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 12:06 -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: 2024-12-20 08:33:16 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 08:55:09 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1313.3 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: 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 268.335 65.822 321.395 rifi_penalties 128.068 50.302 190.567 nls2_fit 96.517 3.054 65.797 rifi_fit 63.298 0.669 68.471 rifi_visualization 45.812 2.101 49.742 make_pen 24.250 8.610 33.186 TI_fit 29.963 2.349 20.757 rifi_fragmentation 7.993 1.653 10.275 fold_change 7.844 0.236 8.478 rifi_stats 7.362 0.256 7.678 rifi_preprocess 4.165 1.080 4.584 * 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 | 29.963 | 2.349 | 20.757 | |
TUgether | 1.165 | 0.283 | 1.434 | |
apply_Ttest_delay | 0.265 | 0.041 | 0.309 | |
apply_ancova | 0.775 | 0.086 | 0.867 | |
apply_event_position | 0.258 | 0.028 | 0.290 | |
apply_manova | 1.528 | 0.108 | 1.646 | |
apply_t_test | 1.631 | 0.009 | 1.656 | |
apply_t_test_ti | 0.413 | 0.004 | 0.467 | |
check_input | 0.803 | 0.008 | 0.812 | |
dataframe_summary | 0.193 | 0.021 | 0.215 | |
dataframe_summary_TI | 0.101 | 0.009 | 0.114 | |
dataframe_summary_events | 1.774 | 0.055 | 1.858 | |
dataframe_summary_events_HL_int | 1.415 | 0.039 | 1.463 | |
dataframe_summary_events_ps_itss | 0.547 | 0.024 | 0.584 | |
dataframe_summary_events_velocity | 0.536 | 0.025 | 0.571 | |
event_dataframe | 1.826 | 0.046 | 1.919 | |
finding_PDD | 0.542 | 0.126 | 0.665 | |
finding_TI | 0.904 | 0.226 | 1.121 | |
fold_change | 7.844 | 0.236 | 8.478 | |
fragment_HL | 1.463 | 0.226 | 1.698 | |
fragment_TI | 1.151 | 0.139 | 1.311 | |
fragment_delay | 2.589 | 0.646 | 3.317 | |
fragment_inty | 1.568 | 0.285 | 1.827 | |
gff3_preprocess | 1.209 | 0.128 | 1.346 | |
make_df | 1.791 | 0.635 | 1.675 | |
make_pen | 24.250 | 8.610 | 33.186 | |
nls2_fit | 96.517 | 3.054 | 65.797 | |
predict_ps_itss | 0.678 | 0.083 | 0.924 | |
rifi_fit | 63.298 | 0.669 | 68.471 | |
rifi_fragmentation | 7.993 | 1.653 | 10.275 | |
rifi_penalties | 128.068 | 50.302 | 190.567 | |
rifi_preprocess | 4.165 | 1.080 | 4.584 | |
rifi_stats | 7.362 | 0.256 | 7.678 | |
rifi_summary | 4.708 | 0.067 | 4.869 | |
rifi_visualization | 45.812 | 2.101 | 49.742 | |
rifi_wrapper | 268.335 | 65.822 | 321.395 | |
segment_pos | 0.432 | 0.005 | 0.457 | |
viz_pen_obj | 0.016 | 0.010 | 0.027 | |