Laura Puente Santamaría
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/TFEA.ChIP |
| Branch: RELEASE_3_11 |
| Last Commit: b65b6f8 |
| Last Changed Date: 2020-04-27 15:12:47 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:59:47 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE TFEA.ChIP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1794/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TFEA.ChIP 1.8.0 Laura Puente Santamaría
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: TFEA.ChIP |
| Version: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2020-10-17 05:52:10 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:00:30 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 500.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TFEA.ChIP.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/TFEA.ChIP.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.8.0’
* 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 ... 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 (user + system) or elapsed time > 5s
user system elapsed
GSEA_run 8.887 0.824 9.763
contingency_matrix 8.971 0.529 9.511
set_user_data 5.862 0.103 5.970
GeneID2entrez 4.309 0.057 8.614
* 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: OK
TFEA.ChIP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TFEA.ChIP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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)
TFEA.ChIP.Rcheck/tests/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 converted.
Done! 1 genes of 1 successfully converted.
Done! 1 genes of 1 successfully converted.
Done! 2 genes of 2 successfully converted.
Done! 16777 genes of 17527 successfully converted.
Couldn't find Entrez IDs for 750 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, 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
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! 10546 genes of 11667 successfully converted.
Couldn't find Entrez IDs for 1121 genes.
Done! 16777 genes of 17527 successfully converted.
Couldn't find Entrez IDs for 750 genes.
Done! 10546 genes of 11667 successfully converted.
Couldn't find Entrez IDs for 1121 genes.
RUNIT TEST PROTOCOL -- Sat Oct 17 06:00:21 2020
***********************************************
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
55.472 3.744 62.784
TFEA.ChIP.Rcheck/TFEA.ChIP-Ex.timings
| name | user | system | elapsed | |
| GR2tfbs_db | 1.029 | 0.078 | 1.106 | |
| GSEA_EnrichmentScore | 0.000 | 0.001 | 0.002 | |
| GSEA_run | 8.887 | 0.824 | 9.763 | |
| GeneID2entrez | 4.309 | 0.057 | 8.614 | |
| Select_genes | 0.149 | 0.051 | 0.200 | |
| contingency_matrix | 8.971 | 0.529 | 9.511 | |
| getCMstats | 0.061 | 0.011 | 0.072 | |
| get_chip_index | 0.092 | 0.037 | 0.130 | |
| makeTFBSmatrix | 0.057 | 0.090 | 0.147 | |
| plot_CM | 0.568 | 0.062 | 0.634 | |
| plot_ES | 0.841 | 0.107 | 0.950 | |
| plot_RES | 0.942 | 0.118 | 1.063 | |
| preprocessInputData | 2.385 | 0.386 | 2.797 | |
| rankTFs | 0.042 | 0.004 | 0.047 | |
| set_user_data | 5.862 | 0.103 | 5.970 | |
| txt2GR | 0.047 | 0.004 | 0.052 | |