Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1755/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rifi 1.10.0 (landing page) Jens Georg
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | 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 | ||||||||||
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: 1.10.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings rifi_1.10.0.tar.gz |
StartedAt: 2024-11-20 08:28:30 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 08:38:45 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 615.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rifi.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:rifi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings rifi_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/rifi.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘rifi/DESCRIPTION’ ... OK * this is package ‘rifi’ version ‘1.10.0’ * 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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/rifi/man/predict_ps_itss.Rd:57: unexpected '}' See ‘/media/volume/teran2_disk/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 76.680 65.267 135.059 rifi_penalties 35.241 44.076 79.562 nls2_fit 27.046 1.295 20.720 rifi_visualization 21.893 1.614 27.455 rifi_fit 17.172 0.073 18.778 make_pen 6.852 7.142 14.124 TI_fit 9.103 1.853 7.211 * 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 ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/rifi.Rcheck/00check.log’ for details.
rifi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL rifi ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}' Warning: /media/volume/teran2_disk/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 | 9.103 | 1.853 | 7.211 | |
TUgether | 0.628 | 0.148 | 1.064 | |
apply_Ttest_delay | 0.079 | 0.007 | 0.086 | |
apply_ancova | 0.204 | 0.027 | 0.233 | |
apply_event_position | 0.062 | 0.012 | 0.073 | |
apply_manova | 1.140 | 0.117 | 1.686 | |
apply_t_test | 0.421 | 0.105 | 0.626 | |
apply_t_test_ti | 0.106 | 0.022 | 0.129 | |
check_input | 0.198 | 0.001 | 0.200 | |
dataframe_summary | 0.051 | 0.005 | 0.057 | |
dataframe_summary_TI | 0.026 | 0.002 | 0.027 | |
dataframe_summary_events | 0.840 | 0.019 | 0.866 | |
dataframe_summary_events_HL_int | 0.353 | 0.011 | 0.463 | |
dataframe_summary_events_ps_itss | 0.133 | 0.005 | 0.201 | |
dataframe_summary_events_velocity | 0.133 | 0.002 | 0.135 | |
event_dataframe | 0.465 | 0.004 | 0.471 | |
finding_PDD | 0.139 | 0.118 | 0.298 | |
finding_TI | 0.227 | 0.156 | 0.411 | |
fold_change | 2.031 | 0.112 | 3.181 | |
fragment_HL | 0.376 | 0.139 | 0.557 | |
fragment_TI | 0.284 | 0.043 | 0.327 | |
fragment_delay | 0.608 | 0.285 | 0.926 | |
fragment_inty | 0.447 | 0.173 | 0.922 | |
gff3_preprocess | 0.346 | 0.051 | 0.404 | |
make_df | 0.476 | 0.284 | 0.773 | |
make_pen | 6.852 | 7.142 | 14.124 | |
nls2_fit | 27.046 | 1.295 | 20.720 | |
predict_ps_itss | 0.163 | 0.030 | 0.196 | |
rifi_fit | 17.172 | 0.073 | 18.778 | |
rifi_fragmentation | 2.073 | 0.996 | 3.136 | |
rifi_penalties | 35.241 | 44.076 | 79.562 | |
rifi_preprocess | 1.101 | 0.683 | 2.533 | |
rifi_stats | 2.053 | 0.116 | 2.596 | |
rifi_summary | 1.272 | 0.008 | 1.344 | |
rifi_visualization | 21.893 | 1.614 | 27.455 | |
rifi_wrapper | 76.680 | 65.267 | 135.059 | |
segment_pos | 0.116 | 0.001 | 0.118 | |
viz_pen_obj | 0.007 | 0.000 | 0.007 | |