Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-04-02 19:32 -0400 (Wed, 02 Apr 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
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 1755/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rifi 1.10.0 (landing page) Jens Georg
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | 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 | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | TIMEOUT | skipped | ||||||||||
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: 1.10.0 |
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_1.10.0.tar.gz |
StartedAt: 2025-04-01 08:05:29 -0400 (Tue, 01 Apr 2025) |
EndedAt: 2025-04-01 08:27:20 -0400 (Tue, 01 Apr 2025) |
EllapsedTime: 1310.4 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_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/rifi.Rcheck’ * using R version 4.4.3 (2025-02-28) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rifi/DESCRIPTION’ ... OK * this is package ‘rifi’ version ‘1.10.0’ * 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-3.20-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /Users/biocbuild/bbs-3.20-bioc/meat/rifi/man/predict_ps_itss.Rd:57: unexpected '}' See ‘/Users/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 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 258.451 70.263 317.355 rifi_penalties 126.566 51.382 181.014 nls2_fit 100.235 5.832 73.108 rifi_fit 64.163 0.794 71.148 rifi_visualization 48.116 2.304 53.537 make_pen 23.188 8.247 33.293 TI_fit 28.184 2.302 20.473 rifi_fragmentation 7.637 1.584 9.831 rifi_stats 7.566 0.239 8.352 fold_change 7.462 0.233 8.346 rifi_preprocess 4.462 1.577 5.256 rifi_summary 4.735 0.066 5.163 * 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-3.20-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-3.20-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /Users/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 | 28.184 | 2.302 | 20.473 | |
TUgether | 1.178 | 0.257 | 1.495 | |
apply_Ttest_delay | 0.249 | 0.043 | 0.308 | |
apply_ancova | 0.751 | 0.091 | 0.878 | |
apply_event_position | 0.249 | 0.037 | 0.303 | |
apply_manova | 1.373 | 0.067 | 1.517 | |
apply_t_test | 1.666 | 0.027 | 1.779 | |
apply_t_test_ti | 0.417 | 0.006 | 0.445 | |
check_input | 0.789 | 0.007 | 0.843 | |
dataframe_summary | 0.186 | 0.021 | 0.212 | |
dataframe_summary_TI | 0.100 | 0.007 | 0.117 | |
dataframe_summary_events | 1.807 | 0.059 | 1.994 | |
dataframe_summary_events_HL_int | 1.365 | 0.032 | 1.486 | |
dataframe_summary_events_ps_itss | 0.560 | 0.024 | 0.622 | |
dataframe_summary_events_velocity | 0.529 | 0.025 | 0.585 | |
event_dataframe | 2.781 | 0.201 | 3.137 | |
finding_PDD | 0.515 | 0.126 | 0.789 | |
finding_TI | 0.874 | 0.251 | 1.416 | |
fold_change | 7.462 | 0.233 | 8.346 | |
fragment_HL | 1.420 | 0.218 | 1.681 | |
fragment_TI | 1.057 | 0.141 | 1.312 | |
fragment_delay | 2.384 | 0.509 | 3.045 | |
fragment_inty | 1.507 | 0.294 | 1.922 | |
gff3_preprocess | 1.118 | 0.132 | 1.365 | |
make_df | 1.738 | 0.616 | 1.734 | |
make_pen | 23.188 | 8.247 | 33.293 | |
nls2_fit | 100.235 | 5.832 | 73.108 | |
predict_ps_itss | 0.645 | 0.080 | 0.878 | |
rifi_fit | 64.163 | 0.794 | 71.148 | |
rifi_fragmentation | 7.637 | 1.584 | 9.831 | |
rifi_penalties | 126.566 | 51.382 | 181.014 | |
rifi_preprocess | 4.462 | 1.577 | 5.256 | |
rifi_stats | 7.566 | 0.239 | 8.352 | |
rifi_summary | 4.735 | 0.066 | 5.163 | |
rifi_visualization | 48.116 | 2.304 | 53.537 | |
rifi_wrapper | 258.451 | 70.263 | 317.355 | |
segment_pos | 0.417 | 0.004 | 0.461 | |
viz_pen_obj | 0.013 | 0.010 | 0.024 | |