get_ans_type’
  ‘DelayedArray:::.reduce_array_dimensions’
  ‘DelayedArray:::RleArraySeed’ ‘DelayedArray:::colblock_APPLY’
  ‘DelayedArray:::get_Nindex_lengths’
  ‘DelayedArray:::get_verbose_block_processing’
  ‘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 ... OK
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/DelayedMatrixStats.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DelayedMatrixStats
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘DelayedMatrixStats’ ...
** using staged installation
** R
** 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)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum


Attaching package: 'DelayedMatrixStats'

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

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

> 
> test_check("DelayedMatrixStats")
Loading required package: rhdf5
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 15084 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> setAutoBlockSize(8)
automatic block size set to 8 bytes (was 1e+08)
> test_check("DelayedMatrixStats")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 15080 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
    user   system  elapsed 
1293.636  426.653 1207.443 

name	user	system	elapsed
colAlls	0.095	0.003	0.098
colAnyNAs	0.685	0.076	0.762
colAvgsPerRowSet	0.352	0.017	0.369
colCollapse	0.284	0.033	0.317
colCounts	0.215	0.002	0.217
colCummaxs	0.240	0.009	0.251
colDiffs	0.169	0.011	0.181
colIQRDiffs	0.255	0.003	0.258
colIQRs	0.009	0.000	0.010
colLogSumExps	0.040	0.000	0.041
colMads	0.180	0.001	0.181
colMeans2	0.040	0.001	0.040
colMedians	0.036	0.000	0.037
colOrderStats	0.077	0.005	0.083
colProds	0.089	0.009	0.097
colQuantiles	0.042	0.001	0.043
colRanks	0.031	0.001	0.033
colSums2	0.030	0.001	0.031
colTabulates	0.389	0.005	0.394
colVars	0.107	0.008	0.114
colWeightedMads	0.005	0.001	0.007
colWeightedMeans	0.075	0.000	0.076
colWeightedMedians	0.021	0.000	0.021
colWeightedVars	0.140	0.002	0.142