Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-04 12:07 -0400 (Sat, 04 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" | 4853 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (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 1785/2341 | 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 12.7.1 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: 2025-10-03 10:49:16 -0000 (Fri, 03 Oct 2025) |
EndedAt: 2025-10-03 11:29:17 -0000 (Fri, 03 Oct 2025) |
EllapsedTime: 2400.4 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 | 15.948 | 1.072 | 10.942 | |
TUgether | 0.630 | 0.271 | 0.803 | |
apply_Ttest_delay | 0.141 | 0.032 | 0.174 | |
apply_ancova | 0.458 | 0.080 | 0.539 | |
apply_event_position | 0.166 | 0.007 | 0.174 | |
apply_manova | 0.858 | 0.132 | 0.992 | |
apply_t_test | 0.987 | 0.016 | 1.005 | |
apply_t_test_ti | 0.235 | 0.000 | 0.236 | |
check_input | 0.467 | 0.000 | 0.468 | |
dataframe_summary | 0.116 | 0.008 | 0.124 | |
dataframe_summary_TI | 0.061 | 0.008 | 0.069 | |
dataframe_summary_events | 1.172 | 0.043 | 1.219 | |
dataframe_summary_events_HL_int | 0.891 | 0.084 | 0.977 | |
dataframe_summary_events_ps_itss | 0.376 | 0.036 | 0.413 | |
dataframe_summary_events_velocity | 0.345 | 0.040 | 0.386 | |
event_dataframe | 1.049 | 0.072 | 1.124 | |
finding_PDD | 0.309 | 0.177 | 0.413 | |
finding_TI | 0.485 | 0.199 | 0.619 | |
fold_change | 4.483 | 0.363 | 4.860 | |
fragment_HL | 0.843 | 0.223 | 0.962 | |
fragment_TI | 0.598 | 0.107 | 0.706 | |
fragment_delay | 1.362 | 0.399 | 1.632 | |
fragment_inty | 0.834 | 0.312 | 1.054 | |
gff3_preprocess | 0.575 | 0.123 | 0.702 | |
make_df | 1.062 | 0.555 | 1.108 | |
make_pen | 12.491 | 9.264 | 18.018 | |
nls2_fit | 57.083 | 2.911 | 35.489 | |
predict_ps_itss | 0.372 | 0.083 | 0.457 | |
rifi_fit | 38.942 | 1.828 | 40.923 | |
rifi_fragmentation | 4.242 | 1.467 | 5.299 | |
rifi_penalties | 68.669 | 54.688 | 103.741 | |
rifi_preprocess | 2.317 | 0.969 | 2.888 | |
rifi_stats | 4.574 | 0.260 | 4.848 | |
rifi_summary | 2.896 | 0.064 | 2.970 | |
rifi_visualization | 44.577 | 0.918 | 45.596 | |