Jared O'Connell
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/BaseSpaceR |
| Branch: RELEASE_3_9 |
| Last Commit: 55c63db |
| Last Changed Date: 2019-05-02 11:53:41 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:27:42 -0400 (Wed, 16 Oct 2019).
| Package 106/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BaseSpaceR 1.28.0 Jared O'Connell
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: BaseSpaceR |
| Version: 1.28.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BaseSpaceR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BaseSpaceR_1.28.0.tar.gz |
| StartedAt: 2019-10-16 02:03:48 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:04:46 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 57.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BaseSpaceR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BaseSpaceR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BaseSpaceR_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BaseSpaceR.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '1.28.0' * 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 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-3.9-bioc/meat/BaseSpaceR.Rcheck/00check.log' for details.
BaseSpaceR.Rcheck/00install.out
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### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/BaseSpaceR_1.28.0.tar.gz && rm -rf BaseSpaceR.buildbin-libdir && mkdir BaseSpaceR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BaseSpaceR.buildbin-libdir BaseSpaceR_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL BaseSpaceR_1.28.0.zip && rm BaseSpaceR_1.28.0.tar.gz BaseSpaceR_1.28.0.zip
###
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% 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 271k 100 271k 0 0 1323k 0 --:--:-- --:--:-- --:--:-- 1368k
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_1.28.0.zip
* DONE (BaseSpaceR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'BaseSpaceR' successfully unpacked and MD5 sums checked
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BaseSpaceR.Rcheck/examples_i386/BaseSpaceR-Ex.timings
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BaseSpaceR.Rcheck/examples_x64/BaseSpaceR-Ex.timings
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