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BioC 3.4: CHECK report for QuartPAC on morelia

This page was generated on 2017-04-15 16:26:07 -0400 (Sat, 15 Apr 2017).

Package 983/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuartPAC 1.6.0
Gregory Ryslik
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/QuartPAC
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / 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: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QuartPAC_1.6.0.tar.gz
StartedAt: 2017-04-15 06:43:58 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 06:47:59 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 241.8 seconds
RetCode: 0
Status:  OK 
CheckDir: QuartPAC.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QuartPAC_1.6.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/QuartPAC.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QuartPAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QuartPAC’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
QuartPAC-package          52.339  0.365  56.443
makeAlignedSuperStructure 19.627  0.152  21.776
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/QuartPAC.Rcheck/00check.log’
for details.


QuartPAC.Rcheck/00install.out:

* 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
* DONE (QuartPAC)

QuartPAC.Rcheck/QuartPAC-Ex.timings:

nameusersystemelapsed
QuartPAC-package52.339 0.36556.443
getMutations0.0370.0101.888
makeAlignedSuperStructure19.627 0.15221.776
quartCluster0.0000.0000.001