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CHECK report for Pbase on tokay2

This page was generated on 2019-10-16 12:30:21 -0400 (Wed, 16 Oct 2019).

Package 1183/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pbase 0.24.0
Sebastian Gibb
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/Pbase
Branch: RELEASE_3_9
Last Commit: 3d70662
Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: Pbase
Version: 0.24.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Pbase_0.24.0.tar.gz
StartedAt: 2019-10-16 05:51:53 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:04:16 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 742.7 seconds
RetCode: 1
Status:  ERROR  
CheckDir: Pbase.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Pbase_0.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Pbase.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 'Pbase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Pbase' version '0.24.0'
* 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-3.9-bioc/tmpdir/Rtmp4KpVdt/R.INSTALL1544577628fa/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-3.9-bioc/tmpdir/Rtmp4KpVdt/R.INSTALL1544577628fa/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-3.9-bioc/tmpdir/Rtmp4KpVdt/R.INSTALL1544577628fa/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-3.9-bioc/tmpdir/Rtmp4KpVdt/R.INSTALL1544577628fa/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-3.9-bioc/tmpdir/Rtmp4KpVdt/R.INSTALL1544577628fa/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-3.9-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  [aut, cre]
  Johannes Rainer  [aut, cre]
  Sebastian Gibb  [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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'Pbase-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mapToGenome-methods
> ### Title: Map range coordinates between proteins and genome space
> ### Aliases: mapToGenome mapToGenome-methods mapToGenome,ANY,ANY-method
> ###   mapToGenome,Proteins,GRangesList-method
> ###   mapToGenome,Proteins,EnsDb-method pmapToGenome pmapToGenome-methods
> ###   pmapToGenome,ANY,ANY-method pmapToGenome,Proteins,GRangesList-method
> ### Keywords: methods utilities
> 
> ### ** Examples
> 
> 
> data(p)
> 
> grl <- etrid2grl(acols(p)$ENST)
Error: subscript contains invalid names
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'Pbase-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mapToGenome-methods
> ### Title: Map range coordinates between proteins and genome space
> ### Aliases: mapToGenome mapToGenome-methods mapToGenome,ANY,ANY-method
> ###   mapToGenome,Proteins,GRangesList-method
> ###   mapToGenome,Proteins,EnsDb-method pmapToGenome pmapToGenome-methods
> ###   pmapToGenome,ANY,ANY-method pmapToGenome,Proteins,GRangesList-method
> ### Keywords: methods utilities
> 
> ### ** Examples
> 
> 
> data(p)
> 
> grl <- etrid2grl(acols(p)$ENST)
Error: subscript contains invalid names
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  8: subset_along_ROWS(x, i, drop = drop)
  9: extractROWS(x, i)
  10: extractROWS(x, i)
  11: normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE)
  12: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
  13: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
  14: .subscript_error("subscript contains invalid ", what)
  15: stop(wmsg(...), call. = FALSE)
  
  == testthat results  ===========================================================
  [ OK: 249 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: mapToGenome,Proteins,EnsDb with Uniprot IDs (@test_mapToGenome-ensembldb.R#190) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  8: subset_along_ROWS(x, i, drop = drop)
  9: extractROWS(x, i)
  10: extractROWS(x, i)
  11: normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE)
  12: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
  13: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
  14: .subscript_error("subscript contains invalid ", what)
  15: stop(wmsg(...), call. = FALSE)
  
  == testthat results  ===========================================================
  [ OK: 249 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: mapToGenome,Proteins,EnsDb with Uniprot IDs (@test_mapToGenome-ensembldb.R#190) 
  
  Error: testthat unit tests failed
  Execution halted
* 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: 4 ERRORs, 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-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/3.9/bioc/src/contrib/Pbase_0.24.0.tar.gz && rm -rf Pbase.buildbin-libdir && mkdir Pbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Pbase.buildbin-libdir Pbase_0.24.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Pbase_0.24.0.zip && rm Pbase_0.24.0.tar.gz Pbase_0.24.0.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 3717k  100 3717k    0     0  27.9M      0 --:--:-- --:--:-- --:--:-- 29.2M

install for i386

* installing *source* package 'Pbase' ...
** using staged installation
** 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-3.9-bioc/tmpdir/Rtmp4KpVdt/R.INSTALL1544577628fa/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-3.9-bioc/tmpdir/Rtmp4KpVdt/R.INSTALL1544577628fa/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-3.9-bioc/tmpdir/Rtmp4KpVdt/R.INSTALL1544577628fa/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-3.9-bioc/tmpdir/Rtmp4KpVdt/R.INSTALL1544577628fa/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-3.9-bioc/tmpdir/Rtmp4KpVdt/R.INSTALL1544577628fa/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 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 'Pbase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Pbase' as Pbase_0.24.0.zip
* DONE (Pbase)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Pbase' successfully unpacked and MD5 sums checked

Tests output

Pbase.Rcheck/tests_i386/testthat.Rout.fail


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")
> 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, 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: 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 0.24.0

-- 1. Error: mapToGenome,Proteins,EnsDb with Uniprot IDs (@test_mapToGenome-ense
subscript contains invalid names
1: etrid2grl(acols(p)$ENST, ens) at testthat/test_mapToGenome-ensembldb.R:190
2: grl[etrid]
3: grl[etrid]
4: callNextMethod(x = x, i = i)
5: eval(call, callEnv)
6: eval(call, callEnv)
7: .nextMethod(x = x, i = i)
8: subset_along_ROWS(x, i, drop = drop)
9: extractROWS(x, i)
10: extractROWS(x, i)
11: normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE)
12: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
13: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
14: .subscript_error("subscript contains invalid ", what)
15: stop(wmsg(...), call. = FALSE)

== testthat results  ===========================================================
[ OK: 249 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
1. Error: mapToGenome,Proteins,EnsDb with Uniprot IDs (@test_mapToGenome-ensembldb.R#190) 

Error: testthat unit tests failed
Execution halted

Pbase.Rcheck/tests_x64/testthat.Rout.fail


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")
> 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, 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: 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 0.24.0

-- 1. Error: mapToGenome,Proteins,EnsDb with Uniprot IDs (@test_mapToGenome-ense
subscript contains invalid names
1: etrid2grl(acols(p)$ENST, ens) at testthat/test_mapToGenome-ensembldb.R:190
2: grl[etrid]
3: grl[etrid]
4: callNextMethod(x = x, i = i)
5: eval(call, callEnv)
6: eval(call, callEnv)
7: .nextMethod(x = x, i = i)
8: subset_along_ROWS(x, i, drop = drop)
9: extractROWS(x, i)
10: extractROWS(x, i)
11: normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE)
12: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
13: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
14: .subscript_error("subscript contains invalid ", what)
15: stop(wmsg(...), call. = FALSE)

== testthat results  ===========================================================
[ OK: 249 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
1. Error: mapToGenome,Proteins,EnsDb with Uniprot IDs (@test_mapToGenome-ensembldb.R#190) 

Error: testthat unit tests failed
Execution halted

Example timings

Pbase.Rcheck/examples_i386/Pbase-Ex.timings

nameusersystemelapsed
Pparams-class000
Proteins-class 9.30 1.2710.96
calculateHeavyLabels0.150.030.19

Pbase.Rcheck/examples_x64/Pbase-Ex.timings

nameusersystemelapsed
Pparams-class000
Proteins-class13.42 0.3113.73
calculateHeavyLabels0.250.020.26