############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/biodb_1.0.4.tar.gz && rm -rf biodb.buildbin-libdir && mkdir biodb.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biodb.buildbin-libdir biodb_1.0.4.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL biodb_1.0.4.zip && rm biodb_1.0.4.tar.gz biodb_1.0.4.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 405k 100 405k 0 0 1199k 0 --:--:-- --:--:-- --:--:-- 1204k install for i386 * installing *source* package 'biodb' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c closeMatchPpm.cpp -o closeMatchPpm.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-100-ms_matching.cpp -o test-100-ms_matching.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat.h:1, from test-runner.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()': C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h:145:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] } ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()': C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h:152:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] } ^ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o biodb.dll tmp.def RcppExports.o closeMatchPpm.o test-100-ms_matching.o test-runner.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/biodb.buildbin-libdir/00LOCK-biodb/00new/biodb/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'biodb' finding HTML links ... done BiodbCompounddbConn-class html BiodbConfig-class html BiodbConn-class html BiodbConnBase-class html BiodbConnObserver-class html BiodbCsvEntry-class html BiodbDbInfo-class html BiodbDbsInfo-class html BiodbDownloadable-class html BiodbEditable-class html BiodbEntry-class html BiodbEntryField-class html BiodbEntryFields-class html BiodbFactory-class html BiodbHtmlEntry-class html BiodbJsonEntry-class html BiodbListEntry-class html BiodbMain-class html BiodbMassdbConn-class html BiodbObserver-class html BiodbPersistentCache-class html BiodbRemotedbConn-class html BiodbRequest html BiodbRequestScheduler-class html BiodbRequestSchedulerRule html BiodbSdfEntry-class html BiodbSqlBinaryOp html BiodbSqlExpr html BiodbSqlField html BiodbSqlList html BiodbSqlLogicalOp html BiodbSqlQuery html BiodbSqlValue html BiodbTestMsgAck-class html BiodbTxtEntry-class html BiodbUrl html BiodbWritable-class html BiodbXmlEntry-class html CompCsvFileConn-class html CompCsvFileEntry-class html CompSqliteConn-class html CompSqliteEntry-class html CsvFileConn-class html ExtConnClass html ExtCpp html ExtDefinitions html ExtDescriptionFile html ExtEntryClass html ExtFileGenerator html ExtGenerator html ExtGitignore html ExtLicense html ExtMakefile html ExtPackage html ExtPackageFile html ExtRbuildignore html ExtReadme html ExtTests html ExtTravisFile html ExtVignette html FileTemplate html MassCsvFileConn-class html MassCsvFileEntry-class html MassSqliteConn-class html MassSqliteEntry-class html Progress html Range html SqliteConn-class html biodb-package html closeMatchPpm html connNameToClassPrefix html createBiodbTestInstance html df2str html error html error0 html genNewExtPkg html getConnClassName html getConnTypes html getEntryClassName html getEntryTypes html getLicenses html getLogger html getPkgName html getReposName html getTestOutputDir html listTestRefEntries html logDebug html logDebug0 html logInfo html logInfo0 html logTrace html logTrace0 html lst2str html newInst html runGenericTests html testContext html testThat html upgradeExtPkg html warn html warn0 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 'biodb' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c closeMatchPpm.cpp -o closeMatchPpm.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-100-ms_matching.cpp -o test-100-ms_matching.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat.h:1, from test-runner.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()': C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h:145:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] } ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()': C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h:152:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] } ^ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o biodb.dll tmp.def RcppExports.o closeMatchPpm.o test-100-ms_matching.o test-runner.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/biodb.buildbin-libdir/biodb/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'biodb' as biodb_1.0.4.zip * DONE (biodb) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'biodb' successfully unpacked and MD5 sums checked