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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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 1787/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rifi 1.12.0  (landing page)
Jens Georg
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/rifi
git_branch: RELEASE_3_21
git_last_commit: b02f67c
git_last_commit_date: 2025-04-15 12:51:32 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


CHECK results for rifi on merida1

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.

raw results


Summary

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

Command output

##############################################################################
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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_1.12.0.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.


Installation output

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)

Tests output


Example timings

rifi.Rcheck/rifi-Ex.timings

nameusersystemelapsed
TI_fit30.365 4.78721.937
TUgether2.1090.4262.569
apply_Ttest_delay0.2470.0440.308
apply_ancova0.7560.1050.912
apply_event_position0.2430.0350.294
apply_manova1.4330.2031.720
apply_t_test1.6260.0461.762
apply_t_test_ti0.4320.0050.465
check_input0.7990.0100.856
dataframe_summary0.1930.0210.226
dataframe_summary_TI0.1170.0090.127
dataframe_summary_events1.7060.0511.846
dataframe_summary_events_HL_int1.4210.0461.616
dataframe_summary_events_ps_itss0.5380.0290.576
dataframe_summary_events_velocity0.5830.0290.617
event_dataframe1.7200.0441.898
finding_PDD0.5300.1360.689
finding_TI0.8460.2191.142
fold_change7.3570.3488.144
fragment_HL1.3930.2391.665
fragment_TI1.0870.1221.269
fragment_delay2.4400.6293.079
fragment_inty1.4830.3011.820
gff3_preprocess1.1290.1271.310
make_df1.7920.7181.764
make_pen22.389 8.52932.235
nls2_fit98.343 5.20171.237
predict_ps_itss0.6570.0770.791
rifi_fit62.585 0.80667.364
rifi_fragmentation 7.971 1.78811.049
rifi_penalties123.802 51.747186.113
rifi_preprocess4.0861.0674.474
rifi_stats7.2790.3667.696
rifi_summary4.6100.0754.930
rifi_visualization52.346 2.23057.148
rifi_wrapper258.378 74.334319.752
segment_pos0.4190.0040.426
viz_pen_obj0.0130.0100.023