Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:33:46 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the SRAdb package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1784/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SRAdb 1.52.0 (landing page) Jack Zhu
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: SRAdb |
Version: 1.52.0 |
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SRAdb.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SRAdb_1.52.0.tar.gz |
StartedAt: 2021-05-06 07:15:08 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 07:16:34 -0400 (Thu, 06 May 2021) |
EllapsedTime: 85.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SRAdb.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SRAdb.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SRAdb_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SRAdb.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'SRAdb/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SRAdb' version '1.52.0' * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'SRAdb' 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 ... NOTE The following files look like leftovers: 'SRAdb/SRAdb-package.Rd' Please remove them from your package. * 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 'RCurl' which was already attached by Depends. Please remove these calls from your code. Packages in Depends field not imported from: 'RSQLite' 'graph' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .socketWrite: no visible global function definition for 'write.socket' .socketWrite: no visible global function definition for 'read.socket' IGVsocket: no visible global function definition for 'make.socket' colDescriptions: no visible global function definition for 'dbGetQuery' entityGraph: no visible global function definition for 'na.omit' entityGraph: no visible global function definition for 'new' entityGraph : <anonymous>: no visible global function definition for 'addEdge' getFASTQfile: no visible global function definition for 'download.file' getFASTQinfo: no visible global function definition for 'dbGetQuery' getSRA: no visible global function definition for 'dbGetQuery' getSRAdbFile: no visible global function definition for 'download.file' getSRAdbFile: no visible global function definition for 'dbConnect' getSRAdbFile: no visible global function definition for 'SQLite' getSRAdbFile: no visible global function definition for 'dbGetQuery' getSRAdbFile: no visible global function definition for 'dbDisconnect' getSRAfile: no visible global function definition for 'download.file' getSRAinfo: no visible global function definition for 'na.omit' sraConvert: no visible global function definition for 'dbGetQuery' startIGV: no visible global function definition for 'browseURL' Undefined global functions or variables: SQLite addEdge browseURL dbConnect dbDisconnect dbGetQuery download.file make.socket na.omit new read.socket write.socket Consider adding importFrom("methods", "new") importFrom("stats", "na.omit") importFrom("utils", "browseURL", "download.file", "make.socket", "read.socket", "write.socket") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 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: 4 NOTEs See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SRAdb.Rcheck/00check.log' for details.
SRAdb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SRAdb_1.52.0.tar.gz && rm -rf SRAdb.buildbin-libdir && mkdir SRAdb.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SRAdb.buildbin-libdir SRAdb_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SRAdb_1.52.0.zip && rm SRAdb_1.52.0.tar.gz SRAdb_1.52.0.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 553k 100 553k 0 0 25.1M 0 --:--:-- --:--:-- --:--:-- 27.0M install for i386 * installing *source* package 'SRAdb' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'SRAdb' finding HTML links ... done IGVclear html IGVcollapse html IGVgenome html IGVgoto html IGVload html IGVsession html IGVsnapshot html IGVsocket html IGVsort html SRAdb-package html ascpR html ascpSRA html colDescriptions html entityGraph html getFASTQfile html getFASTQinfo html getSRA html getSRAdbFile html getSRAfile html getSRAinfo html listSRAfile html sraConvert html sraGraph html startIGV 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 'SRAdb' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'SRAdb' as SRAdb_1.52.0.zip * DONE (SRAdb) * installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library' package 'SRAdb' successfully unpacked and MD5 sums checked
SRAdb.Rcheck/examples_i386/SRAdb-Ex.timings
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SRAdb.Rcheck/examples_x64/SRAdb-Ex.timings
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