Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:37:05 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 ... | ||||||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings rifi_1.8.0.tar.gz |
StartedAt: 2024-05-04 02:59:27 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 03:09:16 -0400 (Sat, 04 May 2024) |
EllapsedTime: 588.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rifi.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings rifi_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/rifi.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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: /home/biocbuild/bbs-3.19-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /home/biocbuild/bbs-3.19-bioc/meat/rifi/man/predict_ps_itss.Rd:57: unexpected '}' See ‘/home/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 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 106.581 60.657 126.037 rifi_penalties 44.187 34.932 62.172 nls2_fit 33.699 1.223 21.174 rifi_visualization 27.434 2.325 29.761 rifi_fit 21.432 0.403 21.836 make_pen 8.682 6.355 12.160 TI_fit 9.940 1.028 6.932 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/rifi.Rcheck/00check.log’ for details.
rifi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL rifi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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-3.19-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /home/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 | 9.940 | 1.028 | 6.932 | |
TUgether | 0.401 | 0.180 | 0.517 | |
apply_Ttest_delay | 0.090 | 0.011 | 0.102 | |
apply_ancova | 0.275 | 0.012 | 0.286 | |
apply_event_position | 0.089 | 0.004 | 0.094 | |
apply_manova | 0.525 | 0.027 | 0.554 | |
apply_t_test | 0.596 | 0.032 | 0.628 | |
apply_t_test_ti | 0.157 | 0.000 | 0.156 | |
check_input | 0.294 | 0.001 | 0.295 | |
dataframe_summary | 0.096 | 0.000 | 0.097 | |
dataframe_summary_TI | 0.039 | 0.000 | 0.040 | |
dataframe_summary_events | 0.669 | 0.008 | 0.678 | |
dataframe_summary_events_HL_int | 0.537 | 0.027 | 0.566 | |
dataframe_summary_events_ps_itss | 0.21 | 0.00 | 0.21 | |
dataframe_summary_events_velocity | 0.221 | 0.000 | 0.220 | |
event_dataframe | 0.691 | 0.036 | 0.727 | |
finding_PDD | 0.180 | 0.097 | 0.232 | |
finding_TI | 0.301 | 0.153 | 0.390 | |
fold_change | 2.760 | 0.200 | 2.959 | |
fragment_HL | 0.515 | 0.196 | 0.614 | |
fragment_TI | 0.363 | 0.036 | 0.399 | |
fragment_delay | 0.844 | 0.278 | 1.018 | |
fragment_inty | 0.639 | 0.151 | 0.728 | |
gff3_preprocess | 0.516 | 0.040 | 0.558 | |
make_df | 0.573 | 0.276 | 0.524 | |
make_pen | 8.682 | 6.355 | 12.160 | |
nls2_fit | 33.699 | 1.223 | 21.174 | |
predict_ps_itss | 0.263 | 0.019 | 0.283 | |
rifi_fit | 21.432 | 0.403 | 21.836 | |
rifi_fragmentation | 2.664 | 0.764 | 3.132 | |
rifi_penalties | 44.187 | 34.932 | 62.172 | |
rifi_preprocess | 1.452 | 0.496 | 1.529 | |
rifi_stats | 2.784 | 0.111 | 2.896 | |
rifi_summary | 1.730 | 0.036 | 1.766 | |
rifi_visualization | 27.434 | 2.325 | 29.761 | |
rifi_wrapper | 106.581 | 60.657 | 126.037 | |
segment_pos | 0.166 | 0.007 | 0.172 | |
viz_pen_obj | 0.01 | 0.00 | 0.01 | |