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This page was generated on 2025-10-27 12:45 -0400 (Mon, 27 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 1801/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rifi 1.13.1 (landing page) Jens Georg
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | ||||||||
|
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: /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_1.13.1.tar.gz |
| StartedAt: 2025-10-26 21:27:12 -0400 (Sun, 26 Oct 2025) |
| EndedAt: 2025-10-26 21:30:37 -0400 (Sun, 26 Oct 2025) |
| EllapsedTime: 205.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rifi.Rcheck |
| Warnings: 2 |
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### 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_1.13.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/rifi.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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: /Users/biocbuild/bbs-3.22-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
Warning: /Users/biocbuild/bbs-3.22-bioc/meat/rifi/man/predict_ps_itss.Rd:57: unexpected '}'
See ‘/Users/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: /Users/biocbuild/bbs-3.22-bioc/meat/rifi.Rcheck/00_pkg_src/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
Warning: /Users/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 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-3.22-bioc/meat/rifi.Rcheck/00_pkg_src/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
Warning: /Users/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 31.001 13.199 39.462
rifi_penalties 13.451 9.590 22.134
nls2_fit 10.628 0.540 6.805
rifi_visualization 10.320 0.691 11.014
rifi_fit 6.689 0.173 6.876
* 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-3.22-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-arm64/Resources/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: /Users/biocbuild/bbs-3.22-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /Users/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 | 3.669 | 0.638 | 2.506 | |
| TUgether | 0.115 | 0.034 | 0.145 | |
| apply_Ttest_delay | 0.031 | 0.009 | 0.040 | |
| apply_ancova | 0.079 | 0.030 | 0.109 | |
| apply_event_position | 0.026 | 0.006 | 0.033 | |
| apply_manova | 0.179 | 0.020 | 0.199 | |
| apply_t_test | 0.467 | 0.041 | 0.508 | |
| apply_t_test_ti | 0.043 | 0.001 | 0.044 | |
| check_input | 0.082 | 0.002 | 0.085 | |
| dataframe_summary | 0.026 | 0.003 | 0.030 | |
| dataframe_summary_TI | 0.014 | 0.002 | 0.016 | |
| dataframe_summary_events | 0.205 | 0.008 | 0.213 | |
| dataframe_summary_events_HL_int | 0.167 | 0.005 | 0.172 | |
| dataframe_summary_events_ps_itss | 0.072 | 0.004 | 0.077 | |
| dataframe_summary_events_velocity | 0.076 | 0.005 | 0.081 | |
| event_dataframe | 0.205 | 0.006 | 0.211 | |
| finding_PDD | 0.058 | 0.027 | 0.080 | |
| finding_TI | 0.093 | 0.038 | 0.125 | |
| fold_change | 0.758 | 0.041 | 0.800 | |
| fragment_HL | 0.155 | 0.056 | 0.204 | |
| fragment_TI | 0.099 | 0.025 | 0.124 | |
| fragment_delay | 0.227 | 0.074 | 0.292 | |
| fragment_inty | 0.164 | 0.071 | 0.228 | |
| gff3_preprocess | 0.197 | 0.040 | 0.238 | |
| make_df | 0.213 | 0.134 | 0.235 | |
| make_pen | 2.444 | 1.769 | 4.037 | |
| nls2_fit | 10.628 | 0.540 | 6.805 | |
| predict_ps_itss | 0.057 | 0.016 | 0.073 | |
| rifi_fit | 6.689 | 0.173 | 6.876 | |
| rifi_fragmentation | 0.770 | 0.307 | 1.050 | |
| rifi_penalties | 13.451 | 9.590 | 22.134 | |
| rifi_preprocess | 0.454 | 0.224 | 0.570 | |
| rifi_stats | 0.789 | 0.049 | 0.843 | |
| rifi_summary | 0.500 | 0.013 | 0.513 | |
| rifi_visualization | 10.320 | 0.691 | 11.014 | |
| rifi_wrapper | 31.001 | 13.199 | 39.462 | |
| segment_pos | 0.045 | 0.001 | 0.046 | |
| viz_pen_obj | 0.003 | 0.000 | 0.004 | |