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CHECK report for sangerseqR on tokay2

This page was generated on 2020-10-17 11:57:44 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE sangerseqR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1572/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sangerseqR 1.24.0
Jonathon Hill
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/sangerseqR
Branch: RELEASE_3_11
Last Commit: 5c894ad
Last Changed Date: 2020-04-27 14:38:32 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sangerseqR
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sangerseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings sangerseqR_1.24.0.tar.gz
StartedAt: 2020-10-17 07:56:15 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:59:45 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 209.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: sangerseqR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sangerseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings sangerseqR_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/sangerseqR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sangerseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sangerseqR' version '1.24.0'
* 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 'sangerseqR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpugnJhR/R.INSTALL1534131d359e/sangerseqR/man/sangerseq-class.Rd:36: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpugnJhR/R.INSTALL1534131d359e/sangerseqR/man/sangerseq-class.Rd:39: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpugnJhR/R.INSTALL1534131d359e/sangerseqR/man/scf-class.Rd:28: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/sangerseqR.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 ... NOTE
chromatogram,sangerseq: no visible global function definition for 'par'
chromatogram,sangerseq: no visible global function definition for
  'quantile'
chromatogram,sangerseq: no visible global function definition for 'IQR'
chromatogram,sangerseq: no visible global function definition for 'pdf'
chromatogram,sangerseq: no visible global function definition for
  'rect'
chromatogram,sangerseq: no visible global function definition for
  'lines'
chromatogram,sangerseq: no visible global function definition for
  'mtext'
chromatogram,sangerseq: no visible global function definition for
  'axis'
chromatogram,sangerseq: no visible global function definition for
  'dev.off'
Undefined global functions or variables:
  IQR axis dev.off lines mtext par pdf quantile rect
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "axis", "lines", "mtext", "par", "rect")
  importFrom("stats", "IQR", "quantile")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
makeBaseCalls  12.59   0.04   12.67
setAllelePhase 11.67   0.05   11.72
chromatogram   10.70   0.11   10.81
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
makeBaseCalls  17.11   0.00   17.11
chromatogram   14.84   0.03   14.88
setAllelePhase 14.66   0.09   14.75
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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-3.11-bioc/meat/sangerseqR.Rcheck/00check.log'
for details.



Installation output

sangerseqR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/sangerseqR_1.24.0.tar.gz && rm -rf sangerseqR.buildbin-libdir && mkdir sangerseqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sangerseqR.buildbin-libdir sangerseqR_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL sangerseqR_1.24.0.zip && rm sangerseqR_1.24.0.tar.gz sangerseqR_1.24.0.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 1208k  100 1208k    0     0  16.3M      0 --:--:-- --:--:-- --:--:-- 18.1M

install for i386

* installing *source* package 'sangerseqR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sangerseqR'
    finding HTML links ... done
    PolyPeakParser                          html  
    abif-class                              html  
    chromatogram                            html  
    makeBaseCalls                           html  
    read.abif                               html  
    read.scf                                html  
    readsangerseq                           html  
    sangerseq-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpugnJhR/R.INSTALL1534131d359e/sangerseqR/man/sangerseq-class.Rd:36: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpugnJhR/R.INSTALL1534131d359e/sangerseqR/man/sangerseq-class.Rd:39: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
    sangerseqAccessors                      html  
    finding level-2 HTML links ... done

    sangerseqR-package                      html  
    scf-class                               html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpugnJhR/R.INSTALL1534131d359e/sangerseqR/man/scf-class.Rd:28: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
    setAllelePhase                          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 'sangerseqR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sangerseqR' as sangerseqR_1.24.0.zip
* DONE (sangerseqR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'sangerseqR' successfully unpacked and MD5 sums checked

Tests output

sangerseqR.Rcheck/tests_i386/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> BiocGenerics:::testPackage("sangerseqR")

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows


Attaching package: 'Biostrings'

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

    strsplit



RUNIT TEST PROTOCOL -- Sat Oct 17 07:59:31 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sangerseqR RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
    4.0     0.2     4.2 

sangerseqR.Rcheck/tests_x64/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> BiocGenerics:::testPackage("sangerseqR")

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows


Attaching package: 'Biostrings'

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

    strsplit



RUNIT TEST PROTOCOL -- Sat Oct 17 07:59:36 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sangerseqR RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   3.76    0.29    4.04 

Example timings

sangerseqR.Rcheck/examples_i386/sangerseqR-Ex.timings

nameusersystemelapsed
PolyPeakParser000
abif-class0.220.030.28
chromatogram10.70 0.1110.81
makeBaseCalls12.59 0.0412.67
read.abif0.110.020.13
read.scf0.100.000.11
readsangerseq0.180.000.18
sangerseq-class0.180.000.18
sangerseqAccessors0.040.000.04
scf-class0.060.000.06
setAllelePhase11.67 0.0511.72

sangerseqR.Rcheck/examples_x64/sangerseqR-Ex.timings

nameusersystemelapsed
PolyPeakParser000
abif-class0.200.010.22
chromatogram14.84 0.0314.88
makeBaseCalls17.11 0.0017.11
read.abif0.190.000.19
read.scf0.080.000.07
readsangerseq0.160.000.16
sangerseq-class0.180.000.19
sangerseqAccessors0.080.000.08
scf-class0.080.000.07
setAllelePhase14.66 0.0914.75