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 12:35:02 -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: /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_1.9.0.tar.gz |
StartedAt: 2024-05-29 23:37:51 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 23:47:48 -0400 (Wed, 29 May 2024) |
EllapsedTime: 597.2 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_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/rifi.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * 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 ‘1.9.0’ * 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 104.900 62.220 126.989 rifi_penalties 46.199 37.048 64.889 rifi_visualization 33.133 2.148 35.282 nls2_fit 33.261 0.985 20.879 rifi_fit 21.591 0.413 22.003 make_pen 9.242 6.985 12.936 TI_fit 10.303 1.067 7.091 * 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-3.20-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 ‘/home/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: /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 | 10.303 | 1.067 | 7.091 | |
TUgether | 0.448 | 0.191 | 0.573 | |
apply_Ttest_delay | 0.117 | 0.012 | 0.128 | |
apply_ancova | 0.271 | 0.076 | 0.347 | |
apply_event_position | 0.097 | 0.016 | 0.112 | |
apply_manova | 0.552 | 0.047 | 0.600 | |
apply_t_test | 0.599 | 0.052 | 0.651 | |
apply_t_test_ti | 0.138 | 0.036 | 0.175 | |
check_input | 0.295 | 0.044 | 0.340 | |
dataframe_summary | 0.091 | 0.016 | 0.107 | |
dataframe_summary_TI | 0.041 | 0.000 | 0.041 | |
dataframe_summary_events | 0.708 | 0.020 | 0.728 | |
dataframe_summary_events_HL_int | 0.548 | 0.028 | 0.576 | |
dataframe_summary_events_ps_itss | 0.213 | 0.000 | 0.213 | |
dataframe_summary_events_velocity | 0.182 | 0.020 | 0.202 | |
event_dataframe | 0.689 | 0.012 | 0.701 | |
finding_PDD | 0.193 | 0.093 | 0.241 | |
finding_TI | 0.312 | 0.101 | 0.365 | |
fold_change | 2.810 | 0.087 | 2.898 | |
fragment_HL | 0.547 | 0.170 | 0.611 | |
fragment_TI | 0.432 | 0.028 | 0.460 | |
fragment_delay | 0.931 | 0.371 | 1.190 | |
fragment_inty | 0.651 | 0.228 | 0.803 | |
gff3_preprocess | 0.540 | 0.107 | 0.648 | |
make_df | 0.610 | 0.341 | 0.587 | |
make_pen | 9.242 | 6.985 | 12.936 | |
nls2_fit | 33.261 | 0.985 | 20.879 | |
predict_ps_itss | 0.264 | 0.032 | 0.296 | |
rifi_fit | 21.591 | 0.413 | 22.003 | |
rifi_fragmentation | 2.836 | 0.977 | 3.450 | |
rifi_penalties | 46.199 | 37.048 | 64.889 | |
rifi_preprocess | 1.467 | 0.529 | 1.553 | |
rifi_stats | 2.920 | 0.199 | 3.120 | |
rifi_summary | 1.815 | 0.043 | 1.859 | |
rifi_visualization | 33.133 | 2.148 | 35.282 | |
rifi_wrapper | 104.900 | 62.220 | 126.989 | |
segment_pos | 0.167 | 0.000 | 0.167 | |
viz_pen_obj | 0.006 | 0.004 | 0.010 | |