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CHECK report for DelayedMatrixStats on tokay1

This page was generated on 2018-04-12 13:30:43 -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: rm -rf DelayedMatrixStats.buildbin-libdir DelayedMatrixStats.Rcheck && mkdir DelayedMatrixStats.buildbin-libdir DelayedMatrixStats.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DelayedMatrixStats.buildbin-libdir DelayedMatrixStats_1.0.3.tar.gz >DelayedMatrixStats.Rcheck\00install.out 2>&1 && cp DelayedMatrixStats.Rcheck\00install.out DelayedMatrixStats-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DelayedMatrixStats.buildbin-libdir --install="check:DelayedMatrixStats-install.out" --force-multiarch --no-vignettes --timings DelayedMatrixStats_1.0.3.tar.gz
StartedAt: 2018-04-11 23:25:26 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:40:08 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 881.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: DelayedMatrixStats.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DelayedMatrixStats.buildbin-libdir DelayedMatrixStats.Rcheck && mkdir DelayedMatrixStats.buildbin-libdir DelayedMatrixStats.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DelayedMatrixStats.buildbin-libdir DelayedMatrixStats_1.0.3.tar.gz >DelayedMatrixStats.Rcheck\00install.out 2>&1 && cp DelayedMatrixStats.Rcheck\00install.out DelayedMatrixStats-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DelayedMatrixStats.buildbin-libdir --install="check:DelayedMatrixStats-install.out" --force-multiarch --no-vignettes --timings DelayedMatrixStats_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DelayedMatrixStats.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.0.3'
* 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 whether package 'DelayedMatrixStats' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colCollapse.Rd:83: missing file link '['
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colCummaxs.Rd:131: missing file link 'cumprod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colCummaxs.Rd:132: missing file link 'cummin'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colCummaxs.Rd:132: missing file link 'cummax'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colIQRDiffs.Rd:117: missing file link 'var'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colIQRDiffs.Rd:172: missing file link 'var'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colProds.Rd:78: missing file link 'is.nan'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DelayedMatrixStats.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 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 ...
** 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/DelayedMatrixStats.Rcheck/00check.log'
for details.

Installation output

DelayedMatrixStats.Rcheck/00install.out


install for i386

* installing *source* package 'DelayedMatrixStats' ...
** R
** inst
** preparing 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  
    colCollapse                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colCollapse.Rd:83: missing file link '['
    colCounts                               html  
    colCummaxs                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colCummaxs.Rd:131: missing file link 'cumprod'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colCummaxs.Rd:132: missing file link 'cummin'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colCummaxs.Rd:132: missing file link 'cummax'
    colDiffs                                html  
    colIQRDiffs                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colIQRDiffs.Rd:117: missing file link 'var'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colIQRDiffs.Rd:172: missing file link 'var'
    colIQRs                                 html  
    colLogSumExps                           html  
    colMads                                 html  
    colMeans2                               html  
    colMedians                              html  
    colOrderStats                           html  
    colProds                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQlDfLI/R.INSTALL1470705e1022/DelayedMatrixStats/man/colProds.Rd:78: missing file link 'is.nan'
    colQuantiles                            html  
    colRanks                                html  
    colSums2                                html  
    colTabulates                            html  
    colVars                                 html  
    colWeightedMads                         html  
    colWeightedMeans                        html  
    colWeightedMedians                      html  
    from_DelayedArray_to_simple_seed_class
                                            html  
    rowAvgsPerColSet                        html  
    rowblock_APPLY                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DelayedMatrixStats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DelayedMatrixStats' as DelayedMatrixStats_1.0.3.zip
* DONE (DelayedMatrixStats)
In R CMD INSTALL
In R CMD INSTALL

Tests output

DelayedMatrixStats.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 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 
 306.68    1.90  308.73

DelayedMatrixStats.Rcheck/tests_x64/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-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: 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 
 415.89    2.01  419.37

Example timings

DelayedMatrixStats.Rcheck/examples_i386/DelayedMatrixStats-Ex.timings

nameusersystemelapsed
colAlls0.250.000.25
colAnyNAs0.420.040.45
colCollapse0.220.000.22
colCounts0.210.000.20
colCummaxs0.200.030.23
colDiffs0.060.000.13
colIQRDiffs0.140.010.15
colIQRs0.010.000.02
colLogSumExps0.070.000.06
colMads0.060.000.06
colMeans20.020.000.01
colMedians0.010.000.02
colOrderStats0.040.000.03
colProds0.060.000.06
colQuantiles0.030.000.03
colRanks0.020.000.02
colSums20.010.000.02
colTabulates0.080.000.07
colVars0.060.000.07
colWeightedMads000
colWeightedMeans0.030.000.03
colWeightedMedians0.020.000.01
rowAvgsPerColSet0.030.000.03

DelayedMatrixStats.Rcheck/examples_x64/DelayedMatrixStats-Ex.timings

nameusersystemelapsed
colAlls0.490.040.58
colAnyNAs0.930.000.93
colCollapse0.590.010.61
colCounts0.440.000.44
colCummaxs0.200.000.25
colDiffs0.110.020.27
colIQRDiffs0.250.000.28
colIQRs0.020.000.01
colLogSumExps0.090.010.11
colMads0.090.000.10
colMeans20.050.000.11
colMedians0.030.000.03
colOrderStats0.080.000.20
colProds0.090.020.13
colQuantiles0.050.000.04
colRanks0.030.000.05
colSums20.030.000.03
colTabulates0.190.000.20
colVars0.090.000.10
colWeightedMads0.020.000.12
colWeightedMeans0.060.000.32
colWeightedMedians0.030.000.03
rowAvgsPerColSet0.050.000.05