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This page was generated on 2025-10-07 12:04 -0400 (Tue, 07 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 1785/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rifi 1.13.1  (landing page)
Jens Georg
Snapshot Date: 2025-10-06 13:45 -0400 (Mon, 06 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)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    TIMEOUT  skipped


CHECK results for rifi on nebbiolo2

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: /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: 2025-10-07 03:35:45 -0400 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 03:46:06 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 620.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rifi.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### 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 Patched (2025-08-23 r88802)
* 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       107.691 83.910 141.598
rifi_penalties      47.118 43.190  70.534
nls2_fit            37.675  2.102  23.541
rifi_visualization  30.082  1.434  31.518
rifi_fit            23.294  0.402  23.697
make_pen             8.702  7.317  12.861
TI_fit              10.023  0.904   6.684
* 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.


Installation output

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)

Tests output


Example timings

rifi.Rcheck/rifi-Ex.timings

nameusersystemelapsed
TI_fit10.023 0.904 6.684
TUgether0.4140.2060.559
apply_Ttest_delay0.1130.0140.128
apply_ancova0.2990.0320.331
apply_event_position0.0950.0050.099
apply_manova0.5650.0590.624
apply_t_test0.6390.0170.656
apply_t_test_ti0.1560.0000.155
check_input0.3060.0010.306
dataframe_summary0.0810.0020.083
dataframe_summary_TI0.0440.0010.045
dataframe_summary_events0.6990.0200.720
dataframe_summary_events_HL_int0.5290.0320.561
dataframe_summary_events_ps_itss0.2080.0070.215
dataframe_summary_events_velocity0.2080.0210.229
event_dataframe0.6450.0140.659
finding_PDD0.2150.1220.287
finding_TI0.3100.1510.412
fold_change2.8080.1232.931
fragment_HL0.5540.1830.649
fragment_TI0.3860.0350.421
fragment_delay0.9050.2801.062
fragment_inty0.6310.2510.735
gff3_preprocess0.4910.0470.538
make_df0.7260.3670.705
make_pen 8.702 7.31712.861
nls2_fit37.675 2.10223.541
predict_ps_itss0.2540.0450.298
rifi_fit23.294 0.40223.697
rifi_fragmentation2.8280.8773.377
rifi_penalties47.11843.19070.534
rifi_preprocess1.5820.6281.760
rifi_stats3.0590.1833.244
rifi_summary1.8820.0601.941
rifi_visualization30.082 1.43431.518
rifi_wrapper107.691 83.910141.598
segment_pos0.1680.0010.168
viz_pen_obj0.010.000.01