Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:40 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 132/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BaseSpaceR 1.49.0 (landing page) Jared O'Connell
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the BaseSpaceR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BaseSpaceR.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: BaseSpaceR |
Version: 1.49.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BaseSpaceR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BaseSpaceR_1.49.0.tar.gz |
StartedAt: 2024-08-20 22:30:24 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 22:31:14 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 49.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BaseSpaceR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BaseSpaceR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BaseSpaceR_1.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BaseSpaceR.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'BaseSpaceR/DESCRIPTION' ... OK * this is package 'BaseSpaceR' version '1.49.0' * 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 whether package 'BaseSpaceR' 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 ... NOTE Problems with news in 'NEWS': Cannot process chunk/lines: BUG FIXES Cannot process chunk/lines: Changed Access token and projects ID used in the vignette to reflect changes in Cannot process chunk/lines: the permission enforcements performed by BaseSpace * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to 'Rsamtools' in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE asBamFile: no visible global function definition for 'BamFile' GET,ServiceURI: no visible global function definition for 'basicHeaderGatherer' GET,ServiceURI: no visible global function definition for 'basicTextGatherer' GET,ServiceURI: no visible global function definition for 'getForm' GET,ServiceURI: no visible global function definition for 'curlOptions' POST,ServiceURI: no visible global function definition for 'basicHeaderGatherer' POST,ServiceURI: no visible global function definition for 'basicTextGatherer' POST,ServiceURI: no visible global function definition for 'curlPerform' POSTForm,ServiceURI: no visible global function definition for 'basicHeaderGatherer' POSTForm,ServiceURI: no visible global function definition for 'basicTextGatherer' POSTForm,ServiceURI: no visible global function definition for 'postForm' POSTForm,ServiceURI: no visible global function definition for 'curlOptions' getBAMs,AppResults: no visible binding for global variable 'BamFileList' getFiles,AppAuth : .toDisk: no visible global function definition for 'CFILE' getFiles,AppAuth : .toDisk: no visible global function definition for 'curlPerform' getFiles,AppAuth : .toMem: no visible global function definition for 'getURLContent' getFiles,AppAuth : .toMem: no visible binding for global variable 'dsize' Undefined global functions or variables: BamFile BamFileList CFILE basicHeaderGatherer basicTextGatherer curlOptions curlPerform dsize getForm getURLContent postForm * checking Rd files ... WARNING checkRd: (5) Genomes-class.Rd:49-52: \item in \describe must have non-empty label checkRd: (5) Genomes-class.Rd:53-58: \item in \describe must have non-empty label checkRd: (5) Genomes-class.Rd:59-62: \item in \describe must have non-empty label checkRd: (5) Projects-class.Rd:55-58: \item in \describe must have non-empty label checkRd: (5) Projects-class.Rd:59-64: \item in \describe must have non-empty label checkRd: (5) Projects-class.Rd:65-68: \item in \describe must have non-empty label checkRd: (5) Runs-class.Rd:55-58: \item in \describe must have non-empty label checkRd: (5) Runs-class.Rd:59-64: \item in \describe must have non-empty label checkRd: (5) Runs-class.Rd:65-68: \item in \describe must have non-empty label checkRd: (5) Samples-class.Rd:63-66: \item in \describe must have non-empty label checkRd: (5) Samples-class.Rd:67-72: \item in \describe must have non-empty label checkRd: (5) Samples-class.Rd:73-76: \item in \describe must have non-empty label checkRd: (5) Users-class.Rd:33-36: \item in \describe must have non-empty label checkRd: (5) Users-class.Rd:37-41: \item in \describe must have non-empty label * 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 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 WARNING, 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/BaseSpaceR.Rcheck/00check.log' for details.
BaseSpaceR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BaseSpaceR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'BaseSpaceR' ... ** using staged installation ** R ** data ** 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 (BaseSpaceR)
BaseSpaceR.Rcheck/BaseSpaceR-Ex.timings
name | user | system | elapsed | |
AppAuth-class | 0.24 | 0.06 | 0.58 | |
AppResults-class | 0 | 0 | 0 | |
AppSessionAuth | 0 | 0 | 0 | |
AppSessions-class | 0 | 0 | 0 | |
Coverage | 0.00 | 0.02 | 0.02 | |
Error | 0 | 0 | 0 | |
Files-class | 0.06 | 0.04 | 0.48 | |
FilesExtra | 0.08 | 0.02 | 0.39 | |
Genomes-class | 0.13 | 0.01 | 0.67 | |
Projects-class | 0.20 | 0.00 | 0.83 | |
Response-class | 0 | 0 | 0 | |
Runs-class | 0.17 | 0.05 | 1.64 | |
Samples-class | 0.14 | 0.05 | 1.05 | |
ServiceURI-class | 0 | 0 | 0 | |
Users-class | 0.06 | 0.03 | 0.28 | |
Variants | 0.05 | 0.03 | 0.49 | |
data-aAuth | 0.05 | 0.02 | 0.11 | |