Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-09-10 17:33 -0400 (Tue, 10 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4495 |
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 707/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Tiago Lubiana
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the FCBF package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FCBF.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: FCBF |
Version: 2.12.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:FCBF.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings FCBF_2.12.0.tar.gz |
StartedAt: 2024-09-08 23:02:22 -0400 (Sun, 08 Sep 2024) |
EndedAt: 2024-09-08 23:07:18 -0400 (Sun, 08 Sep 2024) |
EllapsedTime: 295.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: FCBF.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:FCBF.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings FCBF_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/FCBF.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘FCBF/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FCBF’ version ‘2.12.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘FCBF’ can be installed ... OK * 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 whether startup messages can be suppressed ... 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 ... OK * 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 fcbf 21.112 0.596 21.709 scDengue 14.452 0.180 14.632 su_plot 8.262 0.175 8.438 get_su_for_feature_table_and_vector 7.972 0.204 8.175 get_ig_for_feature_table_and_vector 7.429 0.068 7.497 discretize_exprs 5.306 0.344 5.650 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘FCBF-Vignette.Rmd’ using rmarkdown Quitting from lines 178-205 [unnamed-chunk-10] (FCBF-Vignette.Rmd) Error: processing vignette 'FCBF-Vignette.Rmd' failed with diagnostics: Required packages are missing: kernlab --- failed re-building ‘FCBF-Vignette.Rmd’ SUMMARY: processing the following file failed: ‘FCBF-Vignette.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.19-bioc/meat/FCBF.Rcheck/00check.log’ for details.
FCBF.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL FCBF ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘FCBF’ ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in fun(libname, pkgname) : Package 'FCBF' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'FCBF' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (FCBF)
FCBF.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(FCBF) Warning message: In fun(libname, pkgname) : Package 'FCBF' is deprecated and will be removed from Bioconductor version 3.20 > > test_check("FCBF") [1] "Number of features features = 8" [1] "Number of prospective features = 7" [1] "Number of final features = 2" [1] "Number of features features = 8" [1] "Number of prospective features = 1" [ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ] > > proc.time() user system elapsed 7.731 0.379 8.099
FCBF.Rcheck/FCBF-Ex.timings
name | user | system | elapsed | |
discretize_exprs | 5.306 | 0.344 | 5.650 | |
discretize_exprs_supervised | 2.013 | 0.152 | 2.164 | |
discretize_gene_supervised | 0.401 | 0.080 | 0.481 | |
fcbf | 21.112 | 0.596 | 21.709 | |
get_IG_for_vector_pair | 2.824 | 0.151 | 2.976 | |
get_SU_for_vector_pair | 2.171 | 0.093 | 2.264 | |
get_ig_for_feature_table_and_vector | 7.429 | 0.068 | 7.497 | |
get_su_for_feature_table_and_vector | 7.972 | 0.204 | 8.175 | |
scDengue | 14.452 | 0.180 | 14.632 | |
su_plot | 8.262 | 0.175 | 8.438 | |