Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-30 12:37:18 -0400 (Thu, 30 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" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 1715/2233 | 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 | 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: 1.9.0 |
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: 2024-05-30 06:33:33 -0400 (Thu, 30 May 2024) |
EndedAt: 2024-05-30 06:58:50 -0400 (Thu, 30 May 2024) |
EllapsedTime: 1516.4 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 269.488 74.450 358.982 rifi_penalties 131.559 57.729 217.855 nls2_fit 103.329 6.228 82.244 rifi_fit 66.818 1.337 82.777 rifi_visualization 50.498 2.369 62.647 make_pen 24.769 9.010 37.337 TI_fit 29.953 2.514 23.320 rifi_fragmentation 8.197 1.871 11.205 rifi_stats 8.030 0.414 10.024 fold_change 8.133 0.225 9.904 rifi_preprocess 4.404 1.309 5.597 rifi_summary 4.939 0.074 5.885 * 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 | 29.953 | 2.514 | 23.320 | |
TUgether | 1.177 | 0.247 | 1.596 | |
apply_Ttest_delay | 0.263 | 0.040 | 0.339 | |
apply_ancova | 0.807 | 0.112 | 1.089 | |
apply_event_position | 0.257 | 0.029 | 0.327 | |
apply_manova | 1.526 | 0.059 | 1.816 | |
apply_t_test | 1.645 | 0.014 | 1.885 | |
apply_t_test_ti | 0.414 | 0.006 | 0.457 | |
check_input | 0.826 | 0.010 | 0.955 | |
dataframe_summary | 0.227 | 0.021 | 0.276 | |
dataframe_summary_TI | 0.103 | 0.008 | 0.126 | |
dataframe_summary_events | 1.858 | 0.065 | 2.215 | |
dataframe_summary_events_HL_int | 1.475 | 0.041 | 1.810 | |
dataframe_summary_events_ps_itss | 0.561 | 0.026 | 0.696 | |
dataframe_summary_events_velocity | 0.558 | 0.029 | 0.706 | |
event_dataframe | 1.984 | 0.053 | 2.425 | |
finding_PDD | 0.601 | 0.155 | 0.854 | |
finding_TI | 0.945 | 0.259 | 1.374 | |
fold_change | 8.133 | 0.225 | 9.904 | |
fragment_HL | 1.538 | 0.256 | 1.982 | |
fragment_TI | 1.163 | 0.146 | 1.516 | |
fragment_delay | 2.691 | 0.682 | 3.664 | |
fragment_inty | 1.601 | 0.314 | 2.145 | |
gff3_preprocess | 1.183 | 0.122 | 1.517 | |
make_df | 1.798 | 0.651 | 1.765 | |
make_pen | 24.769 | 9.010 | 37.337 | |
nls2_fit | 103.329 | 6.228 | 82.244 | |
predict_ps_itss | 0.675 | 0.079 | 0.899 | |
rifi_fit | 66.818 | 1.337 | 82.777 | |
rifi_fragmentation | 8.197 | 1.871 | 11.205 | |
rifi_penalties | 131.559 | 57.729 | 217.855 | |
rifi_preprocess | 4.404 | 1.309 | 5.597 | |
rifi_stats | 8.030 | 0.414 | 10.024 | |
rifi_summary | 4.939 | 0.074 | 5.885 | |
rifi_visualization | 50.498 | 2.369 | 62.647 | |
rifi_wrapper | 269.488 | 74.450 | 358.982 | |
segment_pos | 0.457 | 0.008 | 0.549 | |
viz_pen_obj | 0.016 | 0.010 | 0.028 | |