Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 1787/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rifi 1.12.0 (landing page) Jens Georg
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | 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. |
Package: rifi |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rifi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rifi_1.12.0.tar.gz |
StartedAt: 2025-10-14 09:13:45 -0400 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 09:36:16 -0400 (Tue, 14 Oct 2025) |
EllapsedTime: 1351.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rifi.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rifi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rifi_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/rifi.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rifi/DESCRIPTION’ ... OK * this is package ‘rifi’ version ‘1.12.0’ * 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 ... 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: /Users/biocbuild/bbs-3.21-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /Users/biocbuild/bbs-3.21-bioc/meat/rifi/man/predict_ps_itss.Rd:57: unexpected '}' See ‘/Users/biocbuild/bbs-3.21-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: /Users/biocbuild/bbs-3.21-bioc/meat/rifi.Rcheck/00_pkg_src/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /Users/biocbuild/bbs-3.21-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 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: /Users/biocbuild/bbs-3.21-bioc/meat/rifi.Rcheck/00_pkg_src/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /Users/biocbuild/bbs-3.21-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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed rifi_wrapper 258.378 74.334 319.752 rifi_penalties 123.802 51.747 186.113 nls2_fit 98.343 5.201 71.237 rifi_fit 62.585 0.806 67.364 rifi_visualization 52.346 2.230 57.148 TI_fit 30.365 4.787 21.937 make_pen 22.389 8.529 32.235 rifi_fragmentation 7.971 1.788 11.049 fold_change 7.357 0.348 8.144 rifi_stats 7.279 0.366 7.696 rifi_preprocess 4.086 1.067 4.474 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/rifi.Rcheck/00check.log’ for details.
rifi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rifi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘rifi’ ... ** this is package ‘rifi’ version ‘1.12.0’ ** 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: /Users/biocbuild/bbs-3.21-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /Users/biocbuild/bbs-3.21-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 | 30.365 | 4.787 | 21.937 | |
TUgether | 2.109 | 0.426 | 2.569 | |
apply_Ttest_delay | 0.247 | 0.044 | 0.308 | |
apply_ancova | 0.756 | 0.105 | 0.912 | |
apply_event_position | 0.243 | 0.035 | 0.294 | |
apply_manova | 1.433 | 0.203 | 1.720 | |
apply_t_test | 1.626 | 0.046 | 1.762 | |
apply_t_test_ti | 0.432 | 0.005 | 0.465 | |
check_input | 0.799 | 0.010 | 0.856 | |
dataframe_summary | 0.193 | 0.021 | 0.226 | |
dataframe_summary_TI | 0.117 | 0.009 | 0.127 | |
dataframe_summary_events | 1.706 | 0.051 | 1.846 | |
dataframe_summary_events_HL_int | 1.421 | 0.046 | 1.616 | |
dataframe_summary_events_ps_itss | 0.538 | 0.029 | 0.576 | |
dataframe_summary_events_velocity | 0.583 | 0.029 | 0.617 | |
event_dataframe | 1.720 | 0.044 | 1.898 | |
finding_PDD | 0.530 | 0.136 | 0.689 | |
finding_TI | 0.846 | 0.219 | 1.142 | |
fold_change | 7.357 | 0.348 | 8.144 | |
fragment_HL | 1.393 | 0.239 | 1.665 | |
fragment_TI | 1.087 | 0.122 | 1.269 | |
fragment_delay | 2.440 | 0.629 | 3.079 | |
fragment_inty | 1.483 | 0.301 | 1.820 | |
gff3_preprocess | 1.129 | 0.127 | 1.310 | |
make_df | 1.792 | 0.718 | 1.764 | |
make_pen | 22.389 | 8.529 | 32.235 | |
nls2_fit | 98.343 | 5.201 | 71.237 | |
predict_ps_itss | 0.657 | 0.077 | 0.791 | |
rifi_fit | 62.585 | 0.806 | 67.364 | |
rifi_fragmentation | 7.971 | 1.788 | 11.049 | |
rifi_penalties | 123.802 | 51.747 | 186.113 | |
rifi_preprocess | 4.086 | 1.067 | 4.474 | |
rifi_stats | 7.279 | 0.366 | 7.696 | |
rifi_summary | 4.610 | 0.075 | 4.930 | |
rifi_visualization | 52.346 | 2.230 | 57.148 | |
rifi_wrapper | 258.378 | 74.334 | 319.752 | |
segment_pos | 0.419 | 0.004 | 0.426 | |
viz_pen_obj | 0.013 | 0.010 | 0.023 | |