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This page was generated on 2021-10-26 14:06:53 -0400 (Tue, 26 Oct 2021).

INSTALL results for biodb on riesling1

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.

raw results

Package 175/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodb 1.1.16  (landing page)
Pierrick Roger
Snapshot Date: 2021-10-25 14:50:11 -0400 (Mon, 25 Oct 2021)
git_url: https://git.bioconductor.org/packages/biodb
git_branch: master
git_last_commit: c231763
git_last_commit_date: 2021-10-19 06:21:44 -0400 (Tue, 19 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: biodb
Version: 1.1.16
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/biodb_1.1.16.tar.gz && rm -rf biodb.buildbin-libdir && mkdir biodb.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biodb.buildbin-libdir biodb_1.1.16.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL biodb_1.1.16.zip && rm biodb_1.1.16.tar.gz biodb_1.1.16.zip
StartedAt: 2021-10-25 17:28:23 -0400 (Mon, 25 Oct 2021)
EndedAt: 2021-10-25 17:31:23 -0400 (Mon, 25 Oct 2021)
EllapsedTime: 180.2 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/biodb_1.1.16.tar.gz && rm -rf biodb.buildbin-libdir && mkdir biodb.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biodb.buildbin-libdir biodb_1.1.16.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL biodb_1.1.16.zip && rm biodb_1.1.16.tar.gz biodb_1.1.16.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2665k  100 2665k    0     0  3290k      0 --:--:-- --:--:-- --:--:-- 3290k

install for i386

* installing *source* package 'biodb' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/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"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/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"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/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"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/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 D:/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat.h:1,
                 from test-runner.cpp:7:
D:/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()':
D:/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat/testthat.h:145:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
D:/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()':
D:/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 -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/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"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/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"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/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"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/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"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/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 D:/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat.h:1,
                 from test-runner.cpp:7:
D:/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()':
D:/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat/testthat.h:145:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
D:/biocbuild/bbs-3.14-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()':
D:/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 -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/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_1.1.16.zip
* DONE (biodb)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'biodb' successfully unpacked and MD5 sums checked