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CHECK report for Pbase on tokay2

This page was generated on 2018-10-17 08:38:47 -0400 (Wed, 17 Oct 2018).

Package 1067/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pbase 0.20.0
Sebastian Gibb
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Pbase
Branch: RELEASE_3_7
Last Commit: 8f2d5a5
Last Changed Date: 2018-04-30 10:35:33 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Pbase
Version: 0.20.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Pbase_0.20.0.tar.gz
StartedAt: 2018-10-17 03:52:31 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:04:49 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 737.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Pbase.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Pbase_0.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Pbase.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '0.20.0'
* 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-3.7-bioc/tmpdir/RtmpkrUjZy/R.INSTALL24c83c527244/Pbase/man/Proteins-class.Rd:121: file link 'proteins' in package 'ensembldb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkrUjZy/R.INSTALL24c83c527244/Pbase/man/Proteins-class.Rd:126: file link 'listColumns' in package 'ensembldb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkrUjZy/R.INSTALL24c83c527244/Pbase/man/Proteins-class.Rd:232: file link 'cleave' in package 'cleaver' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkrUjZy/R.INSTALL24c83c527244/Pbase/man/coordinate-mapping-methods.Rd:124: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkrUjZy/R.INSTALL24c83c527244/Pbase/man/coordinate-mapping-methods.Rd:129: file link 'mapToTranscripts' in package 'GenomicFeatures' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Pbase.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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
* 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 ... NOTE
  Failed with error:  'package 'Gviz' could not be loaded'
  Error in .requirePackage(package) : 
    unable to find required package 'Pbase'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
* 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
coordinate-mapping-methods 18.02   9.42   41.24
Proteins-class             12.51   1.70   14.64
etrid2grl                   0.64   0.02    8.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
coordinate-mapping-methods 18.67   9.13   41.32
Proteins-class             11.91   1.10   13.01
etrid2grl                   0.72   0.00    8.19
* 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-3.7-bioc/meat/Pbase.Rcheck/00check.log'
for details.

Installation output

Pbase.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Pbase_0.20.0.tar.gz && rm -rf Pbase.buildbin-libdir && mkdir Pbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Pbase.buildbin-libdir Pbase_0.20.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Pbase_0.20.0.zip && rm Pbase_0.20.0.tar.gz Pbase_0.20.0.zip
###
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##############################################################################


  % 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 3717k  100 3717k    0     0  33.8M      0 --:--:-- --:--:-- --:--:-- 36.3M

install for i386

* installing *source* package 'Pbase' ...
** R
** data
** inst
** byte-compile and prepare 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-3.7-bioc/tmpdir/RtmpkrUjZy/R.INSTALL24c83c527244/Pbase/man/Proteins-class.Rd:121: file link 'proteins' in package 'ensembldb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkrUjZy/R.INSTALL24c83c527244/Pbase/man/Proteins-class.Rd:126: file link 'listColumns' in package 'ensembldb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkrUjZy/R.INSTALL24c83c527244/Pbase/man/Proteins-class.Rd:232: file link 'cleave' in package 'cleaver' does not exist and so has been treated as a topic
    calculateHeavyLabels                    html  
    coordinate-mapping-methods              html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkrUjZy/R.INSTALL24c83c527244/Pbase/man/coordinate-mapping-methods.Rd:124: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpkrUjZy/R.INSTALL24c83c527244/Pbase/man/coordinate-mapping-methods.Rd:129: file link 'mapToTranscripts' in package 'GenomicFeatures' does not exist and so has been treated as a topic
    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_0.20.0.zip
* DONE (Pbase)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Pbase' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Pbase.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid

This is Pbase version 0.20.0

== testthat results  ===========================================================
OK: 254 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  49.62   27.34   80.42

Pbase.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid

This is Pbase version 0.20.0

== testthat results  ===========================================================
OK: 254 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  45.26   23.98   73.25

Example timings

Pbase.Rcheck/examples_i386/Pbase-Ex.timings

nameusersystemelapsed
Pparams-class000
Proteins-class12.51 1.7014.64
calculateHeavyLabels0.230.000.23
coordinate-mapping-methods18.02 9.4241.24
etrid2grl0.640.028.11
p0.910.000.90

Pbase.Rcheck/examples_x64/Pbase-Ex.timings

nameusersystemelapsed
Pparams-class000
Proteins-class11.91 1.1013.01
calculateHeavyLabels0.190.000.19
coordinate-mapping-methods18.67 9.1341.32
etrid2grl0.720.008.19
p0.540.050.59