Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-19 12:04 -0400 (Tue, 19 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4536 |
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 1767/2317 | 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 | TIMEOUT | skipped | ||||||||||
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: 1.13.1 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings rifi_1.13.1.tar.gz |
StartedAt: 2025-08-19 02:13:54 -0400 (Tue, 19 Aug 2025) |
EndedAt: 2025-08-19 02:24:12 -0400 (Tue, 19 Aug 2025) |
EllapsedTime: 618.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rifi.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings rifi_1.13.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/rifi.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 ‘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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed rifi_wrapper 101.630 75.218 133.271 rifi_penalties 48.354 47.648 75.520 nls2_fit 37.257 2.706 23.416 rifi_visualization 29.708 2.280 31.991 rifi_fit 22.411 0.685 23.097 make_pen 8.386 7.194 12.448 TI_fit 11.159 1.760 7.564 * 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: 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/rifi.Rcheck/00check.log’ for details.
rifi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL rifi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 | 11.159 | 1.760 | 7.564 | |
TUgether | 0.389 | 0.172 | 0.509 | |
apply_Ttest_delay | 0.091 | 0.028 | 0.119 | |
apply_ancova | 1.068 | 0.337 | 1.405 | |
apply_event_position | 0.094 | 0.009 | 0.103 | |
apply_manova | 0.534 | 0.012 | 0.546 | |
apply_t_test | 0.651 | 0.044 | 0.695 | |
apply_t_test_ti | 0.159 | 0.009 | 0.168 | |
check_input | 0.311 | 0.023 | 0.334 | |
dataframe_summary | 0.089 | 0.007 | 0.097 | |
dataframe_summary_TI | 0.043 | 0.001 | 0.045 | |
dataframe_summary_events | 0.647 | 0.011 | 0.658 | |
dataframe_summary_events_HL_int | 0.528 | 0.018 | 0.545 | |
dataframe_summary_events_ps_itss | 0.198 | 0.005 | 0.202 | |
dataframe_summary_events_velocity | 0.203 | 0.005 | 0.208 | |
event_dataframe | 0.652 | 0.019 | 0.672 | |
finding_PDD | 0.206 | 0.120 | 0.276 | |
finding_TI | 0.308 | 0.146 | 0.400 | |
fold_change | 2.808 | 0.189 | 2.997 | |
fragment_HL | 0.551 | 0.165 | 0.637 | |
fragment_TI | 0.399 | 0.044 | 0.443 | |
fragment_delay | 0.847 | 0.291 | 1.031 | |
fragment_inty | 0.542 | 0.216 | 0.682 | |
gff3_preprocess | 0.524 | 0.068 | 0.593 | |
make_df | 0.813 | 0.486 | 0.810 | |
make_pen | 8.386 | 7.194 | 12.448 | |
nls2_fit | 37.257 | 2.706 | 23.416 | |
predict_ps_itss | 0.276 | 0.034 | 0.311 | |
rifi_fit | 22.411 | 0.685 | 23.097 | |
rifi_fragmentation | 2.828 | 0.911 | 3.415 | |
rifi_penalties | 48.354 | 47.648 | 75.520 | |
rifi_preprocess | 1.571 | 0.606 | 1.748 | |
rifi_stats | 2.988 | 0.142 | 3.130 | |
rifi_summary | 1.962 | 0.106 | 2.068 | |
rifi_visualization | 29.708 | 2.280 | 31.991 | |
rifi_wrapper | 101.630 | 75.218 | 133.271 | |
segment_pos | 0.172 | 0.000 | 0.172 | |
viz_pen_obj | 0.01 | 0.00 | 0.01 | |