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This page was generated on 2025-10-27 12:45 -0400 (Mon, 27 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.7.7 Venturaarm644.5.1 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 1801/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rifi 1.13.1  (landing page)
Jens Georg
Snapshot Date: 2025-10-26 13:45 -0400 (Sun, 26 Oct 2025)
git_url: https://git.bioconductor.org/packages/rifi
git_branch: devel
git_last_commit: fa604e1
git_last_commit_date: 2025-06-27 12:04:57 -0400 (Fri, 27 Jun 2025)
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for rifi on kjohnson3

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: 1.13.1
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

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_1.13.1.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.


Installation output

rifi.Rcheck/00install.out

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###
### 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)

Tests output


Example timings

rifi.Rcheck/rifi-Ex.timings

nameusersystemelapsed
TI_fit3.6690.6382.506
TUgether0.1150.0340.145
apply_Ttest_delay0.0310.0090.040
apply_ancova0.0790.0300.109
apply_event_position0.0260.0060.033
apply_manova0.1790.0200.199
apply_t_test0.4670.0410.508
apply_t_test_ti0.0430.0010.044
check_input0.0820.0020.085
dataframe_summary0.0260.0030.030
dataframe_summary_TI0.0140.0020.016
dataframe_summary_events0.2050.0080.213
dataframe_summary_events_HL_int0.1670.0050.172
dataframe_summary_events_ps_itss0.0720.0040.077
dataframe_summary_events_velocity0.0760.0050.081
event_dataframe0.2050.0060.211
finding_PDD0.0580.0270.080
finding_TI0.0930.0380.125
fold_change0.7580.0410.800
fragment_HL0.1550.0560.204
fragment_TI0.0990.0250.124
fragment_delay0.2270.0740.292
fragment_inty0.1640.0710.228
gff3_preprocess0.1970.0400.238
make_df0.2130.1340.235
make_pen2.4441.7694.037
nls2_fit10.628 0.540 6.805
predict_ps_itss0.0570.0160.073
rifi_fit6.6890.1736.876
rifi_fragmentation0.7700.3071.050
rifi_penalties13.451 9.59022.134
rifi_preprocess0.4540.2240.570
rifi_stats0.7890.0490.843
rifi_summary0.5000.0130.513
rifi_visualization10.320 0.69111.014
rifi_wrapper31.00113.19939.462
segment_pos0.0450.0010.046
viz_pen_obj0.0030.0000.004