Back to Build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-06 08:10 -0400 (Fri, 06 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4711 |
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 1734/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rifi 1.9.0 (landing page) Jens Georg
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
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. |
Package: rifi |
Version: 1.9.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings rifi_1.9.0.tar.gz |
StartedAt: 2024-09-06 04:18:50 -0400 (Fri, 06 Sep 2024) |
EndedAt: 2024-09-06 04:28:26 -0400 (Fri, 06 Sep 2024) |
EllapsedTime: 576.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rifi.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings rifi_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/rifi.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘rifi/DESCRIPTION’ ... OK * this is package ‘rifi’ version ‘1.9.0’ * 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: /home/biocbuild/bbs-3.20-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /home/biocbuild/bbs-3.20-bioc/meat/rifi/man/predict_ps_itss.Rd:57: unexpected '}' See ‘/home/biocbuild/bbs-3.20-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 ... 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 ... 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 104.324 60.434 124.981 rifi_penalties 43.238 33.095 60.342 nls2_fit 32.502 1.066 20.738 rifi_visualization 26.304 1.822 28.126 rifi_fit 21.569 0.684 22.253 make_pen 8.753 6.418 12.073 TI_fit 9.015 0.735 5.779 * 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-3.20-bioc/meat/rifi.Rcheck/00check.log’ for details.
rifi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL rifi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘rifi’ ... ** 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-3.20-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /home/biocbuild/bbs-3.20-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)
rifi.Rcheck/rifi-Ex.timings
name | user | system | elapsed | |
TI_fit | 9.015 | 0.735 | 5.779 | |
TUgether | 0.394 | 0.122 | 0.460 | |
apply_Ttest_delay | 0.098 | 0.008 | 0.106 | |
apply_ancova | 0.282 | 0.031 | 0.315 | |
apply_event_position | 0.078 | 0.012 | 0.090 | |
apply_manova | 0.502 | 0.016 | 0.518 | |
apply_t_test | 0.600 | 0.004 | 0.604 | |
apply_t_test_ti | 0.150 | 0.000 | 0.149 | |
check_input | 0.292 | 0.000 | 0.291 | |
dataframe_summary | 0.083 | 0.000 | 0.083 | |
dataframe_summary_TI | 0.034 | 0.008 | 0.041 | |
dataframe_summary_events | 0.684 | 0.060 | 0.744 | |
dataframe_summary_events_HL_int | 0.501 | 0.012 | 0.513 | |
dataframe_summary_events_ps_itss | 0.191 | 0.003 | 0.196 | |
dataframe_summary_events_velocity | 0.186 | 0.000 | 0.186 | |
event_dataframe | 0.701 | 0.016 | 0.717 | |
finding_PDD | 0.186 | 0.097 | 0.232 | |
finding_TI | 0.315 | 0.198 | 0.422 | |
fold_change | 2.827 | 0.136 | 2.963 | |
fragment_HL | 0.552 | 0.129 | 0.601 | |
fragment_TI | 0.419 | 0.036 | 0.454 | |
fragment_delay | 0.900 | 0.222 | 1.016 | |
fragment_inty | 0.551 | 0.204 | 0.679 | |
gff3_preprocess | 0.494 | 0.076 | 0.570 | |
make_df | 0.565 | 0.239 | 0.504 | |
make_pen | 8.753 | 6.418 | 12.073 | |
nls2_fit | 32.502 | 1.066 | 20.738 | |
predict_ps_itss | 0.211 | 0.036 | 0.247 | |
rifi_fit | 21.569 | 0.684 | 22.253 | |
rifi_fragmentation | 2.682 | 0.838 | 3.215 | |
rifi_penalties | 43.238 | 33.095 | 60.342 | |
rifi_preprocess | 1.491 | 0.484 | 1.563 | |
rifi_stats | 2.796 | 0.156 | 2.951 | |
rifi_summary | 1.762 | 0.044 | 1.806 | |
rifi_visualization | 26.304 | 1.822 | 28.126 | |
rifi_wrapper | 104.324 | 60.434 | 124.981 | |
segment_pos | 0.163 | 0.003 | 0.167 | |
viz_pen_obj | 0.009 | 0.001 | 0.009 | |