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CHECK report for MatrixGenerics on merida1

This page was generated on 2021-05-06 12:35:36 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MatrixGenerics package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1011/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MatrixGenerics 1.2.1  (landing page)
Peter Hickey
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MatrixGenerics
Branch: RELEASE_3_12
Last Commit: abcc9ca
Last Changed Date: 2021-01-29 00:12:47 -0400 (Fri, 29 Jan 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: MatrixGenerics
Version: 1.2.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MatrixGenerics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MatrixGenerics_1.2.1.tar.gz
StartedAt: 2021-05-06 03:19:11 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:19:46 -0400 (Thu, 06 May 2021)
EllapsedTime: 34.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MatrixGenerics.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MatrixGenerics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MatrixGenerics_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/MatrixGenerics.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MatrixGenerics/DESCRIPTION’ ... OK
* this is package ‘MatrixGenerics’ version ‘1.2.1’
* 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 ‘MatrixGenerics’ 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 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
Unexported objects imported by ':::' calls:
  ‘methods:::fromNextMethod’ ‘methods:::getGenericFromCall’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.load_next_suggested_package_to_search’
* 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 examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/MatrixGenerics.Rcheck/00check.log’
for details.



Installation output

MatrixGenerics.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MatrixGenerics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘MatrixGenerics’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (MatrixGenerics)

Tests output

MatrixGenerics.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(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

> 
> test_check("MatrixGenerics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 310 ]
> 
> proc.time()
   user  system elapsed 
  1.761   0.131   1.870 

Example timings

MatrixGenerics.Rcheck/MatrixGenerics-Ex.timings

nameusersystemelapsed
rowAlls0.0030.0010.004
rowAnyNAs0.0010.0010.002
rowAnys0.0020.0010.003
rowAvgsPerColSet0.0040.0010.005
rowCollapse0.0010.0010.002
rowCounts0.0020.0010.002
rowCummaxs0.0010.0010.002
rowCummins0.0020.0010.003
rowCumprods0.0020.0010.003
rowCumsums0.0010.0010.002
rowDiffs0.0020.0010.003
rowIQRDiffs0.0040.0010.004
rowIQRs0.0050.0000.007
rowLogSumExps0.0020.0010.002
rowMadDiffs0.0040.0010.005
rowMads0.0020.0010.003
rowMaxs0.0010.0010.002
rowMeans20.0010.0010.003
rowMedians0.0020.0010.003
rowMins0.0010.0010.003
rowOrderStats0.0010.0010.002
rowProds0.0020.0010.002
rowQuantiles0.0070.0010.008
rowRanges0.0010.0010.002
rowRanks0.0020.0010.003
rowSdDiffs0.0040.0020.006
rowSds0.0020.0010.003
rowSums20.0010.0000.002
rowTabulates0.0030.0010.004
rowVarDiffs0.0020.0010.004
rowVars0.0010.0000.002
rowWeightedMads0.0020.0000.003
rowWeightedMeans0.0020.0000.003
rowWeightedMedians0.0020.0010.003
rowWeightedSds0.0030.0010.004
rowWeightedVars0.0010.0000.002