Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-03 11:38:46 -0400 (Fri, 03 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
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 1714/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rifi 1.9.0 (landing page) Jens Georg
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | 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 | see weekly results here | ||||||||||||
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: 1.9.0 |
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_1.9.0.tar.gz |
StartedAt: 2024-05-02 10:15:42 -0400 (Thu, 02 May 2024) |
EndedAt: 2024-05-02 10:41:50 -0400 (Thu, 02 May 2024) |
EllapsedTime: 1568.5 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_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/rifi.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rifi/DESCRIPTION’ ... OK * this is package ‘rifi’ version ‘1.9.0’ * 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 275.897 79.317 381.339 rifi_penalties 130.228 52.833 220.736 nls2_fit 100.140 3.396 79.533 rifi_fit 65.591 0.882 82.435 rifi_visualization 52.176 2.770 65.191 make_pen 25.291 9.664 40.186 TI_fit 31.097 2.433 24.854 rifi_fragmentation 8.122 1.727 11.605 fold_change 8.482 0.268 10.496 rifi_stats 7.361 0.348 9.765 rifi_preprocess 4.311 1.258 5.452 rifi_summary 4.630 0.093 6.604 * 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 | 31.097 | 2.433 | 24.854 | |
TUgether | 1.238 | 0.297 | 1.751 | |
apply_Ttest_delay | 0.266 | 0.044 | 0.353 | |
apply_ancova | 0.786 | 0.091 | 0.994 | |
apply_event_position | 0.261 | 0.029 | 0.329 | |
apply_manova | 1.553 | 0.111 | 1.908 | |
apply_t_test | 1.725 | 0.018 | 2.036 | |
apply_t_test_ti | 0.418 | 0.006 | 0.483 | |
check_input | 0.854 | 0.011 | 0.971 | |
dataframe_summary | 0.243 | 0.023 | 0.302 | |
dataframe_summary_TI | 0.106 | 0.008 | 0.126 | |
dataframe_summary_events | 1.888 | 0.059 | 2.140 | |
dataframe_summary_events_HL_int | 1.478 | 0.042 | 1.691 | |
dataframe_summary_events_ps_itss | 0.563 | 0.025 | 0.659 | |
dataframe_summary_events_velocity | 0.559 | 0.029 | 0.659 | |
event_dataframe | 1.923 | 0.058 | 2.291 | |
finding_PDD | 0.559 | 0.146 | 0.818 | |
finding_TI | 0.954 | 0.259 | 1.406 | |
fold_change | 8.482 | 0.268 | 10.496 | |
fragment_HL | 1.582 | 0.271 | 2.060 | |
fragment_TI | 1.219 | 0.133 | 1.559 | |
fragment_delay | 2.710 | 0.635 | 3.674 | |
fragment_inty | 1.749 | 0.353 | 2.381 | |
gff3_preprocess | 1.194 | 0.095 | 1.481 | |
make_df | 1.872 | 0.703 | 1.940 | |
make_pen | 25.291 | 9.664 | 40.186 | |
nls2_fit | 100.140 | 3.396 | 79.533 | |
predict_ps_itss | 0.677 | 0.090 | 0.934 | |
rifi_fit | 65.591 | 0.882 | 82.435 | |
rifi_fragmentation | 8.122 | 1.727 | 11.605 | |
rifi_penalties | 130.228 | 52.833 | 220.736 | |
rifi_preprocess | 4.311 | 1.258 | 5.452 | |
rifi_stats | 7.361 | 0.348 | 9.765 | |
rifi_summary | 4.630 | 0.093 | 6.604 | |
rifi_visualization | 52.176 | 2.770 | 65.191 | |
rifi_wrapper | 275.897 | 79.317 | 381.339 | |
segment_pos | 0.446 | 0.006 | 0.554 | |
viz_pen_obj | 0.014 | 0.011 | 0.027 | |