Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-08 13:19:51 -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 nebbiolo1


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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings rifi_1.0.0.tar.gz
StartedAt: 2022-08-07 21:42:41 -0400 (Sun, 07 Aug 2022)
EndedAt: 2022-08-07 21:51:17 -0400 (Sun, 07 Aug 2022)
EllapsedTime: 515.4 seconds
RetCode: 0
Status:   OK  
CheckDir: rifi.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings rifi_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/rifi.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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       105.248 52.112 117.777
rifi_penalties      49.681 34.615  66.832
rifi_visualization  32.795  2.197  34.993
rifi_fit            23.902  0.620  24.523
nls2_fit            15.799  2.057  10.018
make_pen             9.726  7.163  12.777
TI_fit              10.302  0.897   7.084
* 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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL rifi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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_fit10.302 0.897 7.084
TUgether0.4980.1900.624
apply_Ttest_delay0.1190.0080.127
apply_ancova0.3220.0490.371
apply_event_position0.1010.0230.124
apply_manova0.5620.0290.590
apply_t_test0.7340.0630.798
apply_t_test_ti0.2010.0130.212
check_input0.3850.0070.393
dataframe_summary0.0950.0080.103
dataframe_summary_TI0.0440.0000.044
dataframe_summary_events0.8740.0610.934
dataframe_summary_events_HL_int0.6850.0430.729
dataframe_summary_events_ps_itss0.2680.0080.276
dataframe_summary_events_velocity0.2790.0190.299
event_dataframe0.7940.0440.838
finding_PDD0.2140.1300.277
finding_TI0.3210.1720.425
fold_change2.9270.1603.088
fragment_HL0.6520.1390.701
fragment_TI0.4310.0240.455
fragment_delay0.9760.2171.096
fragment_inty0.6200.1980.737
gff3_preprocess0.6310.0600.695
make_df0.6910.2760.623
make_pen 9.726 7.16312.777
nls2_fit15.799 2.05710.018
predict_ps_itss0.2530.0400.292
rifi_fit23.902 0.62024.523
rifi_fragmentation3.1920.9313.771
rifi_penalties49.68134.61566.832
rifi_preprocess1.6280.5021.751
rifi_stats4.7870.1884.975
rifi_summary2.0310.0602.091
rifi_visualization32.795 2.19734.993
rifi_wrapper105.248 52.112117.777
segment_pos0.1570.0110.167
viz_pen_obj0.010.000.01