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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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

Package 2120/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFEA.ChIP 1.27.0  (landing page)
Laura Puente Santamaría
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/TFEA.ChIP
git_branch: devel
git_last_commit: 34b5d7e
git_last_commit_date: 2024-10-29 10:24:34 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for TFEA.ChIP on nebbiolo1

To the developers/maintainers of the TFEA.ChIP package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: TFEA.ChIP
Version: 1.27.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:TFEA.ChIP.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings TFEA.ChIP_1.27.0.tar.gz
StartedAt: 2024-12-24 02:51:51 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 02:58:48 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 416.6 seconds
RetCode: 0
Status:   OK  
CheckDir: TFEA.ChIP.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:TFEA.ChIP.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings TFEA.ChIP_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/TFEA.ChIP.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘TFEA.ChIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TFEA.ChIP’ version ‘1.27.0’
* 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 ... INFO
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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    15.372  0.076  15.447
GSEA_run   11.394  0.197  11.591
getCMstats  7.246  0.074   7.320
plot_CM     6.244  0.042   6.286
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/TFEA.ChIP.Rcheck/00check.log’
for details.


Installation output

TFEA.ChIP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL TFEA.ChIP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 cell types in ENCODE's tiers 1, 2, and 2.5. 
To download the full ReMap2022 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! 16540 genes of 17527 successfully converted.

Couldn't find Entrez IDs for 987 genes.

Loading required namespace: DESeq2
Done! 10426 genes of 11667 successfully converted.

Couldn't find Entrez IDs for 1241 genes.

Done! 16540 genes of 17527 successfully converted.

Couldn't find Entrez IDs for 987 genes.

Done! 10426 genes of 11667 successfully converted.

Couldn't find Entrez IDs for 1241 genes.



RUNIT TEST PROTOCOL -- Tue Dec 24 02:57:56 2024 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TFEA.ChIP RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
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 
 46.229   1.177  47.404 

Example timings

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

nameusersystemelapsed
GSEA_EnrichmentScore000
GSEA_run11.394 0.19711.591
GeneID2entrez0.5250.0010.526
Select_genes0.0920.0180.110
contingency_matrix4.6410.0254.666
getCMstats7.2460.0747.320
get_chip_index0.0240.0120.036
makeChIPGeneDB0.0800.0030.082
matrixDB_to_listDB000
plot_CM6.2440.0426.286
plot_ES0.3580.0040.363
plot_RES1.3300.1131.425
preprocessInputData1.2260.2961.522
rankTFs15.372 0.07615.447
set_user_data1.0630.0071.069
txt2GR0.0300.0010.030