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BioC 3.4: CHECK report for cleanUpdTSeq on malbec1

This page was generated on 2017-04-15 16:11:31 -0400 (Sat, 15 Apr 2017).

Package 210/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cleanUpdTSeq 1.12.0
Sarah Sheppard ; Jianhong Ou
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/cleanUpdTSeq
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  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cleanUpdTSeq
Version: 1.12.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings cleanUpdTSeq_1.12.0.tar.gz
StartedAt: 2017-04-14 21:36:05 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:40:23 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 257.6 seconds
RetCode: 0
Status:  OK 
CheckDir: cleanUpdTSeq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings cleanUpdTSeq_1.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/cleanUpdTSeq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cleanUpdTSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cleanUpdTSeq’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘BSgenome’ ‘BSgenome.Drerio.UCSC.danRer7’
  ‘GenomicRanges’ ‘seqinr’ ‘e1071’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘cleanUpdTSeq’ 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
* 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
BED2GRangesSeq: no visible global function definition for ‘IRanges’
buildClassifier: no visible global function definition for ‘as.formula’
getDownstreamSequence: no visible global function definition for
  ‘IRanges’
getDownstreamSequence: no visible global function definition for
  ‘seqlengths’
getUpstreamSequence: no visible global function definition for
  ‘IRanges’
getUpstreamSequence: no visible global function definition for
  ‘seqlengths’
predictTestSet: no visible global function definition for ‘as.formula’
predictTestSet: no visible global function definition for ‘predict’
predictTestSet: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  IRanges as.formula predict seqlengths write.table
Consider adding
  importFrom("stats", "as.formula", "predict")
  importFrom("utils", "write.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 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
data.NaiveBayes 28.016  0.164  28.200
predictTestSet  25.676  0.056  25.794
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/cleanUpdTSeq.Rcheck/00check.log’
for details.


cleanUpdTSeq.Rcheck/00install.out:

* installing *source* package ‘cleanUpdTSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cleanUpdTSeq)

cleanUpdTSeq.Rcheck/cleanUpdTSeq-Ex.timings:

nameusersystemelapsed
BED2GRangesSeq0.0280.0000.028
PASclassifier-class0.0400.0000.039
buildClassifier0.0000.0000.001
buildFeatureVector2.2440.0282.307
classifier0.0320.0040.035
cleanUpdTSeq-package0.0040.0000.003
data.NaiveBayes28.016 0.16428.200
getDownstreamSequence0.120.000.12
getUpstreamSequence0.1240.0000.123
predictTestSet25.676 0.05625.794