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BioC 3.5: CHECK report for QuartPAC on tokay2

This page was generated on 2017-10-18 14:24:15 -0400 (Wed, 18 Oct 2017).

Package 1044/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuartPAC 1.8.1
Gregory Ryslik
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/QuartPAC
Branch: RELEASE_3_5
Last Commit: ac07fb3
Last Changed Date: 2017-07-12 23:15:08 -0400 (Wed, 12 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: QuartPAC
Version: 1.8.1
Command: rm -rf QuartPAC.buildbin-libdir QuartPAC.Rcheck && mkdir QuartPAC.buildbin-libdir QuartPAC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QuartPAC.buildbin-libdir QuartPAC_1.8.1.tar.gz >QuartPAC.Rcheck\00install.out 2>&1 && cp QuartPAC.Rcheck\00install.out QuartPAC-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=QuartPAC.buildbin-libdir --install="check:QuartPAC-install.out" --force-multiarch --no-vignettes --timings QuartPAC_1.8.1.tar.gz
StartedAt: 2017-10-18 02:17:43 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:24:03 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 379.5 seconds
RetCode: 0
Status:  OK  
CheckDir: QuartPAC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf QuartPAC.buildbin-libdir QuartPAC.Rcheck && mkdir QuartPAC.buildbin-libdir QuartPAC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QuartPAC.buildbin-libdir QuartPAC_1.8.1.tar.gz >QuartPAC.Rcheck\00install.out 2>&1 && cp QuartPAC.Rcheck\00install.out QuartPAC-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=QuartPAC.buildbin-libdir --install="check:QuartPAC-install.out" --force-multiarch --no-vignettes --timings QuartPAC_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/QuartPAC.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'QuartPAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'QuartPAC' version '1.8.1'
* 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 'QuartPAC' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
alignPositions: no visible global function definition for
  'PhredQuality'
alignPositions: no visible global function definition for
  'pairwiseAlignment'
constructCanonicalNumbering: no visible global function definition for
  'pattern'
constructCanonicalNumbering: no visible global function definition for
  'subject'
constructCanonicalNumbering: no visible global function definition for
  'start'
getMutations : <anonymous>: no visible global function definition for
  'read.table'
getRangeLocInfo: no visible global function definition for 'aggregate'
quartCluster: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  PhredQuality aggregate capture.output pairwiseAlignment pattern
  read.table start subject
Consider adding
  importFrom("stats", "aggregate", "start")
  importFrom("utils", "capture.output", "read.table")
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
QuartPAC-package          38.82   0.27   39.38
makeAlignedSuperStructure 14.70   0.02   14.88
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
QuartPAC-package          48.31   0.23   48.81
makeAlignedSuperStructure 21.28   0.02   21.52
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/QuartPAC.Rcheck/00check.log'
for details.


QuartPAC.Rcheck/00install.out:


install for i386

* installing *source* package 'QuartPAC' ...
** 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 'QuartPAC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QuartPAC' as QuartPAC_1.8.1.zip
* DONE (QuartPAC)

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

nameusersystemelapsed
QuartPAC-package38.82 0.2739.38
getMutations0.060.000.12
makeAlignedSuperStructure14.70 0.0214.88
quartCluster000

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

nameusersystemelapsed
QuartPAC-package48.31 0.2348.81
getMutations0.040.020.12
makeAlignedSuperStructure21.28 0.0221.52
quartCluster000