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This page was generated on 2021-09-24 15:05:59 -0400 (Fri, 24 Sep 2021).

CHECK results for TFEA.ChIP on nebbiolo1

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raw results

Package 1909/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFEA.ChIP 1.12.0  (landing page)
Laura Puente Santamaría
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/TFEA.ChIP
git_branch: RELEASE_3_13
git_last_commit: ef83d9d
git_last_commit_date: 2021-05-19 12:32:25 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TFEA.ChIP
Version: 1.12.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TFEA.ChIP.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TFEA.ChIP_1.12.0.tar.gz
StartedAt: 2021-09-23 11:48:50 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 11:53:54 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 303.9 seconds
RetCode: 0
Status:   OK  
CheckDir: TFEA.ChIP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TFEA.ChIP.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TFEA.ChIP_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/TFEA.ChIP.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’
* 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 ... NOTE
rankTFs: no visible binding for global variable ‘arg.ES’
rankTFs: no visible binding for global variable ‘ES’
rankTFs: no visible binding for global variable ‘TF’
Undefined global functions or variables:
  ES TF arg.ES
* 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 (user + system) or elapsed time > 5s
                     user system elapsed
rankTFs            11.402  0.348  11.750
GSEA_run            5.866  0.255   6.123
plot_CM             5.731  0.308   6.040
getCMstats          5.528  0.280   5.809
contingency_matrix  5.176  0.252   5.429
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/TFEA.ChIP.Rcheck/00check.log’
for details.



Installation output

TFEA.ChIP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL TFEA.ChIP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘TFEA.ChIP’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TFEA.ChIP)

Tests output

TFEA.ChIP.Rcheck/tests/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 converted.

Done! 1 genes of 1 successfully converted.

Done! 1 genes of 1 successfully converted.

Done! 2 genes of 2 successfully converted.

Done! 16675 genes of 17527 successfully converted.

Couldn't find Entrez IDs for 852 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, 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, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Done! 10494 genes of 11667 successfully converted.

Couldn't find Entrez IDs for 1173 genes.

Done! 16675 genes of 17527 successfully converted.

Couldn't find Entrez IDs for 852 genes.

Done! 10494 genes of 11667 successfully converted.

Couldn't find Entrez IDs for 1173 genes.



RUNIT TEST PROTOCOL -- Thu Sep 23 11:53:51 2021 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TFEA.ChIP RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
Warning message:
Some genes returned 1:many mapping to ENTREZ ID. Genes were assigned the first ENTREZ ID match found.
 
> 
> proc.time()
   user  system elapsed 
 40.374   1.208  41.571 

Example timings

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

nameusersystemelapsed
GR2tfbs_db0.5640.0120.576
GSEA_EnrichmentScore0.0000.0010.001
GSEA_run5.8660.2556.123
GeneID2entrez0.2640.0000.264
Select_genes0.0860.0270.115
contingency_matrix5.1760.2525.429
getCMstats5.5280.2805.809
get_chip_index0.0270.0200.047
makeTFBSmatrix0.0230.0640.086
plot_CM5.7310.3086.040
plot_ES0.4380.0150.454
plot_RES0.7980.0680.847
preprocessInputData1.2110.3121.523
rankTFs11.402 0.34811.750
set_user_data2.5480.0802.628
txt2GR0.0290.0040.034