| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 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" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1793/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rifi 1.13.1 (landing page) Jens Georg
| 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 | TIMEOUT | ||||||||||
|
To the developers/maintainers of the rifi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rifi.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: rifi |
| Version: 1.13.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rifi_1.13.1.tar.gz |
| StartedAt: 2025-10-17 12:49:21 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 13:29:22 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 2400.5 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: rifi.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rifi_1.13.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/rifi.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rifi/DESCRIPTION’ ... OK
* this is package ‘rifi’ version ‘1.13.1’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
R/.ipynb_checkpoints
vignettes/.ipynb_checkpoints
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rifi’ can be installed ... WARNING
Found the following significant warnings:
Note: next used in wrong context: no loop is visible
Warning: /home/biocbuild/bbs-3.22-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
Warning: /home/biocbuild/bbs-3.22-bioc/meat/rifi/man/predict_ps_itss.Rd:57: unexpected '}'
See ‘/home/biocbuild/bbs-3.22-bioc/meat/rifi.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...Warning: /home/biocbuild/bbs-3.22-bioc/meat/rifi.Rcheck/00_pkg_src/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
Warning: /home/biocbuild/bbs-3.22-bioc/meat/rifi.Rcheck/00_pkg_src/rifi/man/predict_ps_itss.Rd:57: unexpected '}'
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 ... WARNING
prepare_Rd: ./man/apply_Ttest_delay.Rd:55: unexpected '}'
prepare_Rd: ./man/predict_ps_itss.Rd:57: unexpected '}'
* checking Rd metadata ... OK
* checking Rd cross-references ...Warning: /home/biocbuild/bbs-3.22-bioc/meat/rifi.Rcheck/00_pkg_src/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
Warning: /home/biocbuild/bbs-3.22-bioc/meat/rifi.Rcheck/00_pkg_src/rifi/man/predict_ps_itss.Rd:57: unexpected '}'
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 ...
rifi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL rifi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘rifi’ ... ** this is package ‘rifi’ version ‘1.13.1’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: next used in wrong context: no loop is visible ** help Warning: /home/biocbuild/bbs-3.22-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /home/biocbuild/bbs-3.22-bioc/meat/rifi/man/predict_ps_itss.Rd:57: unexpected '}' *** 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 (rifi)
rifi.Rcheck/rifi-Ex.timings
| name | user | system | elapsed | |
| TI_fit | 16.221 | 0.922 | 10.734 | |
| TUgether | 0.707 | 0.223 | 0.847 | |
| apply_Ttest_delay | 0.168 | 0.028 | 0.197 | |
| apply_ancova | 0.484 | 0.048 | 0.534 | |
| apply_event_position | 0.158 | 0.016 | 0.175 | |
| apply_manova | 1.004 | 0.111 | 1.119 | |
| apply_t_test | 1.035 | 0.076 | 1.114 | |
| apply_t_test_ti | 0.253 | 0.020 | 0.273 | |
| check_input | 0.470 | 0.048 | 0.520 | |
| dataframe_summary | 0.111 | 0.020 | 0.131 | |
| dataframe_summary_TI | 0.060 | 0.012 | 0.072 | |
| dataframe_summary_events | 1.157 | 0.064 | 1.223 | |
| dataframe_summary_events_HL_int | 0.848 | 0.024 | 0.874 | |
| dataframe_summary_events_ps_itss | 0.336 | 0.004 | 0.342 | |
| dataframe_summary_events_velocity | 0.354 | 0.008 | 0.363 | |
| event_dataframe | 1.133 | 0.028 | 1.164 | |
| finding_PDD | 0.344 | 0.190 | 0.477 | |
| finding_TI | 0.519 | 0.225 | 0.684 | |
| fold_change | 4.710 | 0.495 | 5.225 | |
| fragment_HL | 0.921 | 0.258 | 1.071 | |
| fragment_TI | 0.665 | 0.072 | 0.740 | |
| fragment_delay | 1.421 | 0.414 | 1.712 | |
| fragment_inty | 0.890 | 0.326 | 1.126 | |
| gff3_preprocess | 0.627 | 0.128 | 0.758 | |
| make_df | 1.141 | 0.585 | 1.107 | |
| make_pen | 13.189 | 9.481 | 18.789 | |
| nls2_fit | 57.071 | 3.171 | 36.925 | |
| predict_ps_itss | 0.429 | 0.071 | 0.501 | |
| rifi_fit | 38.568 | 1.292 | 40.158 | |
| rifi_fragmentation | 4.548 | 1.264 | 5.432 | |
| rifi_penalties | 69.268 | 53.120 | 103.399 | |
| rifi_preprocess | 2.389 | 0.708 | 2.869 | |
| rifi_stats | 4.395 | 0.340 | 4.863 | |
| rifi_summary | 2.817 | 0.108 | 2.938 | |
| rifi_visualization | 42.922 | 1.001 | 44.201 | |