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This page was generated on 2022-08-08 13:20:45 -0400 (Mon, 08 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4362
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4180
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

CHECK results for rifi on merida1


To the developers/maintainers of the rifi package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1654/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rifi 1.0.0  (landing page)
Jens Georg
Snapshot Date: 2022-08-07 13:55:12 -0400 (Sun, 07 Aug 2022)
git_url: https://git.bioconductor.org/packages/rifi
git_branch: RELEASE_3_15
git_last_commit: a495442
git_last_commit_date: 2022-04-27 15:48:36 -0400 (Wed, 27 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: rifi
Version: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2022-08-08 07:02:09 -0400 (Mon, 08 Aug 2022)
EndedAt: 2022-08-08 07:18:30 -0400 (Mon, 08 Aug 2022)
EllapsedTime: 981.0 seconds
RetCode: 0
Status:   OK  
CheckDir: rifi.Rcheck
Warnings: 0

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_1.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/rifi.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rifi/DESCRIPTION’ ... OK
* this is package ‘rifi’ version ‘1.0.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rifi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... 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       224.860 35.640 228.438
rifi_penalties     111.135 27.466 135.239
rifi_fit            56.261  0.551  59.347
rifi_visualization  46.106  1.853  48.027
nls2_fit            34.478  3.596  22.032
make_pen            20.888  4.960  25.213
TI_fit              23.602  1.660  15.401
rifi_stats          10.853  0.137  11.001
rifi_fragmentation   6.902  1.094   7.855
fold_change          6.428  0.137   6.574
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


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/4.2/Resources/library’
* installing *source* package ‘rifi’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** 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_fit23.602 1.66015.401
TUgether0.9990.1641.153
apply_Ttest_delay0.2210.0240.246
apply_ancova0.6720.0570.730
apply_event_position0.2330.0190.253
apply_manova1.3060.0521.361
apply_t_test1.4760.0061.483
apply_t_test_ti0.3680.0040.371
check_input0.7230.0050.729
dataframe_summary0.1890.0100.200
dataframe_summary_TI0.0770.0030.080
dataframe_summary_events1.7510.0331.785
dataframe_summary_events_HL_int1.4160.0221.440
dataframe_summary_events_ps_itss0.5070.0160.522
dataframe_summary_events_velocity0.5260.0170.543
event_dataframe1.6250.0291.655
finding_PDD0.4780.0710.531
finding_TI0.7760.1310.889
fold_change6.4280.1376.574
fragment_HL1.2600.1541.382
fragment_TI0.9270.0811.009
fragment_delay2.1530.3362.430
fragment_inty1.4330.2191.617
gff3_preprocess1.1090.0851.198
make_df1.6100.5411.440
make_pen20.888 4.96025.213
nls2_fit34.478 3.59622.032
predict_ps_itss0.5940.0570.653
rifi_fit56.261 0.55159.347
rifi_fragmentation6.9021.0947.855
rifi_penalties111.135 27.466135.239
rifi_preprocess3.8740.8803.995
rifi_stats10.853 0.13711.001
rifi_summary4.6060.0404.652
rifi_visualization46.106 1.85348.027
rifi_wrapper224.860 35.640228.438
segment_pos0.4020.0020.405
viz_pen_obj0.0160.0090.024