Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-30 11:35:51 -0400 (Thu, 30 May 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" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
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 | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 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: 1.8.0 |
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: 2024-05-29 23:16:15 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 23:28:38 -0400 (Wed, 29 May 2024) |
EllapsedTime: 743.2 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 12.7.1 * 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 140.309 60.313 181.229 rifi_penalties 67.313 44.240 109.034 nls2_fit 48.277 3.756 31.194 rifi_visualization 34.124 2.742 37.308 rifi_fit 29.864 0.708 30.868 make_pen 12.971 6.724 19.202 TI_fit 13.069 1.478 8.889 rifi_fragmentation 3.951 1.128 4.992 * 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 | 13.069 | 1.478 | 8.889 | |
TUgether | 0.572 | 0.159 | 0.719 | |
apply_Ttest_delay | 0.138 | 0.019 | 0.159 | |
apply_ancova | 0.390 | 0.043 | 0.438 | |
apply_event_position | 0.113 | 0.010 | 0.125 | |
apply_manova | 0.641 | 0.022 | 0.666 | |
apply_t_test | 0.764 | 0.009 | 0.777 | |
apply_t_test_ti | 0.204 | 0.004 | 0.210 | |
check_input | 0.423 | 0.010 | 0.438 | |
dataframe_summary | 0.116 | 0.010 | 0.127 | |
dataframe_summary_TI | 0.060 | 0.004 | 0.065 | |
dataframe_summary_events | 1.177 | 0.053 | 1.252 | |
dataframe_summary_events_HL_int | 0.875 | 0.042 | 0.930 | |
dataframe_summary_events_ps_itss | 0.349 | 0.021 | 0.372 | |
dataframe_summary_events_velocity | 0.372 | 0.028 | 0.414 | |
event_dataframe | 1.009 | 0.036 | 1.056 | |
finding_PDD | 0.275 | 0.112 | 0.376 | |
finding_TI | 0.458 | 0.163 | 0.601 | |
fold_change | 3.613 | 0.101 | 3.749 | |
fragment_HL | 0.754 | 0.150 | 0.887 | |
fragment_TI | 0.575 | 0.053 | 0.633 | |
fragment_delay | 1.355 | 0.417 | 1.724 | |
fragment_inty | 0.806 | 0.183 | 0.968 | |
gff3_preprocess | 0.691 | 0.059 | 0.758 | |
make_df | 0.899 | 0.383 | 0.859 | |
make_pen | 12.971 | 6.724 | 19.202 | |
nls2_fit | 48.277 | 3.756 | 31.194 | |
predict_ps_itss | 0.340 | 0.027 | 0.371 | |
rifi_fit | 29.864 | 0.708 | 30.868 | |
rifi_fragmentation | 3.951 | 1.128 | 4.992 | |
rifi_penalties | 67.313 | 44.240 | 109.034 | |
rifi_preprocess | 2.330 | 0.813 | 2.711 | |
rifi_stats | 3.928 | 0.185 | 4.154 | |
rifi_summary | 2.588 | 0.067 | 2.688 | |
rifi_visualization | 34.124 | 2.742 | 37.308 | |
rifi_wrapper | 140.309 | 60.313 | 181.229 | |
segment_pos | 0.216 | 0.004 | 0.223 | |
viz_pen_obj | 0.009 | 0.001 | 0.011 | |