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CHECK report for topdownr on tokay2

This page was generated on 2018-10-17 08:44:49 -0400 (Wed, 17 Oct 2018).

Package 1492/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
topdownr 1.2.0
Sebastian Gibb
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/topdownr
Branch: RELEASE_3_7
Last Commit: 8c9dfe3
Last Changed Date: 2018-04-30 10:35:48 -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: topdownr
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:topdownr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings topdownr_1.2.0.tar.gz
StartedAt: 2018-10-17 05:13:45 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 05:19:05 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 320.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: topdownr.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:topdownr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings topdownr_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/topdownr.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 'topdownr/DESCRIPTION' ... OK
* this is package 'topdownr' version '1.2.0'
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'topdownr' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/AbstractTopDownSet-class.Rd:228: file link 'XStringViews' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/FragmentViews-class.Rd:75: file link 'AAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:27: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:48: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:49: file link 'defaultNeutralLoss' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:108: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:134: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:135: file link 'defaultNeutralLoss' in package 'MSnbase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/topdownr.Rcheck/00install.out' for details.
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... 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-3.7-bioc/meat/topdownr.Rcheck/00check.log'
for details.

Installation output

topdownr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/topdownr_1.2.0.tar.gz && rm -rf topdownr.buildbin-libdir && mkdir topdownr.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=topdownr.buildbin-libdir topdownr_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL topdownr_1.2.0.zip && rm topdownr_1.2.0.tar.gz topdownr_1.2.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1889k  100 1889k    0     0  27.0M      0 --:--:-- --:--:-- --:--:-- 29.7M

install for i386

* installing *source* package 'topdownr' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'topdownr'
    finding HTML links ... done
    AbstractTopDownSet-class                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/AbstractTopDownSet-class.Rd:228: file link 'XStringViews' in package 'Biostrings' does not exist and so has been treated as a topic
    FragmentViews-class                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/FragmentViews-class.Rd:75: file link 'AAString' in package 'Biostrings' does not exist and so has been treated as a topic
    NCBSet-class                            html  
    TopDownSet-class                        html  
    default-functions                       html  
    readTopDownFiles                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:27: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:48: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:49: file link 'defaultNeutralLoss' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:108: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:134: file link 'calculateFragments' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmps3hDLj/R.INSTALLa0858fd578b/topdownr/man/readTopDownFiles.Rd:135: file link 'defaultNeutralLoss' in package 'MSnbase' does not exist and so has been treated as a topic
    tds                                     html  
    topdownr-package                        html  
    windows-specific-functions              html  
    writeMethodXmls                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'topdownr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'topdownr' as topdownr_1.2.0.zip
* DONE (topdownr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'topdownr' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

topdownr.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")
> library("topdownr")
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: ProtGenerics
Loading required package: Biostrings
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: XVector

Attaching package: 'Biostrings'

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

    strsplit


This is topdownr version 1.2.0 
  Visit https://sgibb.github.io/topdownr/ to get started.

> 
> test_check("topdownr")
== testthat results  ===========================================================
OK: 550 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  22.29    2.06   25.62

topdownr.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")
> library("topdownr")
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: ProtGenerics
Loading required package: Biostrings
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: XVector

Attaching package: 'Biostrings'

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

    strsplit


This is topdownr version 1.2.0 
  Visit https://sgibb.github.io/topdownr/ to get started.

> 
> test_check("topdownr")
== testthat results  ===========================================================
OK: 550 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  24.53    1.21   26.42

Example timings

topdownr.Rcheck/examples_i386/topdownr-Ex.timings

nameusersystemelapsed
AbstractTopDownSet-class0.750.281.03
FragmentViews-class0.140.020.16
NCBSet-class3.340.233.57
TopDownSet-class1.330.051.40
default-functions0.000.010.01
readTopDownFiles2.250.132.38
windows-specific-functions000
writeMethodXmls1.720.312.03

topdownr.Rcheck/examples_x64/topdownr-Ex.timings

nameusersystemelapsed
AbstractTopDownSet-class0.910.050.96
FragmentViews-class0.140.000.14
NCBSet-class4.440.044.49
TopDownSet-class1.240.081.34
default-functions0.010.000.02
readTopDownFiles2.700.132.82
windows-specific-functions0.020.000.02
writeMethodXmls2.700.453.75