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BioC 3.4: CHECK report for QuartPAC on moscato1

This page was generated on 2016-09-21 03:46:35 -0700 (Wed, 21 Sep 2016).

Package 956/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuartPAC 1.5.0
Gregory Ryslik
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/QuartPAC
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: QuartPAC
Version: 1.5.0
Command: rm -rf QuartPAC.buildbin-libdir QuartPAC.Rcheck && mkdir QuartPAC.buildbin-libdir QuartPAC.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QuartPAC.buildbin-libdir QuartPAC_1.5.0.tar.gz >QuartPAC.Rcheck\00install.out 2>&1 && cp QuartPAC.Rcheck\00install.out QuartPAC-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=QuartPAC.buildbin-libdir --install="check:QuartPAC-install.out" --force-multiarch --no-vignettes --timings QuartPAC_1.5.0.tar.gz
StartedAt: 2016-09-20 14:38:07 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 14:45:11 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 424.1 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QuartPAC.buildbin-libdir QuartPAC_1.5.0.tar.gz >QuartPAC.Rcheck\00install.out 2>&1 && cp QuartPAC.Rcheck\00install.out QuartPAC-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=QuartPAC.buildbin-libdir --install="check:QuartPAC-install.out" --force-multiarch --no-vignettes --timings QuartPAC_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/QuartPAC.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.5.0'
* 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 '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          49.80   1.03   51.54
makeAlignedSuperStructure 20.58   1.03   26.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
QuartPAC-package          64.31   0.64   65.69
makeAlignedSuperStructure 25.44   0.59   26.46
* 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
  'D:/biocbld/bbs-3.4-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_1.5.0.zip
* DONE (QuartPAC)

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

nameusersystemelapsed
QuartPAC-package49.80 1.0351.54
getMutations0.010.000.25
makeAlignedSuperStructure20.58 1.0326.89
quartCluster000

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

nameusersystemelapsed
QuartPAC-package64.31 0.6465.69
getMutations0.060.000.27
makeAlignedSuperStructure25.44 0.5926.46
quartCluster000