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CHECK report for cleaver on tokay1

This page was generated on 2018-04-12 13:22:55 -0400 (Thu, 12 Apr 2018).

Package 239/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cleaver 1.16.0
Sebastian Gibb
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/cleaver
Branch: RELEASE_3_6
Last Commit: b334e4d
Last Changed Date: 2017-10-30 12:40:03 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cleaver
Version: 1.16.0
Command: rm -rf cleaver.buildbin-libdir cleaver.Rcheck && mkdir cleaver.buildbin-libdir cleaver.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cleaver.buildbin-libdir cleaver_1.16.0.tar.gz >cleaver.Rcheck\00install.out 2>&1 && cp cleaver.Rcheck\00install.out cleaver-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cleaver.buildbin-libdir --install="check:cleaver-install.out" --force-multiarch --no-vignettes --timings cleaver_1.16.0.tar.gz
StartedAt: 2018-04-11 22:57:08 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:58:46 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 98.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cleaver.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cleaver.buildbin-libdir cleaver.Rcheck && mkdir cleaver.buildbin-libdir cleaver.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cleaver.buildbin-libdir cleaver_1.16.0.tar.gz >cleaver.Rcheck\00install.out 2>&1 && cp cleaver.Rcheck\00install.out cleaver-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cleaver.buildbin-libdir --install="check:cleaver-install.out" --force-multiarch --no-vignettes --timings cleaver_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cleaver.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 'cleaver/DESCRIPTION' ... OK
* this is package 'cleaver' version '1.16.0'
* 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 'cleaver' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleave-methods.Rd:52: missing file link 'gregexpr'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleaver-package.Rd:7: missing file link 'cleave'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleaver-package.Rd:8: missing file link 'cleavageRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleaver-package.Rd:9: missing file link 'cleavageSites'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleaver-package.Rd:36: missing file link 'cleave'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleaver-package.Rd:36: missing file link 'cleavageRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleaver-package.Rd:37: missing file link 'cleavageSites'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cleaver.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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/cleaver.Rcheck/00check.log'
for details.

Installation output

cleaver.Rcheck/00install.out


install for i386

* installing *source* package 'cleaver' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'cleaver'
    finding HTML links ... done
    cleave-methods                          html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleave-methods.Rd:52: missing file link 'gregexpr'
    cleaver-package                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleaver-package.Rd:7: missing file link 'cleave'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleaver-package.Rd:8: missing file link 'cleavageRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleaver-package.Rd:9: missing file link 'cleavageSites'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleaver-package.Rd:36: missing file link 'cleave'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleaver-package.Rd:36: missing file link 'cleavageRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpYvxSYF/R.INSTALL1a0456f4674f/cleaver/man/cleaver-package.Rd:37: missing file link 'cleavageSites'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'cleaver' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cleaver' as cleaver_1.16.0.zip
* DONE (cleaver)
In R CMD INSTALL
In R CMD INSTALL

Tests output

cleaver.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("cleaver")
Loading required package: cleaver
Loading required package: Biostrings
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
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

== testthat results  ===========================================================
OK: 124 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.79    0.15    4.93

cleaver.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("cleaver")
Loading required package: cleaver
Loading required package: Biostrings
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
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

== testthat results  ===========================================================
OK: 124 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.81    0.09    3.89

Example timings

cleaver.Rcheck/examples_i386/cleaver-Ex.timings

nameusersystemelapsed
cleave-methods0.260.000.27

cleaver.Rcheck/examples_x64/cleaver-Ex.timings

nameusersystemelapsed
cleave-methods0.310.000.32