Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-09-24 22:57 -0400 (Tue, 24 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4760 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4497 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4526 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4475 |
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 1772/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rifi 1.8.0 (landing page) Jens Georg
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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: 1.8.0 |
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_1.8.0.tar.gz |
StartedAt: 2024-09-23 10:44:16 -0400 (Mon, 23 Sep 2024) |
EndedAt: 2024-09-23 11:09:37 -0400 (Mon, 23 Sep 2024) |
EllapsedTime: 1521.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rifi.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### 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_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/rifi.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rifi/DESCRIPTION’ ... OK * this is package ‘rifi’ version ‘1.8.0’ * 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: /Users/biocbuild/bbs-3.19-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /Users/biocbuild/bbs-3.19-bioc/meat/rifi/man/predict_ps_itss.Rd:57: unexpected '}' See ‘/Users/biocbuild/bbs-3.19-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 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 265.154 75.105 362.825 rifi_penalties 130.496 58.013 223.573 nls2_fit 101.468 5.938 77.002 rifi_fit 65.866 1.212 81.572 rifi_visualization 51.081 2.409 63.199 make_pen 24.541 8.961 37.217 TI_fit 29.965 2.514 23.029 rifi_fragmentation 8.062 1.860 12.319 rifi_stats 8.035 0.438 10.346 fold_change 7.965 0.210 9.182 rifi_preprocess 4.389 1.274 5.640 rifi_summary 4.866 0.083 5.940 * 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-3.19-bioc/meat/rifi.Rcheck/00check.log’ for details.
rifi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rifi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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: /Users/biocbuild/bbs-3.19-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /Users/biocbuild/bbs-3.19-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 | 29.965 | 2.514 | 23.029 | |
TUgether | 1.223 | 0.247 | 1.632 | |
apply_Ttest_delay | 0.261 | 0.041 | 0.339 | |
apply_ancova | 0.784 | 0.108 | 0.997 | |
apply_event_position | 0.255 | 0.028 | 0.314 | |
apply_manova | 1.465 | 0.055 | 1.695 | |
apply_t_test | 1.638 | 0.013 | 1.901 | |
apply_t_test_ti | 0.422 | 0.006 | 0.475 | |
check_input | 0.816 | 0.010 | 0.894 | |
dataframe_summary | 0.214 | 0.021 | 0.251 | |
dataframe_summary_TI | 0.102 | 0.007 | 0.117 | |
dataframe_summary_events | 1.802 | 0.062 | 2.023 | |
dataframe_summary_events_HL_int | 1.442 | 0.036 | 1.601 | |
dataframe_summary_events_ps_itss | 0.535 | 0.023 | 0.602 | |
dataframe_summary_events_velocity | 0.636 | 0.032 | 0.721 | |
event_dataframe | 1.916 | 0.045 | 2.185 | |
finding_PDD | 0.564 | 0.141 | 0.766 | |
finding_TI | 0.898 | 0.244 | 1.247 | |
fold_change | 7.965 | 0.210 | 9.182 | |
fragment_HL | 1.525 | 0.252 | 1.901 | |
fragment_TI | 1.161 | 0.142 | 1.459 | |
fragment_delay | 2.720 | 0.679 | 3.622 | |
fragment_inty | 1.656 | 0.326 | 2.147 | |
gff3_preprocess | 1.284 | 0.113 | 1.558 | |
make_df | 1.863 | 0.648 | 1.829 | |
make_pen | 24.541 | 8.961 | 37.217 | |
nls2_fit | 101.468 | 5.938 | 77.002 | |
predict_ps_itss | 0.666 | 0.076 | 0.852 | |
rifi_fit | 65.866 | 1.212 | 81.572 | |
rifi_fragmentation | 8.062 | 1.860 | 12.319 | |
rifi_penalties | 130.496 | 58.013 | 223.573 | |
rifi_preprocess | 4.389 | 1.274 | 5.640 | |
rifi_stats | 8.035 | 0.438 | 10.346 | |
rifi_summary | 4.866 | 0.083 | 5.940 | |
rifi_visualization | 51.081 | 2.409 | 63.199 | |
rifi_wrapper | 265.154 | 75.105 | 362.825 | |
segment_pos | 0.442 | 0.006 | 0.504 | |
viz_pen_obj | 0.016 | 0.011 | 0.029 | |