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CHECK report for EventPointer on merida1

This page was generated on 2019-04-16 12:00:25 -0400 (Tue, 16 Apr 2019).

Package 491/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EventPointer 2.0.1
Juan Pablo Romero
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/EventPointer
Branch: RELEASE_3_8
Last Commit: e700729
Last Changed Date: 2018-12-05 03:54:42 -0400 (Wed, 05 Dec 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: EventPointer
Version: 2.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EventPointer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EventPointer_2.0.1.tar.gz
StartedAt: 2019-04-15 23:51:11 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:56:54 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 342.3 seconds
RetCode: 0
Status:  OK 
CheckDir: EventPointer.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EventPointer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EventPointer_2.0.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/EventPointer.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EventPointer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EventPointer’ version ‘2.0.1’
* 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 ‘EventPointer’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘SGSeq:::addFeatureID’ ‘SGSeq:::addGeneID’ ‘SGSeq:::edges’
  ‘SGSeq:::exonGraph’ ‘SGSeq:::feature2name’ ‘SGSeq:::matchSGFeatures’
  ‘SGSeq:::nodes’ ‘SGSeq:::propagateAnnotation’
  ‘SGSeq:::splitCharacterList’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotate2: no visible global function definition for
  ‘addDummySpliceSites’
annotate2: no visible global function definition for ‘annotatePaths’
annotateFeatures2: no visible global function definition for
  ‘matchTxFeatures’
Undefined global functions or variables:
  addDummySpliceSites annotatePaths matchTxFeatures
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
CDFfromGTF                   6.883  0.166   7.127
CDFfromGTF_Multipath         6.168  0.061   6.555
EventsGTFfromTrancriptomeGTF 6.145  0.032   6.476
* 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-3.8-bioc/meat/EventPointer.Rcheck/00check.log’
for details.



Installation output

EventPointer.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EventPointer
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘EventPointer’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EventPointer)

Tests output

EventPointer.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> BiocGenerics:::testPackage("EventPointer")

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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'Biostrings'

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

    strsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    type

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

    aperm, apply


Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Creating SG Information...Creating SG Information...
 Obtaining Events
  |                                                                            
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  |============                                                          |  17%
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  |=======================                                               |  33%
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  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |==========================================================            |  83%
  |                                                                            
  |======================================================================| 100%


 Obtaining Events
  |                                                                            
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  |============                                                          |  17%
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  |=======================                                               |  33%
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  |===============================================                       |  67%
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  |==========================================================            |  83%
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  |======================================================================| 100%

Creating SG Information...Creating SG Information...Creating SG Information...Creating SG Information...Creating SG Information...Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK

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  |===================================                                   |  50%
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  |======================================================================| 100%

Creating .txt ...
.txt created
Creating .GTF ...
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  |========                                                              |  11%
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  |================                                                      |  22%
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  |=======================                                               |  33%
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  |===============================                                       |  44%
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  |=======================================                               |  56%
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  |===============================================                       |  67%
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  |======================================================                |  78%
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  |==============================================================        |  89%
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  |======================================================================| 100%

.txt created
Creating the sparseMatrix of paths x transcripts...

	******FINISHED******


RUNIT TEST PROTOCOL -- Mon Apr 15 23:56:49 2019 
*********************************************** 
Number of test functions: 13 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
EventPointer RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 24.613   0.935  25.880 

Example timings

EventPointer.Rcheck/EventPointer-Ex.timings

nameusersystemelapsed
CDFfromGTF6.8830.1667.127
CDFfromGTF_Multipath6.1680.0616.555
EventDetection2.3330.0432.406
EventDetectionMultipath1.3410.0071.361
EventPointer0.0670.0070.077
EventPointer_IGV4.0700.0204.221
EventPointer_RNASeq0.1240.0030.127
EventPointer_RNASeq_IGV4.6350.0324.812
EventPointer_RNASeq_TranRef0.0220.0040.026
EventsGTFfromTrancriptomeGTF6.1450.0326.476
GetPSI_FromTranRef0.0480.0030.051
PSI_Statistic0.1440.0030.149
PrepareBam_EP0.0000.0000.001
getbootstrapkallisto0.5830.0310.639