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CHECK report for EventPointer on merida2

This page was generated on 2019-04-09 13:34:38 -0400 (Tue, 09 Apr 2019).

Package 514/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EventPointer 2.1.4
Juan Pablo Romero
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/EventPointer
Branch: master
Last Commit: bf5b1af
Last Changed Date: 2019-04-08 07:59:54 -0400 (Mon, 08 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: EventPointer
Version: 2.1.4
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_2.1.4.tar.gz
StartedAt: 2019-04-09 00:47:29 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:53:29 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 360.1 seconds
RetCode: 1
Status:  ERROR 
CheckDir: EventPointer.Rcheck
Warnings: NA

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_2.1.4.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/EventPointer.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘2.1.4’
* 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                   6.647  0.132   6.843
EventsGTFfromTrancriptomeGTF 5.818  0.029   5.922
CDFfromGTF_Multipath         5.483  0.042   5.597
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  EventPointer RUnit Tests - 14 test functions, 0 errors, 1 failure
  FAILURE in test_FindPrimers: Error in checkIdentical("Dir = Complete path where primer3web_v4_0_0_default_settings.txt file and primer3_config directory are stored",  : 
    FALSE 
   
  
  Test files with failing tests
  
     test_FindPrimers.R 
       test_FindPrimers 
  
  
  Error in BiocGenerics:::testPackage("EventPointer") : 
    unit tests failed for package EventPointer
  Execution halted
* 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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-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/3.6/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.fail


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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.

> 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, 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, rowsum


Attaching package: 'Matrix'

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

    expand

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


 Obtaining Events
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  |==========================================================            |  83%
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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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Creating .txt ...
.txt created
Creating .GTF ...
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.txt created
Creating the sparseMatrix of paths x transcripts...

	******FINISHED******
Timing stopped at: 0.001 0 0.001
Error in checkIdentical("Dir = Complete path where primer3web_v4_0_0_default_settings.txt file and primer3_config directory are stored",  : 
  FALSE 
 


RUNIT TEST PROTOCOL -- Tue Apr  9 00:53:19 2019 
*********************************************** 
Number of test functions: 14 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
EventPointer RUnit Tests - 14 test functions, 0 errors, 1 failure
FAILURE in test_FindPrimers: Error in checkIdentical("Dir = Complete path where primer3web_v4_0_0_default_settings.txt file and primer3_config directory are stored",  : 
  FALSE 
 

Test files with failing tests

   test_FindPrimers.R 
     test_FindPrimers 


Error in BiocGenerics:::testPackage("EventPointer") : 
  unit tests failed for package EventPointer
Execution halted

Example timings

EventPointer.Rcheck/EventPointer-Ex.timings

nameusersystemelapsed
CDFfromGTF6.6470.1326.843
CDFfromGTF_Multipath5.4830.0425.597
EventDetection1.8630.0301.915
EventDetectionMultipath1.3170.0091.342
EventPointer0.0730.0110.084
EventPointer_IGV3.4600.0153.498
EventPointer_RNASeq0.1140.0030.118
EventPointer_RNASeq_IGV4.1330.0304.197
EventPointer_RNASeq_TranRef0.0240.0040.029
EventsGTFfromTrancriptomeGTF5.8180.0295.922
FindPrimers0.0010.0000.000
GetPSI_FromTranRef0.0280.0030.032
PSI_Statistic0.1320.0030.136
PrepareBam_EP0.0010.0000.001
getbootstrapkallisto0.4330.0280.471