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CHECK report for DelayedMatrixStats on veracruz1

This page was generated on 2018-04-12 13:45:58 -0400 (Thu, 12 Apr 2018).

Package 349/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DelayedMatrixStats 1.0.3
Peter Hickey
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/DelayedMatrixStats
Branch: RELEASE_3_6
Last Commit: e29a344
Last Changed Date: 2018-02-13 20:41:40 -0400 (Tue, 13 Feb 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DelayedMatrixStats
Version: 1.0.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DelayedMatrixStats_1.0.3.tar.gz
StartedAt: 2018-04-12 02:41:48 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:50:37 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 528.2 seconds
RetCode: 0
Status:  OK 
CheckDir: DelayedMatrixStats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DelayedMatrixStats_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/DelayedMatrixStats.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.3’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘DelayedArray:::.as_array_or_matrix’
  ‘DelayedArray:::.execute_delayed_ops’
  ‘DelayedArray:::.get_DelayedArray_dim_before_transpose’
  ‘DelayedArray:::.get_DelayedArray_dimnames_before_transpose’
  ‘DelayedArray:::.get_ans_type’
  ‘DelayedArray:::.reduce_array_dimensions’
  ‘DelayedArray:::RleArraySeed’ ‘DelayedArray:::colblock_APPLY’
  ‘DelayedArray:::extract_block’ ‘DelayedArray:::get_Nindex_lengths’
  ‘DelayedArray:::get_Nindex_names_along’
  ‘DelayedArray:::get_max_block_length’
  ‘DelayedArray:::get_max_spacings_for_linear_blocks’
  ‘DelayedArray:::get_verbose_block_processing’
  ‘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 installed files from ‘inst/doc’ ... 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-3.6-bioc/meat/DelayedMatrixStats.Rcheck/00check.log’
for details.



Installation output

DelayedMatrixStats.Rcheck/00install.out

* installing *source* package ‘DelayedMatrixStats’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DelayedMatrixStats)

Tests output

DelayedMatrixStats.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply


Attaching package: 'DelayedMatrixStats'

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

    colAlls, colAnyMissings, colAnyNAs, colAnys, 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, 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

> 
> test_check("DelayedMatrixStats")

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: rhdf5
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 8855 SKIPPED: 0 FAILED: 0
> options(DelayedArray.block.size = 8L)
> test_check("DelayedMatrixStats")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 8855 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
418.040   1.826 426.467 

Example timings

DelayedMatrixStats.Rcheck/DelayedMatrixStats-Ex.timings

nameusersystemelapsed
colAlls0.5280.0140.558
colAnyNAs0.6190.0150.644
colCollapse0.2790.0050.289
colCounts0.3320.0030.336
colCummaxs0.1280.0040.132
colDiffs0.2850.0050.297
colIQRDiffs0.2470.0150.265
colIQRs0.0080.0000.011
colLogSumExps0.0850.0040.091
colMads0.0880.0010.096
colMeans20.0290.0000.029
colMedians0.0280.0010.028
colOrderStats0.0440.0010.044
colProds0.0670.0030.073
colQuantiles0.0290.0000.032
colRanks0.0240.0010.025
colSums20.0260.0010.026
colTabulates0.1260.0010.129
colVars0.0660.0030.072
colWeightedMads0.0050.0000.005
colWeightedMeans0.0530.0010.055
colWeightedMedians0.0230.0000.023
rowAvgsPerColSet0.0290.0010.030