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INSTALL report for AnalysisPageServer on tokay1

This page was generated on 2020-04-15 12:24:14 -0400 (Wed, 15 Apr 2020).

Package 52/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnalysisPageServer 1.20.0
Brad Friedman
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/AnalysisPageServer
Branch: RELEASE_3_10
Last Commit: aafd036
Last Changed Date: 2019-10-29 13:09:07 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnalysisPageServer
Version: 1.20.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/AnalysisPageServer_1.20.0.tar.gz && rm -rf AnalysisPageServer.buildbin-libdir && mkdir AnalysisPageServer.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnalysisPageServer.buildbin-libdir AnalysisPageServer_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL AnalysisPageServer_1.20.0.zip && rm AnalysisPageServer_1.20.0.tar.gz AnalysisPageServer_1.20.0.zip
StartedAt: 2020-04-14 18:37:26 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 18:42:55 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 328.8 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/AnalysisPageServer_1.20.0.tar.gz && rm -rf AnalysisPageServer.buildbin-libdir && mkdir AnalysisPageServer.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnalysisPageServer.buildbin-libdir AnalysisPageServer_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL AnalysisPageServer_1.20.0.zip && rm AnalysisPageServer_1.20.0.tar.gz AnalysisPageServer_1.20.0.zip
###
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100 16.7M  100 16.7M    0     0  55.7M      0 --:--:-- --:--:-- --:--:-- 56.4M

install for i386

* installing *source* package 'AnalysisPageServer' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c AnalysisPageSVG.cpp -o AnalysisPageSVG.o
AnalysisPageSVG.cpp: In function 'int matchPlotPoints(XMLElementList, std::deque<double>, std::deque<double>, double, int, int)':
AnalysisPageSVG.cpp:154:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "x and y have different lengths";
        ^
AnalysisPageSVG.cpp:157:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(els.size() < start + n)  {
                 ^
AnalysisPageSVG.cpp:194:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0; i < x.size(); i++)  {
                      ^
AnalysisPageSVG.cpp:210:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_x.size(); i++)  {
                        ^
AnalysisPageSVG.cpp:215:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_y.size(); i++)  {
                        ^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c R_init_AnalysisPageServer.cpp -o R_init_AnalysisPageServer.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c SearchReplace2.cpp -o SearchReplace2.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c catch.c -o catch.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c cor.cpp -o cor.o
cor.cpp: In function 'double basic_cor(const std::deque<double>&, const std::deque<double>&)':
cor.cpp:24:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "different sizes";
        ^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c tinyxml2.cpp -o tinyxml2.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o AnalysisPageServer.dll tmp.def AnalysisPageSVG.o R_init_AnalysisPageServer.o SearchReplace2.o catch.o cor.o tinyxml2.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/AnalysisPageServer.buildbin-libdir/00LOCK-AnalysisPageServer/00new/AnalysisPageServer/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
While loading AnalysisPageServer: urlEncode not found, providing a pure R implementation
While loading AnalysisPageServer: urlDecode not found, providing a pure R implementation
** help
*** installing help indices
  converting help for package 'AnalysisPageServer'
    finding HTML links ... done
    add.event                               html  
    add.event.handler                       html  
    analysis.link                           html  
    analysis.page.link                      html  
    analysis.page.of.current.app            html  
    annotate.analysis.page.svg              html  
    annotate.data.frame                     html  
    apache.httpd.conf                       html  
    aps.dataset.divs                        html  
    aps.one.dataset.div                     html  
    aps.urlEncode                           html  
    array.param                             html  
    autosignal.on.bloated.memory            html  
    bind.memory.checker                     html  
    bool.param                              html  
    build.service                           html  
    check.memory                            html  
    check.same.svgs                         html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpOARGUw/R.INSTALL10401f50671/AnalysisPageServer/man/check.same.svgs.Rd:17: file link 'checkEquals' in package 'RUnit' does not exist and so has been treated as a topic
    check.signal                            html  
    checkPackageInstalled                   html  
    checkRookForkForVignettes               html  
    clear.event.handlers                    html  
    client.ip                               html  
    combobox.param                          html  
    compound.param                          html  
    config.js                               html  
    copy.front.end                          html  
    current.app                             html  
    custom.body.attr                        html  
    custom.body.html                        html  
    custom.html.headers                     html  
    data.frame.to.json                      html  
    data.frame.to.list                      html  
    default.param                           html  
    default.param.set                       html  
    default.service.paramset                html  
    default.stylesheets                     html  
    dieIfWindows                            html  
    dies.ok                                 html  
    embed.APS.dataset                       html  
    encode.datanode                         html  
    eval.within.time                        html  
    event.names                             html  
    execute.handler                         html  
    file.param                              html  
    filterWidget                            html  
    get.APS.libbase.prefix                  html  
    get.APS.outdir                          html  
    get.page                                html  
    getTraceback                            html  
    has.event                               html  
    has.page                                html  
    ignore.lots.of.stuff                    html  
    is.registry                             html  
    kill.process                            html  
    knitAPS                                 html  
    known.param.sizes                       html  
    lives.ok                                html  
    make.standard.ids                       html  
    messageSectionName                      html  
    new.FastRWeb.analysis.page.run          html  
    new.analysis.page                       html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpOARGUw/R.INSTALL10401f50671/AnalysisPageServer/man/new.analysis.page.Rd:133: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
    new.datanode.array                      html  
    new.datanode.html                       html  
    new.datanode.plot                       html  
    new.datanode.simple                     html  
    new.datanode.table                      html  
    new.event.registry                      html  
    new.registry                            html  
    new.response                            html  
    new.rook.analysis.page.app              html  
    pages                                   html  
    param.set                               html  
    paramSetToJSON                          html  
    persistent.param.dependencies           html  
    persistent.params                       html  
    platformIsWindows                       html  
    protect.rapache.memory                  html  
    rapache.app.from.registry               html  
    rapache.trig.app                        html  
    register.page                           html  
    remove.event                            html  
    remove.old.files                        html  
    requestEnv                              html  
    reset.APS.outdir                        html  
    rook.analysis.page.server.landing.page
                                            html  
    search.replace                          html  
    select.param                            html  
    service.link                            html  
    set.APS.libbase.prefix                  html  
    set.APS.outdir                          html  
    setup.APS.knitr                         html  
    simple.param                            html  
    sine.handler                            html  
    slider.param                            html  
    startRookAnalysisPageServer             html  
    static.analysis.page                    html  
    static.analysis.page.query.string       html  
    test.package                            html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpOARGUw/R.INSTALL10401f50671/AnalysisPageServer/man/test.package.Rd:26: file link 'runTestSuite' in package 'RUnit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpOARGUw/R.INSTALL10401f50671/AnalysisPageServer/man/test.package.Rd:26: file link 'require' in package 'base' does not exist and so has been treated as a topic
    trig.registry                           html  
    trigger.event                           html  
    tryKeepConditions                       html  
    tryKeepTraceback                        html  
    uniquify.ids.in.svg.files               html  
    urlDecode                               html  
    urlEncode                               html  
    validate.array.param.value              html  
    validate.bool.param.value               html  
    validate.combobox.param.value           html  
    validate.compound.param.value           html  
    validate.file.param.value               html  
    validate.labeled.param.value            html  
    validate.param.list                     html  
    validate.param.value                    html  
    validate.select.param.value             html  
    validate.text.param.value               html  
    vwc.conditions                          html  
    vwc.error                               html  
    vwc.error.condition                     html  
    vwc.error.traceback                     html  
    vwc.is.error                            html  
    vwc.messages                            html  
    vwc.messages.conditions                 html  
    vwc.messages.tracebacks                 html  
    vwc.n                                   html  
    vwc.n.messages                          html  
    vwc.n.warnings                          html  
    vwc.tracebacks                          html  
    vwc.value                               html  
    vwc.warnings                            html  
    vwc.warnings.conditions                 html  
    vwc.warnings.tracebacks                 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 'AnalysisPageServer' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c AnalysisPageSVG.cpp -o AnalysisPageSVG.o
AnalysisPageSVG.cpp: In function 'int matchPlotPoints(XMLElementList, std::deque<double>, std::deque<double>, double, int, int)':
AnalysisPageSVG.cpp:154:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "x and y have different lengths";
        ^
AnalysisPageSVG.cpp:157:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(els.size() < start + n)  {
                 ^
AnalysisPageSVG.cpp:194:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0; i < x.size(); i++)  {
                      ^
AnalysisPageSVG.cpp:210:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_x.size(); i++)  {
                        ^
AnalysisPageSVG.cpp:215:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_y.size(); i++)  {
                        ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c R_init_AnalysisPageServer.cpp -o R_init_AnalysisPageServer.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c SearchReplace2.cpp -o SearchReplace2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c catch.c -o catch.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c cor.cpp -o cor.o
cor.cpp: In function 'double basic_cor(const std::deque<double>&, const std::deque<double>&)':
cor.cpp:24:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "different sizes";
        ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c tinyxml2.cpp -o tinyxml2.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o AnalysisPageServer.dll tmp.def AnalysisPageSVG.o R_init_AnalysisPageServer.o SearchReplace2.o catch.o cor.o tinyxml2.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/AnalysisPageServer.buildbin-libdir/AnalysisPageServer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnalysisPageServer' as AnalysisPageServer_1.20.0.zip
* DONE (AnalysisPageServer)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'AnalysisPageServer' successfully unpacked and MD5 sums checked