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CHECK report for cleanUpdTSeq on veracruz1

This page was generated on 2018-04-12 13:37:04 -0400 (Thu, 12 Apr 2018).

Package 238/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cleanUpdTSeq 1.16.0
Sarah Sheppard ; Jianhong Ou
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/cleanUpdTSeq
Branch: RELEASE_3_6
Last Commit: 3e4e2d8
Last Changed Date: 2017-10-30 12:40:04 -0400 (Mon, 30 Oct 2017)
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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cleanUpdTSeq
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cleanUpdTSeq_1.16.0.tar.gz
StartedAt: 2018-04-12 01:45:48 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:50:57 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 308.6 seconds
RetCode: 0
Status:  OK 
CheckDir: cleanUpdTSeq.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cleanUpdTSeq_1.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/cleanUpdTSeq.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.0’
* 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
predictTestSet  26.471  0.390  27.344
data.NaiveBayes 26.107  0.325  26.914
* 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-3.6-bioc/meat/cleanUpdTSeq.Rcheck/00check.log’
for details.



Installation output

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)

Tests output

cleanUpdTSeq.Rcheck/tests/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("cleanUpdTSeq") || stop("unable to load Package:cleanUpdTSeq")
Loading required package: cleanUpdTSeq
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
Loading required package: BSgenome.Drerio.UCSC.danRer7
Loading required package: seqinr

Attaching package: 'seqinr'

The following object is masked from 'package:Biostrings':

    translate

Loading required package: e1071
[1] TRUE
> BiocGenerics:::testPackage("cleanUpdTSeq")


RUNIT TEST PROTOCOL -- Thu Apr 12 01:50:52 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
cleanUpdTSeq RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 16.160   0.443  16.896 

Example timings

cleanUpdTSeq.Rcheck/cleanUpdTSeq-Ex.timings

nameusersystemelapsed
BED2GRangesSeq0.1320.0190.157
PASclassifier-class0.0600.0070.067
buildClassifier0.0010.0000.001
buildFeatureVector4.0800.0794.261
classifier0.0450.0050.050
cleanUpdTSeq-package0.0060.0000.006
data.NaiveBayes26.107 0.32526.914
getDownstreamSequence0.2050.0100.221
getUpstreamSequence0.2550.0260.283
predictTestSet26.471 0.39027.344