Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:26 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 2057/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
StarBioTrek 1.28.0 (landing page) Claudia Cava
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the StarBioTrek package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/StarBioTrek.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: StarBioTrek |
Version: 1.28.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:StarBioTrek.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings StarBioTrek_1.28.0.tar.gz |
StartedAt: 2024-04-16 04:27:29 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 04:30:26 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 177.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: StarBioTrek.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:StarBioTrek.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings StarBioTrek_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/StarBioTrek.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 ‘StarBioTrek/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘StarBioTrek’ version ‘1.28.0’ * 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 ‘StarBioTrek’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: data 5.4Mb * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘AnnotationDbi’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE svm_classification: no visible binding for global variable ‘Target’ Undefined global functions or variables: Target * 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 ... WARNING Documented arguments not in \usage in documentation object 'svm_classification': ‘Target’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 LazyData ... WARNING LazyData DB of 5.4 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘StarBioTrek.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘StarBioTrek.Rmd’ ... > knitr::opts_chunk$set(cache = FALSE) > devtools::load_all(".") When sourcing ‘StarBioTrek.R’: Error: Could not find a root 'DESCRIPTION' file that starts with '^Package' in '/tmp/Rtmp8yXbqs/file2defef7fa64aa6/vignettes'. ℹ Are you in your project directory and does your project have a 'DESCRIPTION' file? Execution halted * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/StarBioTrek.Rcheck/00check.log’ for details.
StarBioTrek.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL StarBioTrek ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘StarBioTrek’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (StarBioTrek)
StarBioTrek.Rcheck/StarBioTrek-Ex.timings
name | user | system | elapsed | |
ConvertedIDgenes | 4.753 | 0.144 | 4.897 | |
GE_matrix | 0.045 | 0.000 | 0.045 | |
GE_matrix_mean | 0.043 | 0.000 | 0.043 | |
GetData | 0 | 0 | 0 | |
GetPathData | 0.003 | 0.000 | 0.003 | |
GetPathNet | 0.002 | 0.000 | 0.002 | |
IPPI | 0.000 | 0.000 | 0.001 | |
SelectedSample | 0.112 | 0.012 | 0.124 | |
average | 0.900 | 0.104 | 1.004 | |
circleplot | 0.959 | 0.004 | 0.963 | |
dsscorecrtlk | 0.03 | 0.00 | 0.03 | |
eucdistcrtlk | 0.056 | 0.000 | 0.056 | |
getNETdata | 0 | 0 | 0 | |
listpathnet | 0.352 | 0.000 | 0.352 | |
pathnet | 0.34 | 0.00 | 0.34 | |
plotcrosstalk | 0.008 | 0.000 | 0.008 | |
stdv | 0.028 | 0.000 | 0.028 | |
svm_classification | 0 | 0 | 0 | |