Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-12 17:41 -0400 (Fri, 12 Jul 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" | 4741 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 12.7.4 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: 2024-07-11 10:30:02 -0400 (Thu, 11 Jul 2024) |
EndedAt: 2024-07-11 10:55:56 -0400 (Thu, 11 Jul 2024) |
EllapsedTime: 1554.0 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 269.622 77.392 356.236 rifi_penalties 134.343 58.516 234.832 nls2_fit 103.136 6.200 82.020 rifi_fit 67.309 1.265 82.708 rifi_visualization 51.441 2.474 62.086 make_pen 25.703 9.420 40.960 TI_fit 30.290 2.616 24.365 rifi_fragmentation 8.297 1.871 11.626 fold_change 8.294 0.223 9.881 rifi_stats 8.057 0.408 10.447 rifi_preprocess 4.468 1.267 5.903 rifi_summary 4.907 0.077 6.039 * 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 | 30.290 | 2.616 | 24.365 | |
TUgether | 1.252 | 0.268 | 1.782 | |
apply_Ttest_delay | 0.285 | 0.045 | 0.406 | |
apply_ancova | 0.851 | 0.113 | 1.169 | |
apply_event_position | 0.269 | 0.031 | 0.401 | |
apply_manova | 1.513 | 0.061 | 1.870 | |
apply_t_test | 1.720 | 0.015 | 2.064 | |
apply_t_test_ti | 0.428 | 0.006 | 0.483 | |
check_input | 0.883 | 0.011 | 0.995 | |
dataframe_summary | 0.232 | 0.022 | 0.282 | |
dataframe_summary_TI | 0.103 | 0.007 | 0.123 | |
dataframe_summary_events | 1.907 | 0.068 | 2.219 | |
dataframe_summary_events_HL_int | 1.537 | 0.039 | 1.826 | |
dataframe_summary_events_ps_itss | 0.571 | 0.025 | 0.698 | |
dataframe_summary_events_velocity | 0.659 | 0.034 | 0.822 | |
event_dataframe | 1.905 | 0.048 | 2.280 | |
finding_PDD | 0.600 | 0.162 | 0.893 | |
finding_TI | 0.949 | 0.253 | 1.354 | |
fold_change | 8.294 | 0.223 | 9.881 | |
fragment_HL | 1.564 | 0.264 | 2.030 | |
fragment_TI | 1.185 | 0.142 | 1.589 | |
fragment_delay | 2.741 | 0.690 | 3.843 | |
fragment_inty | 1.683 | 0.360 | 2.323 | |
gff3_preprocess | 1.237 | 0.112 | 1.559 | |
make_df | 1.925 | 0.677 | 1.952 | |
make_pen | 25.703 | 9.420 | 40.960 | |
nls2_fit | 103.136 | 6.200 | 82.020 | |
predict_ps_itss | 0.662 | 0.077 | 0.880 | |
rifi_fit | 67.309 | 1.265 | 82.708 | |
rifi_fragmentation | 8.297 | 1.871 | 11.626 | |
rifi_penalties | 134.343 | 58.516 | 234.832 | |
rifi_preprocess | 4.468 | 1.267 | 5.903 | |
rifi_stats | 8.057 | 0.408 | 10.447 | |
rifi_summary | 4.907 | 0.077 | 6.039 | |
rifi_visualization | 51.441 | 2.474 | 62.086 | |
rifi_wrapper | 269.622 | 77.392 | 356.236 | |
segment_pos | 0.456 | 0.009 | 0.601 | |
viz_pen_obj | 0.016 | 0.012 | 0.036 | |