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This page was generated on 2025-10-03 12:04 -0400 (Fri, 03 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4845
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4632
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4577
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 2182/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFHAZ 1.31.0  (landing page)
Gaia Ceddia
Snapshot Date: 2025-10-02 13:45 -0400 (Thu, 02 Oct 2025)
git_url: https://git.bioconductor.org/packages/TFHAZ
git_branch: devel
git_last_commit: 2fbb6c2
git_last_commit_date: 2025-04-15 11:14:05 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for TFHAZ on nebbiolo2

To the developers/maintainers of the TFHAZ package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TFHAZ.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: TFHAZ
Version: 1.31.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:TFHAZ.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings TFHAZ_1.31.0.tar.gz
StartedAt: 2025-10-03 05:02:15 -0400 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 05:08:44 -0400 (Fri, 03 Oct 2025)
EllapsedTime: 388.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TFHAZ.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:TFHAZ.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings TFHAZ_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/TFHAZ.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘TFHAZ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TFHAZ’ version ‘1.31.0’
* 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 ‘TFHAZ’ can be installed ... WARNING
Found the following significant warnings:
  Warning: no function found corresponding to methods exports from ‘ORFik’ for: ‘organism’
See ‘/home/biocbuild/bbs-3.22-bioc/meat/TFHAZ.Rcheck/00install.out’ for details.
* 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 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 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 LazyData ... 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
dense_zones  8.305  0.084   8.401
accumulation 6.706  0.230   6.954
* 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 WARNING
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/TFHAZ.Rcheck/00check.log’
for details.


Installation output

TFHAZ.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL TFHAZ
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘TFHAZ’ ...
** this is package ‘TFHAZ’ version ‘1.31.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Warning: no function found corresponding to methods exports from ‘ORFik’ for: ‘organism’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: no function found corresponding to methods exports from ‘ORFik’ for: ‘organism’
** testing if installed package can be loaded from final location
Warning: no function found corresponding to methods exports from ‘ORFik’ for: ‘organism’
** testing if installed package keeps a record of temporary installation path
* DONE (TFHAZ)

Tests output


Example timings

TFHAZ.Rcheck/TFHAZ-Ex.timings

nameusersystemelapsed
Ishikawa0.0960.0070.103
TF_acc_w_00.1510.0130.164
TF_dense_w_00.1260.0010.128
TF_dense_w_100.1190.0010.121
TF_dense_w_1000.1200.0010.122
TF_dense_w_10000.1220.0100.132
TF_dense_w_100000.1460.0190.166
accumulation6.7060.2306.954
base_dense_w_100.1150.0010.116
dense_zones8.3050.0848.401
high_accumulation_zones0.2690.0500.319
n_zones_PCA0.0240.0020.026
plot_accumulation000
plot_n_zones0.0080.0000.008
reg_dense_w_100.1240.0020.126
w_analysis0.0070.0010.008