############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/biodb_1.2.2.tar.gz && rm -rf biodb.buildbin-libdir && mkdir biodb.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biodb.buildbin-libdir biodb_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL biodb_1.2.2.zip && rm biodb_1.2.2.tar.gz biodb_1.2.2.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 10 2665k 10 275k 0 0 667k 0 0:00:03 --:--:-- 0:00:03 666k 43 2665k 43 1150k 0 0 817k 0 0:00:03 0:00:01 0:00:02 817k 100 2665k 100 2665k 0 0 1175k 0 0:00:02 0:00:02 --:--:-- 1176k 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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/R/library/testthat/include/testthat.h:1, from test-runner.cpp:7: C:/Users/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()': C:/Users/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat/testthat.h:145:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] } ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()': C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-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 BiodbBiocPersistentCache html BiodbConfig html BiodbConn html BiodbConnBase html BiodbCsvEntry html BiodbCustomPersistentCache html BiodbDbInfo html BiodbDbsInfo html BiodbEntry html BiodbEntryField html BiodbEntryFields html BiodbFactory html BiodbHtmlEntry html BiodbJsonEntry html BiodbListEntry html BiodbMain html BiodbPersistentCache html BiodbRequest html BiodbRequestScheduler html BiodbRequestSchedulerRule html BiodbSdfEntry html BiodbSqlBinaryOp html BiodbSqlExpr html BiodbSqlField html BiodbSqlList html BiodbSqlLogicalOp html BiodbSqlQuery html BiodbSqlValue html BiodbTestMsgAck html BiodbTxtEntry html BiodbUrl html BiodbXmlEntry html CompCsvFileConn html CompCsvFileEntry html CompSqliteConn html CompSqliteEntry html CsvFileConn 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 html MassCsvFileEntry html MassSqliteConn html MassSqliteEntry html Progress html Range html RequestResult html SqliteConn html TestRefEntries html abstractClass html abstractMethod html biodb-package html checkDeprecatedCacheFolders html closeMatchPpm html connNameToClassPrefix html createBiodbTestInstance html df2str html doesRCurlRequestUrlExist html error html error0 html genNewExtPkg html getBaseUrlContent html getBaseUrlRequestResult html getConnClassName html getConnTypes html getDefaultCacheDir html getEntryClassName html getEntryTypes html getLicenses html getLogger html getPkgName html getRCurlContent html getRCurlRequestResult html getReposName html getTestOutputDir html getUrlContent html getUrlRequestResult html listTestRefEntries html loadFileContents html logDebug html logDebug0 html logInfo html logInfo0 html logTrace html logTrace0 html lst2str html makeRCurlOptions html newInst html prepareFileContents html runGenericTests html saveContentsToFiles 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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/R/library/testthat/include/testthat.h:1, from test-runner.cpp:7: C:/Users/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()': C:/Users/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat/testthat.h:145:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] } ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()': C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/biodb.buildbin-libdir/biodb/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'biodb' as biodb_1.2.2.zip * DONE (biodb) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'biodb' successfully unpacked and MD5 sums checked