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This page was generated on 2021-09-20 15:05:07 -0400 (Mon, 20 Sep 2021).

INSTALL results for Cardinal on tokay2

To the developers/maintainers of the Cardinal package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Cardinal.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 241/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 2.10.0  (landing page)
Kylie A. Bemis
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/Cardinal
git_branch: RELEASE_3_13
git_last_commit: 174f14c
git_last_commit_date: 2021-05-19 12:10:59 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Cardinal
Version: 2.10.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Cardinal_2.10.0.tar.gz && rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Cardinal.buildbin-libdir Cardinal_2.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Cardinal_2.10.0.zip && rm Cardinal_2.10.0.tar.gz Cardinal_2.10.0.zip
StartedAt: 2021-09-19 08:16:54 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 08:19:34 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 159.9 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Cardinal_2.10.0.tar.gz && rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Cardinal.buildbin-libdir Cardinal_2.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Cardinal_2.10.0.zip && rm Cardinal_2.10.0.tar.gz Cardinal_2.10.0.zip
###
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##############################################################################


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100 1092k  100 1092k    0     0  3107k      0 --:--:-- --:--:-- --:--:-- 3113k

install for i386

* installing *source* package 'Cardinal' ...
** 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:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c DIP.cpp -o DIP.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dynAlign.cpp -o dynAlign.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imzML.cpp -o imzML.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.cpp -o init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pugixml.cpp -o pugixml.o
pugixml.cpp:2264:16: warning: 'void pugi::impl::{anonymous}::as_utf8_end(char*, size_t, const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN void as_utf8_end(char* buffer, size_t size, const wchar_t* str, size_t length)
                ^~~~~~~~~~~
pugixml.cpp:2258:18: warning: 'size_t pugi::impl::{anonymous}::as_utf8_begin(const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN size_t as_utf8_begin(const wchar_t* str, size_t length)
                  ^~~~~~~~~~~~~
pugixml.cpp:221:18: warning: 'size_t pugi::impl::{anonymous}::strlength_wide(const wchar_t*)' defined but not used [-Wunused-function]
  PUGI__FN size_t strlength_wide(const wchar_t* s)
                  ^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c spatial.cpp -o spatial.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Cardinal.dll tmp.def DIP.o dynAlign.o imzML.o init.o pugixml.o spatial.o utils.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/Cardinal.buildbin-libdir/00LOCK-Cardinal/00new/Cardinal/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Cardinal'
    finding HTML links ... done
    AnnotatedImage-class                    html  
    finding level-2 HTML links ... done

    AnnotatedImagingExperiment-class        html  
    Cardinal-package                        html  
    ImageList-class                         html  
    ImagingExperiment-class                 html  
    ImagingResult-class                     html  
    MSContinuousImagingExperiment-class     html  
    MSImagingExperiment-class               html  
    MSImagingInfo-class                     html  
    MSProcessedImagingExperiment-class      html  
    MassDataFrame-class                     html  
    PCA-methods                             html  
    PLS-methods                             html  
    PositionDataFrame-class                 html  
    SparseImagingExperiment-class           html  
    XDataFrame-class                        html  
    aggregate-methods                       html  
    colocalized-methods                     html  
    colors-functions                        html  
    crossValidate-methods                   html  
    defunct                                 html  
    deprecated                              html  
    findNeighbors-methods                   html  
    image-methods                           html  
    internal                                html  
    legacy                                  html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/Cardinal.buildbin-libdir/00LOCK-Cardinal/00new/Cardinal/help/ImageData.html
    meansTest-methods                       html  
    mz-methods                              html  
    mzAlign-methods                         html  
    mzBin-methods                           html  
    mzFilter-methods                        html  
    normalize-methods                       html  
    peakAlign-methods                       html  
    peakBin-methods                         html  
    peakPick-methods                        html  
    pixelApply-methods                      html  
    plot-methods                            html  
    process-methods                         html  
    readMSIData                             html  
    reduceBaseline-methods                  html  
    reexports                               html  
    selectROI-methods                       html  
    simulateSpectrum                        html  
    slice-methods                           html  
    smoothSignal-methods                    html  
    spatialDGMM-methods                     html  
    spatialFastmap-methods                  html  
    spatialKMeans-methods                   html  
    spatialShrunkenCentroids-methods        html  
    subset-methods                          html  
    topFeatures-methods                     html  
    writeMSIData                            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 'Cardinal' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c DIP.cpp -o DIP.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dynAlign.cpp -o dynAlign.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imzML.cpp -o imzML.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.cpp -o init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pugixml.cpp -o pugixml.o
pugixml.cpp:2264:16: warning: 'void pugi::impl::{anonymous}::as_utf8_end(char*, size_t, const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN void as_utf8_end(char* buffer, size_t size, const wchar_t* str, size_t length)
                ^~~~~~~~~~~
pugixml.cpp:2258:18: warning: 'size_t pugi::impl::{anonymous}::as_utf8_begin(const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN size_t as_utf8_begin(const wchar_t* str, size_t length)
                  ^~~~~~~~~~~~~
pugixml.cpp:221:18: warning: 'size_t pugi::impl::{anonymous}::strlength_wide(const wchar_t*)' defined but not used [-Wunused-function]
  PUGI__FN size_t strlength_wide(const wchar_t* s)
                  ^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c spatial.cpp -o spatial.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Cardinal.dll tmp.def DIP.o dynAlign.o imzML.o init.o pugixml.o spatial.o utils.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/Cardinal.buildbin-libdir/Cardinal/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Cardinal' as Cardinal_2.10.0.zip
* DONE (Cardinal)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'Cardinal' successfully unpacked and MD5 sums checked