| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-24 12:04 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 2204/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TFHAZ 1.31.0 (landing page) Gaia Ceddia
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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. |
| 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: 2025-10-24 04:42:55 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 04:48:26 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 331.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TFHAZ.Rcheck |
| Warnings: 1 |
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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
###
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* 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 7.058 0.168 7.226
accumulation 5.283 0.109 5.391
* 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.
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)
TFHAZ.Rcheck/TFHAZ-Ex.timings
| name | user | system | elapsed | |
| Ishikawa | 0.082 | 0.003 | 0.085 | |
| TF_acc_w_0 | 0.122 | 0.012 | 0.134 | |
| TF_dense_w_0 | 0.110 | 0.000 | 0.111 | |
| TF_dense_w_10 | 0.109 | 0.002 | 0.110 | |
| TF_dense_w_100 | 0.113 | 0.001 | 0.112 | |
| TF_dense_w_1000 | 0.112 | 0.009 | 0.121 | |
| TF_dense_w_10000 | 0.123 | 0.028 | 0.150 | |
| accumulation | 5.283 | 0.109 | 5.391 | |
| base_dense_w_10 | 0.106 | 0.002 | 0.108 | |
| dense_zones | 7.058 | 0.168 | 7.226 | |
| high_accumulation_zones | 0.238 | 0.033 | 0.272 | |
| n_zones_PCA | 0.024 | 0.000 | 0.024 | |
| plot_accumulation | 0 | 0 | 0 | |
| plot_n_zones | 0.006 | 0.000 | 0.008 | |
| reg_dense_w_10 | 0.112 | 0.001 | 0.114 | |
| w_analysis | 0.008 | 0.000 | 0.008 | |