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CHECK report for Pbase on tokay1

This page was generated on 2018-04-12 13:24:26 -0400 (Thu, 12 Apr 2018).

Package 1012/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pbase 0.18.0
Sebastian Gibb
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/Pbase
Branch: RELEASE_3_6
Last Commit: 3366ee9
Last Changed Date: 2017-10-30 12:40:17 -0400 (Mon, 30 Oct 2017)
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: Pbase
Version: 0.18.0
Command: rm -rf Pbase.buildbin-libdir Pbase.Rcheck && mkdir Pbase.buildbin-libdir Pbase.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Pbase.buildbin-libdir Pbase_0.18.0.tar.gz >Pbase.Rcheck\00install.out 2>&1 && cp Pbase.Rcheck\00install.out Pbase-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Pbase.buildbin-libdir --install="check:Pbase-install.out" --force-multiarch --no-vignettes --timings Pbase_0.18.0.tar.gz
StartedAt: 2018-04-12 02:02:23 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:18:23 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 960.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Pbase.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Pbase.buildbin-libdir Pbase.Rcheck && mkdir Pbase.buildbin-libdir Pbase.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Pbase.buildbin-libdir Pbase_0.18.0.tar.gz >Pbase.Rcheck\00install.out 2>&1 && cp Pbase.Rcheck\00install.out Pbase-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Pbase.buildbin-libdir --install="check:Pbase-install.out" --force-multiarch --no-vignettes --timings Pbase_0.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Pbase.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 'Pbase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Pbase' version '0.18.0'
* 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 'Pbase' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIvOwSi/R.INSTALL2a683a7d5592/Pbase/man/Proteins-class.Rd:121: missing file link 'proteins'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIvOwSi/R.INSTALL2a683a7d5592/Pbase/man/Proteins-class.Rd:126: missing file link 'listColumns'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIvOwSi/R.INSTALL2a683a7d5592/Pbase/man/Proteins-class.Rd:232: missing file link 'cleave'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIvOwSi/R.INSTALL2a683a7d5592/Pbase/man/coordinate-mapping-methods.Rd:124: missing file link 'mapToAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIvOwSi/R.INSTALL2a683a7d5592/Pbase/man/coordinate-mapping-methods.Rd:129: missing file link 'mapToTranscripts'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Pbase.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   2.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
  Laurent Gatto <lg390@cam.ac.uk> [aut, cre]
  Johannes Rainer <Johannes.Rainer@eurac.edu> [aut, cre]
  Sebastian Gibb <mail@sebastiangibb.de> [aut, cre]
* 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
coordinate-mapping-methods 14.87   8.86  180.38
Proteins-class             12.95   0.83   60.11
etrid2grl                   0.77   0.05    7.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
coordinate-mapping-methods 15.65   6.99   47.25
Proteins-class             16.48   0.87   17.36
etrid2grl                   1.02   0.00    7.89
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/Pbase.Rcheck/00check.log'
for details.

Installation output

Pbase.Rcheck/00install.out


install for i386

* installing *source* package 'Pbase' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'Pbase'
    finding HTML links ... done
    Pparams-class                           html  
    Proteins-class                          html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIvOwSi/R.INSTALL2a683a7d5592/Pbase/man/Proteins-class.Rd:121: missing file link 'proteins'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIvOwSi/R.INSTALL2a683a7d5592/Pbase/man/Proteins-class.Rd:126: missing file link 'listColumns'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIvOwSi/R.INSTALL2a683a7d5592/Pbase/man/Proteins-class.Rd:232: missing file link 'cleave'
    calculateHeavyLabels                    html  
    coordinate-mapping-methods              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIvOwSi/R.INSTALL2a683a7d5592/Pbase/man/coordinate-mapping-methods.Rd:124: missing file link 'mapToAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIvOwSi/R.INSTALL2a683a7d5592/Pbase/man/coordinate-mapping-methods.Rd:129: missing file link 'mapToTranscripts'
    etrid2grl                               html  
    isReverse                               html  
    p                                       html  
    plotAsAnnotationTrack                   html  
    proteinCoding-methods                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Pbase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Pbase' as Pbase_0.18.0.zip
* DONE (Pbase)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Pbase.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")
> test_check("Pbase")
Loading required package: Pbase
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: Rcpp
Loading required package: Gviz
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
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid

This is Pbase version 0.18.0

== testthat results  ===========================================================
OK: 254 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  36.85   18.07   93.82

Pbase.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")
> test_check("Pbase")
Loading required package: Pbase
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: Rcpp
Loading required package: Gviz
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
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid

This is Pbase version 0.18.0

== testthat results  ===========================================================
OK: 254 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  43.93   18.68   66.53

Example timings

Pbase.Rcheck/examples_i386/Pbase-Ex.timings

nameusersystemelapsed
Pparams-class0.020.000.01
Proteins-class12.95 0.8360.11
calculateHeavyLabels0.270.000.26
coordinate-mapping-methods 14.87 8.86180.38
etrid2grl0.770.057.20
p1.550.011.56

Pbase.Rcheck/examples_x64/Pbase-Ex.timings

nameusersystemelapsed
Pparams-class0.010.000.02
Proteins-class16.48 0.8717.36
calculateHeavyLabels0.240.000.24
coordinate-mapping-methods15.65 6.9947.25
etrid2grl1.020.007.89
p0.700.010.71