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 biodb package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodb.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 178/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biodb 1.0.4 (landing page) Pierrick Roger
| 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: biodb |
Version: 1.0.4 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biodb.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings biodb_1.0.4.tar.gz |
StartedAt: 2021-10-14 20:14:07 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:24:07 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 600.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biodb.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biodb.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings biodb_1.0.4.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/biodb.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 'biodb/DESCRIPTION' ... OK * this is package 'biodb' version '1.0.4' * package encoding: UTF-8 * 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 'biodb' can be installed ... OK * checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: R 1.7Mb libs 2.7Mb * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/biodb/libs/i386/biodb.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/biodb/libs/x64/biodb.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' 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/biodb.Rcheck/00check.log' for details.
biodb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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
biodb.Rcheck/tests_i386/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # vi: fdm=marker > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodb) > Sys.setenv(TESTTHAT_REPORTER="summary") > test_check("biodb") [ FAIL 0 | WARN 19 | SKIP 0 | PASS 1386 ] > > proc.time() user system elapsed 148.45 9.95 160.39 |
biodb.Rcheck/tests_x64/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # vi: fdm=marker > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodb) > Sys.setenv(TESTTHAT_REPORTER="summary") > test_check("biodb") [ FAIL 0 | WARN 19 | SKIP 0 | PASS 1386 ] > > proc.time() user system elapsed 188.92 11.29 248.29 |
biodb.Rcheck/examples_i386/biodb-Ex.timings
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biodb.Rcheck/examples_x64/biodb-Ex.timings
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