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CHECK report for TFEA.ChIP on merida2

This page was generated on 2019-04-09 13:36:15 -0400 (Tue, 09 Apr 2019).

Package 1606/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFEA.ChIP 1.3.5
Laura Puente SantamarĂ­a
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/TFEA.ChIP
Branch: master
Last Commit: 390b328
Last Changed Date: 2019-04-05 09:10:31 -0400 (Fri, 05 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
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: TFEA.ChIP
Version: 1.3.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TFEA.ChIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TFEA.ChIP_1.3.5.tar.gz
StartedAt: 2019-04-09 04:05:08 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:11:09 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 361.5 seconds
RetCode: 1
Status:  ERROR 
CheckDir: TFEA.ChIP.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TFEA.ChIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TFEA.ChIP_1.3.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TFEA.ChIP.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 ‘TFEA.ChIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TFEA.ChIP’ version ‘1.3.5’
* package encoding: UTF-8
* 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 ‘TFEA.ChIP’ 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 ... OK
* 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
GSEA_run           9.589  0.446  10.134
contingency_matrix 8.532  0.486   9.104
set_user_data      6.088  0.111   6.257
GeneID2entrez      1.067  0.056  25.413
* 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 : 
  TFEA.ChIP RUnit Tests - 11 test functions, 1 error, 0 failures
  ERROR in test_contingency_matrix: Error in get_chip_index(TFfilter = "EPAS1") : 
    No ChIP-Seq dataset in the database follows your conditions.
  
  Test files with failing tests
  
     test_TFEA.ChIP.R 
       test_contingency_matrix 
  
  
  Error in BiocGenerics:::testPackage(pkgname = "TFEA.ChIP") : 
    unit tests failed for package TFEA.ChIP
  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
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/TFEA.ChIP.Rcheck/00check.log’
for details.


Installation output

TFEA.ChIP.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TFEA.ChIP
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘TFEA.ChIP’ ...
** R
** data
** 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 (TFEA.ChIP)

Tests output

TFEA.ChIP.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(pkgname = "TFEA.ChIP")

Because of space limitations, TFEA.ChIPs internal database only includes ChIP-seq experiments from the ENCODE project. 
To download the full ReMap database, as well as other ready-to-use databases, visit https://github.com/LauraPS1/TFEA.ChIP_downloads

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Done! 2 genes of 2 successfully translated.

Done! 1 genes of 1 successfully translated.

Done! 1 genes of 1 successfully translated.

Done! 2 genes of 2 successfully translated.

Timing stopped at: 7.854 0.419 8.349
Error in get_chip_index(TFfilter = "EPAS1") : 
  No ChIP-Seq dataset in the database follows your conditions.
In addition: Warning message:
Some genes returned 1:many mapping to ENTREZ ID. Genes were assigned the first ENTREZ ID match found.
 
Done! 16975 genes of 17527 successfully translated.

Couldn't find Entrez IDs for 552 genes.

Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
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, 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

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

Done! 10651 genes of 11667 successfully translated.

Couldn't find Entrez IDs for 1016 genes.

Done! 16975 genes of 17527 successfully translated.

Couldn't find Entrez IDs for 552 genes.

Done! 10651 genes of 11667 successfully translated.

Couldn't find Entrez IDs for 1016 genes.



RUNIT TEST PROTOCOL -- Tue Apr  9 04:11:02 2019 
*********************************************** 
Number of test functions: 11 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
TFEA.ChIP RUnit Tests - 11 test functions, 1 error, 0 failures
ERROR in test_contingency_matrix: Error in get_chip_index(TFfilter = "EPAS1") : 
  No ChIP-Seq dataset in the database follows your conditions.

Test files with failing tests

   test_TFEA.ChIP.R 
     test_contingency_matrix 


Error in BiocGenerics:::testPackage(pkgname = "TFEA.ChIP") : 
  unit tests failed for package TFEA.ChIP
Execution halted

Example timings

TFEA.ChIP.Rcheck/TFEA.ChIP-Ex.timings

nameusersystemelapsed
GR2tfbs_db0.7700.0480.825
GSEA_EnrichmentScore0.0000.0000.001
GSEA_run 9.589 0.44610.134
GeneID2entrez 1.067 0.05625.413
Select_genes0.1500.0150.166
contingency_matrix8.5320.4869.104
getCMstats0.0620.0020.064
get_chip_index0.0790.0100.090
makeTFBSmatrix0.0510.0360.088
plot_CM0.4810.0420.533
plot_ES0.6590.0610.729
plot_RES1.3880.9740.825
preprocessInputData2.3470.2482.620
rankTFs0.0350.0010.037
set_user_data6.0880.1116.257
txt2GR0.0400.0010.043