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This page was generated on 2021-09-22 15:05:12 -0400 (Wed, 22 Sep 2021).

CHECK results for DelayedMatrixStats on tokay2

To the developers/maintainers of the DelayedMatrixStats package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DelayedMatrixStats.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 471/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DelayedMatrixStats 1.14.3  (landing page)
Peter Hickey
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/DelayedMatrixStats
git_branch: RELEASE_3_13
git_last_commit: b8bf535
git_last_commit_date: 2021-08-25 18:52:42 -0400 (Wed, 25 Aug 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DelayedMatrixStats
Version: 1.14.3
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DelayedMatrixStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DelayedMatrixStats_1.14.3.tar.gz
StartedAt: 2021-09-21 21:43:35 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 21:51:23 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 467.7 seconds
RetCode: 0
Status:   OK  
CheckDir: DelayedMatrixStats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DelayedMatrixStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DelayedMatrixStats_1.14.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DelayedMatrixStats.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DelayedMatrixStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DelayedMatrixStats' version '1.14.3'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Missing object imported by a ':::' call: 'DelayedArray:::.reduce_array_dimensions'
Unexported objects imported by ':::' calls:
  'DelayedArray:::.get_ans_type' '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 ... 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/DelayedMatrixStats.Rcheck/00check.log'
for details.



Installation output

DelayedMatrixStats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DelayedMatrixStats_1.14.3.tar.gz && rm -rf DelayedMatrixStats.buildbin-libdir && mkdir DelayedMatrixStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DelayedMatrixStats.buildbin-libdir DelayedMatrixStats_1.14.3.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DelayedMatrixStats_1.14.3.zip && rm DelayedMatrixStats_1.14.3.tar.gz DelayedMatrixStats_1.14.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 44590  100 44590    0     0   283k      0 --:--:-- --:--:-- --:--:--  282k

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'DelayedMatrixStats/longtests/../tests/testthat' to 'DelayedMatrixStats/longtests/testthat'
* installing *source* package 'DelayedMatrixStats' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DelayedMatrixStats'
    finding HTML links ... done
    DelayedMatrixStats                      html  
    colAlls                                 html  
    finding level-2 HTML links ... done

    colAnyNAs                               html  
    colAvgsPerRowSet                        html  
    colCollapse                             html  
    colCounts                               html  
    colCummaxs                              html  
    colDiffs                                html  
    colIQRDiffs                             html  
    colIQRs                                 html  
    colLogSumExps                           html  
    colMads                                 html  
    colMeans2                               html  
    colMedians                              html  
    colOrderStats                           html  
    colProds                                html  
    colQuantiles                            html  
    colRanks                                html  
    colSums2                                html  
    colTabulates                            html  
    colVars                                 html  
    colWeightedMads                         html  
    colWeightedMeans                        html  
    colWeightedMedians                      html  
    colWeightedVars                         html  
    from_DelayedArray_to_simple_seed_class
                                            html  
    reexports                               html  
    subset_by_Nindex                        html  
** 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

install for x64

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'DelayedMatrixStats/longtests/../tests/testthat' to 'DelayedMatrixStats/longtests/testthat'
* installing *source* package 'DelayedMatrixStats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DelayedMatrixStats' as DelayedMatrixStats_1.14.3.zip
* DONE (DelayedMatrixStats)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'DelayedMatrixStats' successfully unpacked and MD5 sums checked

Tests output

DelayedMatrixStats.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 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: 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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand, unname

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep


Attaching package: 'DelayedMatrixStats'

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

    colAnyMissings, rowAnyMissings

> 
> test_check("DelayedMatrixStats")
Loading required package: rhdf5

Attaching package: 'HDF5Array'

The following object is masked from 'package:rhdf5':

    h5ls

== Skipped tests ===============================================================
* On Windows (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 14731 ]
> 
> proc.time()
   user  system elapsed 
 146.57    4.60  151.73 

DelayedMatrixStats.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: 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: 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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand, unname

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep


Attaching package: 'DelayedMatrixStats'

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

    colAnyMissings, rowAnyMissings

> 
> test_check("DelayedMatrixStats")
Loading required package: rhdf5

Attaching package: 'HDF5Array'

The following object is masked from 'package:rhdf5':

    h5ls

== Skipped tests ===============================================================
* On Windows (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 14731 ]
> 
> proc.time()
   user  system elapsed 
 157.60    4.90  168.23 

Example timings

DelayedMatrixStats.Rcheck/examples_i386/DelayedMatrixStats-Ex.timings

nameusersystemelapsed
colAlls0.060.000.06
colAnyNAs0.610.090.72
colAvgsPerRowSet0.190.020.21
colCollapse0.180.030.23
colCounts0.160.000.16
colCummaxs0.190.010.20
colDiffs0.150.050.22
colIQRDiffs0.160.000.15
colIQRs0.010.000.02
colLogSumExps0.040.000.03
colMads0.110.000.11
colMeans20.030.000.03
colMedians0.030.000.03
colOrderStats0.040.000.05
colProds0.080.000.09
colQuantiles0.030.000.03
colRanks0.020.000.02
colSums20.020.000.01
colTabulates0.150.000.16
colVars0.050.010.09
colWeightedMads000
colWeightedMeans0.030.000.03
colWeightedMedians0.030.000.03
colWeightedVars0.060.000.07

DelayedMatrixStats.Rcheck/examples_x64/DelayedMatrixStats-Ex.timings

nameusersystemelapsed
colAlls0.040.030.08
colAnyNAs0.580.060.69
colAvgsPerRowSet0.230.000.24
colCollapse0.140.010.18
colCounts0.090.000.09
colCummaxs0.140.000.14
colDiffs0.130.000.15
colIQRDiffs0.110.020.12
colIQRs000
colLogSumExps0.010.000.02
colMads0.100.000.09
colMeans20.030.000.03
colMedians0.010.000.02
colOrderStats0.050.000.04
colProds0.060.020.10
colQuantiles0.020.000.01
colRanks0.030.000.03
colSums20.010.000.02
colTabulates0.160.000.16
colVars0.060.000.09
colWeightedMads000
colWeightedMeans0.050.000.05
colWeightedMedians0.020.000.01
colWeightedVars0.070.000.08