Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:42 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 | ![]() | ||||||||
palomino3 | 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: 2024-06-24 10:30:56 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 10:57:14 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 1578.3 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_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/rifi.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘1.8.0’ * 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 275.502 79.175 377.971 rifi_penalties 134.989 60.438 236.860 nls2_fit 102.837 6.063 81.128 rifi_fit 67.092 1.248 82.644 rifi_visualization 51.982 2.456 64.466 make_pen 25.538 9.479 39.372 TI_fit 30.476 2.512 23.701 rifi_fragmentation 8.387 1.875 11.738 fold_change 8.258 0.218 9.669 rifi_stats 8.051 0.416 10.173 rifi_preprocess 4.548 1.340 5.803 rifi_summary 4.924 0.081 6.038 * 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 | 30.476 | 2.512 | 23.701 | |
TUgether | 1.264 | 0.246 | 1.702 | |
apply_Ttest_delay | 0.283 | 0.042 | 0.369 | |
apply_ancova | 0.846 | 0.109 | 1.064 | |
apply_event_position | 0.268 | 0.029 | 0.333 | |
apply_manova | 1.542 | 0.056 | 1.785 | |
apply_t_test | 1.720 | 0.012 | 1.945 | |
apply_t_test_ti | 0.460 | 0.007 | 0.530 | |
check_input | 0.856 | 0.010 | 0.972 | |
dataframe_summary | 0.232 | 0.022 | 0.286 | |
dataframe_summary_TI | 0.108 | 0.006 | 0.135 | |
dataframe_summary_events | 1.900 | 0.064 | 2.210 | |
dataframe_summary_events_HL_int | 1.483 | 0.039 | 1.725 | |
dataframe_summary_events_ps_itss | 0.574 | 0.024 | 0.672 | |
dataframe_summary_events_velocity | 0.561 | 0.027 | 0.663 | |
event_dataframe | 1.973 | 0.052 | 2.276 | |
finding_PDD | 0.603 | 0.155 | 0.880 | |
finding_TI | 0.939 | 0.253 | 1.290 | |
fold_change | 8.258 | 0.218 | 9.669 | |
fragment_HL | 1.537 | 0.294 | 2.060 | |
fragment_TI | 1.207 | 0.145 | 1.535 | |
fragment_delay | 2.790 | 0.717 | 3.808 | |
fragment_inty | 1.704 | 0.340 | 2.236 | |
gff3_preprocess | 1.220 | 0.119 | 1.505 | |
make_df | 1.882 | 0.668 | 1.869 | |
make_pen | 25.538 | 9.479 | 39.372 | |
nls2_fit | 102.837 | 6.063 | 81.128 | |
predict_ps_itss | 0.672 | 0.078 | 0.903 | |
rifi_fit | 67.092 | 1.248 | 82.644 | |
rifi_fragmentation | 8.387 | 1.875 | 11.738 | |
rifi_penalties | 134.989 | 60.438 | 236.860 | |
rifi_preprocess | 4.548 | 1.340 | 5.803 | |
rifi_stats | 8.051 | 0.416 | 10.173 | |
rifi_summary | 4.924 | 0.081 | 6.038 | |
rifi_visualization | 51.982 | 2.456 | 64.466 | |
rifi_wrapper | 275.502 | 79.175 | 377.971 | |
segment_pos | 0.459 | 0.006 | 0.572 | |
viz_pen_obj | 0.016 | 0.012 | 0.029 | |