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CHECK report for profileplyr on tokay2

This page was generated on 2019-10-16 12:44:01 -0400 (Wed, 16 Oct 2019).

Package 1256/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
profileplyr 1.0.1
Tom Carroll , Doug Barrows
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/profileplyr
Branch: RELEASE_3_9
Last Commit: 4e6bf6b
Last Changed Date: 2019-05-12 15:29:44 -0400 (Sun, 12 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: profileplyr
Version: 1.0.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:profileplyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings profileplyr_1.0.1.tar.gz
StartedAt: 2019-10-16 06:09:03 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:19:34 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 630.8 seconds
RetCode: 0
Status:  OK  
CheckDir: profileplyr.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:profileplyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings profileplyr_1.0.1.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/profileplyr.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'profileplyr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'profileplyr' version '1.0.1'
* 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 'profileplyr' 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
annotateRanges           26.81   0.93   27.78
as_profileplyr           14.97   0.58   16.33
BamBigwig_to_chipProfile 11.74   0.44   12.28
generateEnrichedHeatmap   5.47   0.16    5.63
annotateRanges_great      2.12   0.61   10.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
annotateRanges           29.72   0.79   30.50
as_profileplyr           14.78   0.75   16.22
BamBigwig_to_chipProfile 10.97   0.11   11.08
annotateRanges_great      3.75   0.80   12.24
* 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: OK

Installation output

profileplyr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/profileplyr_1.0.1.tar.gz && rm -rf profileplyr.buildbin-libdir && mkdir profileplyr.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=profileplyr.buildbin-libdir profileplyr_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL profileplyr_1.0.1.zip && rm profileplyr_1.0.1.tar.gz profileplyr_1.0.1.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
100 1741k  100 1741k    0     0  23.6M      0 --:--:-- --:--:-- --:--:-- 26.1M

install for i386

* installing *source* package 'profileplyr' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'profileplyr'
    finding HTML links ... done
    BamBigwig_to_chipProfile                html  
    K27ac_GRlist_hind_liver_top5000         html  
    annotateRanges                          html  
    annotateRanges_great                    html  
    as_profileplyr                          html  
    clusterRanges                           html  
    convertToEnrichedHeatmapMat             html  
    export_deepToolsMat                     html  
    gene_list_character                     html  
    gene_list_dataframe                     html  
    generateEnrichedHeatmap                 html  
    groupBy                                 html  
    inherit_group_function                  html  
    orderBy                                 html  
    params                                  html  
    profileplyr                             html  
    sampleData                              html  
    subset_GR_GL_common_top                 html  
    subsetbyGeneListOverlap                 html  
    subsetbyRangeOverlap                    html  
    summarize                               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

* installing *source* package 'profileplyr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'profileplyr' as profileplyr_1.0.1.zip
* DONE (profileplyr)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'profileplyr' successfully unpacked and MD5 sums checked

Tests output

profileplyr.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(profileplyr)
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: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

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: 'profileplyr'

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

    params

> 
> test_check("profileplyr")
Read 1 item
== testthat results  ===========================================================
[ OK: 15 | SKIPPED: 0 | WARNINGS: 15 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  20.95    1.56   23.92

profileplyr.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(profileplyr)
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: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

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: 'profileplyr'

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

    params

> 
> test_check("profileplyr")
Read 1 item
== testthat results  ===========================================================
[ OK: 15 | SKIPPED: 0 | WARNINGS: 15 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  26.35    0.82   28.59

Example timings

profileplyr.Rcheck/examples_i386/profileplyr-Ex.timings

nameusersystemelapsed
BamBigwig_to_chipProfile11.74 0.4412.28
annotateRanges26.81 0.9327.78
annotateRanges_great 2.12 0.6110.55
as_profileplyr14.97 0.5816.33
clusterRanges0.450.000.45
convertToEnrichedHeatmapMat1.360.021.38
export_deepToolsMat0.470.151.37
generateEnrichedHeatmap5.470.165.63
groupBy0.570.030.60
orderBy0.260.000.26
params0.130.000.13
sampleData0.150.020.17
subsetbyGeneListOverlap000
subsetbyRangeOverlap000
summarize0.440.010.45

profileplyr.Rcheck/examples_x64/profileplyr-Ex.timings

nameusersystemelapsed
BamBigwig_to_chipProfile10.97 0.1111.08
annotateRanges29.72 0.7930.50
annotateRanges_great 3.75 0.8012.24
as_profileplyr14.78 0.7516.22
clusterRanges1.850.041.89
convertToEnrichedHeatmapMat1.170.001.17
export_deepToolsMat0.310.191.25
generateEnrichedHeatmap4.610.004.61
groupBy0.550.030.59
orderBy0.170.000.17
params0.070.000.06
sampleData0.120.000.13
subsetbyGeneListOverlap000
subsetbyRangeOverlap000
summarize0.690.020.70