Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 | |||||||||
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: 2024-12-21 06:51:57 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 07:02:03 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 605.8 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 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * 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 112.957 33.620 130.936 rifi_penalties 48.752 29.284 75.502 nls2_fit 37.663 2.179 24.132 rifi_visualization 31.441 2.671 34.228 rifi_fit 23.102 0.462 23.642 make_pen 8.438 4.494 12.427 TI_fit 10.329 1.078 6.849 * 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-arm64/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 | 10.329 | 1.078 | 6.849 | |
TUgether | 0.442 | 0.161 | 0.597 | |
apply_Ttest_delay | 0.109 | 0.024 | 0.132 | |
apply_ancova | 0.318 | 0.041 | 0.359 | |
apply_event_position | 0.093 | 0.019 | 0.113 | |
apply_manova | 0.558 | 0.024 | 0.583 | |
apply_t_test | 0.732 | 0.021 | 0.754 | |
apply_t_test_ti | 0.164 | 0.003 | 0.168 | |
check_input | 0.345 | 0.007 | 0.352 | |
dataframe_summary | 0.098 | 0.012 | 0.111 | |
dataframe_summary_TI | 0.047 | 0.005 | 0.052 | |
dataframe_summary_events | 0.845 | 0.037 | 0.886 | |
dataframe_summary_events_HL_int | 0.568 | 0.018 | 0.586 | |
dataframe_summary_events_ps_itss | 0.282 | 0.017 | 0.298 | |
dataframe_summary_events_velocity | 0.253 | 0.013 | 0.266 | |
event_dataframe | 1.669 | 0.132 | 1.802 | |
finding_PDD | 0.195 | 0.068 | 0.252 | |
finding_TI | 0.294 | 0.122 | 0.398 | |
fold_change | 2.539 | 0.103 | 2.642 | |
fragment_HL | 0.512 | 0.161 | 0.650 | |
fragment_TI | 0.376 | 0.068 | 0.443 | |
fragment_delay | 0.813 | 0.238 | 1.021 | |
fragment_inty | 0.591 | 0.204 | 0.774 | |
gff3_preprocess | 0.642 | 0.074 | 0.716 | |
make_df | 0.701 | 0.308 | 0.712 | |
make_pen | 8.438 | 4.494 | 12.427 | |
nls2_fit | 37.663 | 2.179 | 24.132 | |
predict_ps_itss | 0.240 | 0.027 | 0.267 | |
rifi_fit | 23.102 | 0.462 | 23.642 | |
rifi_fragmentation | 2.901 | 0.873 | 3.678 | |
rifi_penalties | 48.752 | 29.284 | 75.502 | |
rifi_preprocess | 1.629 | 0.635 | 1.925 | |
rifi_stats | 2.979 | 0.093 | 3.094 | |
rifi_summary | 1.994 | 0.043 | 2.042 | |
rifi_visualization | 31.441 | 2.671 | 34.228 | |
rifi_wrapper | 112.957 | 33.620 | 130.936 | |
segment_pos | 0.196 | 0.003 | 0.199 | |
viz_pen_obj | 0.014 | 0.003 | 0.016 | |