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BioC 3.5: CHECK report for mBPCR on malbec2

This page was generated on 2017-08-16 13:13:24 -0400 (Wed, 16 Aug 2017).

Package 766/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mBPCR 1.30.0
P.M.V. Rancoita
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/mBPCR
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  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: mBPCR
Version: 1.30.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings mBPCR_1.30.0.tar.gz
StartedAt: 2017-08-16 00:21:29 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:24:36 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 187.3 seconds
RetCode: 0
Status:  OK 
CheckDir: mBPCR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings mBPCR_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/mBPCR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mBPCR/DESCRIPTION’ ... OK
* this is package ‘mBPCR’ version ‘1.30.0’
* 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 ‘mBPCR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
estProfileWithMBPCRforOligoSnpSet: no visible global function
  definition for ‘new’
estProfileWithMBPCRforOligoSnpSet: no visible global function
  definition for ‘integerMatrix’
importCNData: no visible global function definition for ‘read.table’
plotEstProfile: no visible global function definition for ‘x11’
plotEstProfile: no visible global function definition for ‘plot’
plotEstProfile: no visible global function definition for ‘title’
plotEstProfile: no visible global function definition for ‘legend’
plotEstProfile: no visible global function definition for ‘points’
writeEstProfile: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  integerMatrix legend new plot points read.table title write.table x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "legend", "plot", "points", "title")
  importFrom("methods", "new")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
plotEstProfile  9.3  0.028   9.333
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/mBPCR.Rcheck/00check.log’
for details.


mBPCR.Rcheck/00install.out:

* installing *source* package ‘mBPCR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (mBPCR)

mBPCR.Rcheck/mBPCR-Ex.timings:

nameusersystemelapsed
computeMBPCR2.4600.0482.510
estGlobParam0.0080.0000.008
estProfileWithMBPCR3.6560.0003.657
estProfileWithMBPCRforOligoSnpSet0.0040.0000.000
importCNData0.0640.0000.065
logAdd000
plotEstProfile9.3000.0289.333
writeEstProfile3.6680.0003.672