Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-08 11:45 -0400 (Mon, 08 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
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 1722/2243 | 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 | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | NA | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: rifi |
Version: 1.9.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rifi_1.9.0.tar.gz |
StartedAt: 2024-07-06 07:52:15 -0000 (Sat, 06 Jul 2024) |
EndedAt: 2024-07-06 08:05:41 -0000 (Sat, 06 Jul 2024) |
EllapsedTime: 806.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rifi.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rifi_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/rifi.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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: /home/biocbuild/bbs-3.20-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /home/biocbuild/bbs-3.20-bioc/meat/rifi/man/predict_ps_itss.Rd:57: unexpected '}' See ‘/home/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 loading without being on the library search path ... 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 178.929 78.908 202.706 rifi_penalties 67.520 49.256 93.975 rifi_visualization 65.385 1.163 66.683 nls2_fit 53.754 1.764 34.166 rifi_fit 36.615 0.423 37.132 make_pen 12.834 8.830 17.778 TI_fit 15.550 1.632 10.644 rifi_fragmentation 4.215 1.195 5.002 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/rifi.Rcheck/00check.log’ for details.
rifi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL rifi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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: /home/biocbuild/bbs-3.20-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /home/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 | 15.550 | 1.632 | 10.644 | |
TUgether | 0.584 | 0.169 | 0.684 | |
apply_Ttest_delay | 0.129 | 0.024 | 0.154 | |
apply_ancova | 0.404 | 0.048 | 0.452 | |
apply_event_position | 0.149 | 0.028 | 0.177 | |
apply_manova | 0.820 | 0.068 | 0.890 | |
apply_t_test | 0.936 | 0.023 | 0.967 | |
apply_t_test_ti | 0.245 | 0.008 | 0.253 | |
check_input | 0.490 | 0.012 | 0.503 | |
dataframe_summary | 0.120 | 0.000 | 0.121 | |
dataframe_summary_TI | 0.059 | 0.000 | 0.060 | |
dataframe_summary_events | 1.087 | 0.032 | 1.122 | |
dataframe_summary_events_HL_int | 0.900 | 0.004 | 0.907 | |
dataframe_summary_events_ps_itss | 0.353 | 0.004 | 0.358 | |
dataframe_summary_events_velocity | 0.325 | 0.012 | 0.338 | |
event_dataframe | 1.078 | 0.020 | 1.101 | |
finding_PDD | 0.312 | 0.139 | 0.381 | |
finding_TI | 0.520 | 0.191 | 0.639 | |
fold_change | 4.436 | 0.123 | 4.573 | |
fragment_HL | 0.802 | 0.271 | 0.971 | |
fragment_TI | 0.553 | 0.080 | 0.633 | |
fragment_delay | 1.348 | 0.338 | 1.569 | |
fragment_inty | 0.798 | 0.293 | 1.008 | |
gff3_preprocess | 0.711 | 0.119 | 0.833 | |
make_df | 0.957 | 0.284 | 0.774 | |
make_pen | 12.834 | 8.830 | 17.778 | |
nls2_fit | 53.754 | 1.764 | 34.166 | |
predict_ps_itss | 0.373 | 0.072 | 0.446 | |
rifi_fit | 36.615 | 0.423 | 37.132 | |
rifi_fragmentation | 4.215 | 1.195 | 5.002 | |
rifi_penalties | 67.520 | 49.256 | 93.975 | |
rifi_preprocess | 2.173 | 0.837 | 2.454 | |
rifi_stats | 4.421 | 0.164 | 4.594 | |
rifi_summary | 2.860 | 0.080 | 2.946 | |
rifi_visualization | 65.385 | 1.163 | 66.683 | |
rifi_wrapper | 178.929 | 78.908 | 202.706 | |
segment_pos | 0.429 | 0.000 | 0.431 | |
viz_pen_obj | 0.009 | 0.000 | 0.009 | |