Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:58 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the BaseSpaceR package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 119/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BaseSpaceR 1.36.0 (landing page) Jared O'Connell
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: BaseSpaceR |
Version: 1.36.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BaseSpaceR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BaseSpaceR_1.36.0.tar.gz |
StartedAt: 2021-10-14 19:50:50 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 19:52:16 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 86.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BaseSpaceR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BaseSpaceR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BaseSpaceR_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BaseSpaceR.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'BaseSpaceR/DESCRIPTION' ... OK * this is package 'BaseSpaceR' version '1.36.0' * 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 ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... 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 ... 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BaseSpaceR.Rcheck/00check.log' for details.
BaseSpaceR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BaseSpaceR_1.36.0.tar.gz && rm -rf BaseSpaceR.buildbin-libdir && mkdir BaseSpaceR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BaseSpaceR.buildbin-libdir BaseSpaceR_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BaseSpaceR_1.36.0.zip && rm BaseSpaceR_1.36.0.tar.gz BaseSpaceR_1.36.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 273k 100 273k 0 0 1031k 0 --:--:-- --:--:-- --:--:-- 1034k install for i386 * installing *source* package 'BaseSpaceR' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'BaseSpaceR' finding HTML links ... done AppAuth-class html AppResults-class html AppSessionAuth html AppSessions-class html BaseSpaceR-package html Coverage html Error html Files-class html FilesExtra html Genomes-class html Projects-class html Response-class html Runs-class html Samples-class html ServiceURI-class html Users-class html Variants html data-aAuth html private_methods html ** 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 install for x64 * installing *source* package 'BaseSpaceR' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'BaseSpaceR' as BaseSpaceR_1.36.0.zip * DONE (BaseSpaceR) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'BaseSpaceR' successfully unpacked and MD5 sums checked
BaseSpaceR.Rcheck/examples_i386/BaseSpaceR-Ex.timings
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BaseSpaceR.Rcheck/examples_x64/BaseSpaceR-Ex.timings
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