Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:49 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 1738/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rifi 1.7.0 (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 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | 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. |
Package: rifi |
Version: 1.7.0 |
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_1.7.0.tar.gz |
StartedAt: 2024-03-02 09:29:15 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 09:54:27 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 1511.6 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_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/rifi.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 ‘1.7.0’ * 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 R 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 254.954 77.853 359.547 rifi_penalties 126.590 58.812 222.520 nls2_fit 93.076 3.051 72.562 rifi_fit 61.518 0.893 82.692 rifi_visualization 46.575 2.591 59.415 make_pen 23.196 9.546 37.734 TI_fit 28.024 2.337 22.165 rifi_fragmentation 7.722 1.779 11.129 fold_change 7.504 0.237 9.229 rifi_stats 7.201 0.281 9.729 rifi_preprocess 4.111 1.243 5.477 rifi_summary 4.498 0.092 5.477 * 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 | 28.024 | 2.337 | 22.165 | |
TUgether | 1.141 | 0.320 | 1.662 | |
apply_Ttest_delay | 0.250 | 0.043 | 0.328 | |
apply_ancova | 0.761 | 0.090 | 1.028 | |
apply_event_position | 0.255 | 0.028 | 0.330 | |
apply_manova | 1.441 | 0.081 | 1.809 | |
apply_t_test | 1.658 | 0.032 | 1.996 | |
apply_t_test_ti | 0.399 | 0.008 | 0.461 | |
check_input | 0.841 | 0.019 | 0.970 | |
dataframe_summary | 0.202 | 0.023 | 0.268 | |
dataframe_summary_TI | 0.100 | 0.007 | 0.122 | |
dataframe_summary_events | 1.693 | 0.058 | 2.022 | |
dataframe_summary_events_HL_int | 1.354 | 0.036 | 1.605 | |
dataframe_summary_events_ps_itss | 0.503 | 0.026 | 0.603 | |
dataframe_summary_events_velocity | 0.524 | 0.027 | 0.636 | |
event_dataframe | 1.687 | 0.047 | 1.992 | |
finding_PDD | 0.526 | 0.143 | 0.755 | |
finding_TI | 0.874 | 0.258 | 1.279 | |
fold_change | 7.504 | 0.237 | 9.229 | |
fragment_HL | 1.428 | 0.274 | 1.967 | |
fragment_TI | 1.063 | 0.121 | 1.431 | |
fragment_delay | 2.464 | 0.554 | 3.340 | |
fragment_inty | 1.561 | 0.348 | 2.103 | |
gff3_preprocess | 1.149 | 0.130 | 1.537 | |
make_df | 1.807 | 0.708 | 1.924 | |
make_pen | 23.196 | 9.546 | 37.734 | |
nls2_fit | 93.076 | 3.051 | 72.562 | |
predict_ps_itss | 0.625 | 0.081 | 0.898 | |
rifi_fit | 61.518 | 0.893 | 82.692 | |
rifi_fragmentation | 7.722 | 1.779 | 11.129 | |
rifi_penalties | 126.590 | 58.812 | 222.520 | |
rifi_preprocess | 4.111 | 1.243 | 5.477 | |
rifi_stats | 7.201 | 0.281 | 9.729 | |
rifi_summary | 4.498 | 0.092 | 5.477 | |
rifi_visualization | 46.575 | 2.591 | 59.415 | |
rifi_wrapper | 254.954 | 77.853 | 359.547 | |
segment_pos | 0.410 | 0.010 | 0.582 | |
viz_pen_obj | 0.015 | 0.010 | 0.026 | |