Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 92/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
appreci8R 1.24.0 (landing page) Sarah Sandmann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the appreci8R package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/appreci8R.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: appreci8R |
Version: 1.24.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:appreci8R.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings appreci8R_1.24.0.tar.gz |
StartedAt: 2024-12-20 11:20:24 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 11:26:59 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 395.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: appreci8R.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:appreci8R.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings appreci8R_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/appreci8R.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘appreci8R/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘appreci8R’ version ‘1.24.0’ * 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 ‘appreci8R’ 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 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 ... NOTE annotate: no visible global function definition for ‘write.table’ appreci8Rshiny : <anonymous>: no visible global function definition for ‘read.table’ appreci8Rshiny : <anonymous>: no visible global function definition for ‘write.table’ appreci8Rshiny : <anonymous>: no visible global function definition for ‘data’ appreci8Rshiny : <anonymous>: no visible global function definition for ‘ncbi_snp_query’ combineOutput: no visible global function definition for ‘write.table’ determineCharacteristics: no visible global function definition for ‘data’ determineCharacteristics: no visible global function definition for ‘ncbi_snp_query’ determineCharacteristics: no visible global function definition for ‘write.table’ evaluateCovAndBQ: no visible global function definition for ‘write.table’ filterTarget: no visible global function definition for ‘write.table’ finalFiltration: no visible global function definition for ‘write.table’ normalize: no visible global function definition for ‘write.table’ readInput : <anonymous>: no visible global function definition for ‘read.table’ readInput: no visible global function definition for ‘read.table’ Undefined global functions or variables: data ncbi_snp_query read.table write.table Consider adding importFrom("utils", "data", "read.table", "write.table") to your NAMESPACE file. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/appreci8R.Rcheck/00check.log’ for details.
appreci8R.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL appreci8R ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘appreci8R’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’ Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘XtraSNPlocs.Hsapiens.dbSNP144.GRCh37’ Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.1Kgenomes.phase3.hs37d5’ Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.ExAC.r1.0.hs37d5’ Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.gnomADex.r2.1.hs37d5’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’ Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘XtraSNPlocs.Hsapiens.dbSNP144.GRCh37’ Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.1Kgenomes.phase3.hs37d5’ Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.ExAC.r1.0.hs37d5’ Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.gnomADex.r2.1.hs37d5’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’ Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘XtraSNPlocs.Hsapiens.dbSNP144.GRCh37’ Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.1Kgenomes.phase3.hs37d5’ Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.ExAC.r1.0.hs37d5’ Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.gnomADex.r2.1.hs37d5’ ** testing if installed package keeps a record of temporary installation path * DONE (appreci8R)
appreci8R.Rcheck/appreci8R-Ex.timings
name | user | system | elapsed | |
annotate | 0.140 | 0.012 | 0.151 | |
appreci8R-package | 0 | 0 | 0 | |
appreci8Rshiny | 0 | 0 | 0 | |
combineOutput | 0.390 | 0.030 | 0.422 | |
determineCharacteristics | 0.137 | 0.013 | 0.150 | |
evaluateCovAndBQ | 0.170 | 0.014 | 0.185 | |
filterTarget | 0.001 | 0.001 | 0.001 | |
finalFiltration | 0.127 | 0.007 | 0.139 | |
normalize | 0.001 | 0.000 | 0.001 | |