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This page was generated on 2022-01-17 11:08:33 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for TFEA.ChIP on riesling1


To the developers/maintainers of the TFEA.ChIP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TFEA.ChIP.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1938/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFEA.ChIP 1.15.1  (landing page)
Laura Puente SantamarĂ­a
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/TFEA.ChIP
git_branch: master
git_last_commit: 8dfc758
git_last_commit_date: 2021-11-21 01:00:12 -0500 (Sun, 21 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TFEA.ChIP
Version: 1.15.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TFEA.ChIP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TFEA.ChIP_1.15.1.tar.gz
StartedAt: 2022-01-16 20:21:11 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 20:26:30 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 318.8 seconds
RetCode: 0
Status:   OK  
CheckDir: TFEA.ChIP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TFEA.ChIP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TFEA.ChIP_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/TFEA.ChIP.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TFEA.ChIP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TFEA.ChIP' version '1.15.1'
* 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 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    16.83   1.28   18.11
plot_CM     7.17   0.92    8.10
getCMstats  6.30   1.00    7.30
GSEA_run    5.93   0.70    6.63
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/TFEA.ChIP.Rcheck/00check.log'
for details.



Installation output

TFEA.ChIP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL TFEA.ChIP
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'TFEA.ChIP'
    finding HTML links ... done
    ARNT.metadata                           html  
    ARNT.peaks.bed                          html  
    DnaseHS_db                              html  
    Entrez.gene.IDs                         html  
    GR2tfbs_db                              html  
    GSEA.result                             html  
    GSEA_ESpermutations                     html  
    GSEA_EnrichmentScore                    html  
    GSEA_run                                html  
    GeneID2entrez                           html  
    Genes.Upreg                             html  
    Mat01                                   html  
    MetaData                                html  
    Select_genes                            html  
    contingency_matrix                      html  
    getCMstats                              html  
    get_LFC_bar                             html  
    get_chip_index                          html  
    gr.list                                 html  
    highlight_TF                            html  
    hypoxia                                 html  
    hypoxia_DESeq                           html  
    log2.FC                                 html  
    makeTFBSmatrix                          html  
    plot_CM                                 html  
    plot_ES                                 html  
    plot_RES                                html  
    preprocessInputData                     html  
    rankTFs                                 html  
    set_user_data                           html  
    tfbs.database                           html  
    txt2GR                                  html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'bumphunter' is missing or broken
 done

Tests output

TFEA.ChIP.Rcheck/tests/runTests.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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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  |======================================================================| 100%

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  |===================================                                   |  50%
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  |======================================================================| 100%
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! 16646 genes of 17527 successfully converted.

Couldn't find Entrez IDs for 881 genes.

Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

Attaching package: 'IRanges'

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

    windows

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! 10484 genes of 11667 successfully converted.

Couldn't find Entrez IDs for 1183 genes.

Done! 16646 genes of 17527 successfully converted.

Couldn't find Entrez IDs for 881 genes.

Done! 10484 genes of 11667 successfully converted.

Couldn't find Entrez IDs for 1183 genes.



RUNIT TEST PROTOCOL -- Sun Jan 16 20:26:10 2022 
*********************************************** 
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 
  39.84    5.23   45.03 

Example timings

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

nameusersystemelapsed
GR2tfbs_db1.060.061.12
GSEA_EnrichmentScore000
GSEA_run5.930.706.63
GeneID2entrez0.250.000.25
Select_genes0.060.060.12
contingency_matrix4.560.384.94
getCMstats6.31.07.3
get_chip_index0.030.030.06
makeTFBSmatrix0.030.030.06
plot_CM7.170.928.10
plot_ES0.630.130.75
plot_RES1.110.171.28
preprocessInputData1.400.241.64
rankTFs16.83 1.2818.11
set_user_data3.430.073.52
txt2GR0.030.000.03