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BioC 3.5: CHECK report for sangerseqR on tokay2

This page was generated on 2017-08-16 13:23:00 -0400 (Wed, 16 Aug 2017).

Package 1178/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sangerseqR 1.12.0
Jonathon Hill
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/sangerseqR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
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 [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sangerseqR
Version: 1.12.0
Command: rm -rf sangerseqR.buildbin-libdir sangerseqR.Rcheck && mkdir sangerseqR.buildbin-libdir sangerseqR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sangerseqR.buildbin-libdir sangerseqR_1.12.0.tar.gz >sangerseqR.Rcheck\00install.out 2>&1 && cp sangerseqR.Rcheck\00install.out sangerseqR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=sangerseqR.buildbin-libdir --install="check:sangerseqR-install.out" --force-multiarch --no-vignettes --timings sangerseqR_1.12.0.tar.gz
StartedAt: 2017-08-16 02:44:21 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:47:21 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 179.1 seconds
RetCode: 0
Status:  OK  
CheckDir: sangerseqR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf sangerseqR.buildbin-libdir sangerseqR.Rcheck && mkdir sangerseqR.buildbin-libdir sangerseqR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sangerseqR.buildbin-libdir sangerseqR_1.12.0.tar.gz >sangerseqR.Rcheck\00install.out 2>&1 && cp sangerseqR.Rcheck\00install.out sangerseqR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=sangerseqR.buildbin-libdir --install="check:sangerseqR-install.out" --force-multiarch --no-vignettes --timings sangerseqR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/sangerseqR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.12.0'
* 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 ... OK
* 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
  'plot'
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 plot quantile rect
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot", "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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
setAllelePhase 11.74   0.15   11.89
chromatogram    8.59   0.01    8.61
makeBaseCalls   8.00   0.00    8.00
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
setAllelePhase 12.65   0.05   12.71
chromatogram   10.92   0.01   11.00
makeBaseCalls  10.04   0.00   10.05
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/sangerseqR.Rcheck/00check.log'
for details.


sangerseqR.Rcheck/00install.out:


install for i386

* installing *source* package 'sangerseqR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'sangerseqR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sangerseqR' as sangerseqR_1.12.0.zip
* DONE (sangerseqR)

sangerseqR.Rcheck/examples_i386/sangerseqR-Ex.timings:

nameusersystemelapsed
PolyPeakParser000
abif-class0.110.000.11
chromatogram8.590.018.61
makeBaseCalls808
read.abif0.110.000.11
read.scf0.20.00.2
readsangerseq0.30.00.3
sangerseq-class0.250.000.25
sangerseqAccessors0.050.000.05
scf-class0.040.020.06
setAllelePhase11.74 0.1511.89

sangerseqR.Rcheck/examples_x64/sangerseqR-Ex.timings:

nameusersystemelapsed
PolyPeakParser000
abif-class0.160.020.18
chromatogram10.92 0.0111.00
makeBaseCalls10.04 0.0010.05
read.abif0.100.020.11
read.scf0.300.010.31
readsangerseq0.170.000.17
sangerseq-class0.130.000.12
sangerseqAccessors0.040.000.05
scf-class0.070.000.06
setAllelePhase12.65 0.0512.71