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INSTALL report for Cardinal on tokay2

This page was generated on 2018-10-17 08:39:56 -0400 (Wed, 17 Oct 2018).

Package 189/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 1.12.1
Kylie A. Bemis
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Cardinal
Branch: RELEASE_3_7
Last Commit: 8885df8
Last Changed Date: 2018-07-22 17:06:58 -0400 (Sun, 22 Jul 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Cardinal
Version: 1.12.1
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Cardinal_1.12.1.tar.gz && rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Cardinal.buildbin-libdir Cardinal_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Cardinal_1.12.1.zip && rm Cardinal_1.12.1.tar.gz Cardinal_1.12.1.zip
StartedAt: 2018-10-16 18:52:07 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 18:53:58 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 111.3 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Cardinal_1.12.1.tar.gz && rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Cardinal.buildbin-libdir Cardinal_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Cardinal_1.12.1.zip && rm Cardinal_1.12.1.tar.gz Cardinal_1.12.1.zip
###
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100 1044k  100 1044k    0     0  15.9M      0 --:--:-- --:--:-- --:--:-- 17.8M

install for i386

* installing *source* package 'Cardinal' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c dynamicAlign.c -o dynamicAlign.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c fastmap.c -o fastmap.o
fastmap.c: In function 'choose_distant_objects':
fastmap.c:59:24: warning: 'o_b' may be used uninitialized in this function [-Wmaybe-uninitialized]
  pivot_objects->b[col] = o_b;
                        ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c imzML.cpp -o imzML.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c localMaxima.c -o localMaxima.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pugixml.cpp -o pugixml.o
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)
                  ^
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: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)
                ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c smooth.c -o smooth.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c spatial.c -o spatial.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Cardinal.dll tmp.def dynamicAlign.o fastmap.o imzML.o localMaxima.o pugixml.o smooth.o spatial.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Cardinal.buildbin-libdir/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
    Binmat-class                            html  
    finding level-2 HTML links ... done

    Cardinal-package                        html  
    Hashmat-class                           html  
    IAnnotatedDataFrame-class               html  
    ImageData-class                         html  
    MIAPE-Imaging-class                     html  
    MSImageData-class                       html  
    MSImageProcess-class                    html  
    MSImageSet-class                        html  
    OPLS-methods                            html  
    PCA-methods                             html  
    PLS-methods                             html  
    ResultSet-class                         html  
    SImageData-class                        html  
    SImageSet-class                         html  
    batchProcess-methods                    html  
    colors-functions                        html  
    coord-methods                           html  
    coregister-methods                      html  
    cvApply-methods                         html  
    generateImage                           html  
    generateSpectrum                        html  
    iSet-class                              html  
    image-methods                           html  
    imageData-methods                       html  
    mz-methods                              html  
    normalize-methods                       html  
    peakAlign-methods                       html  
    peakFilter-methods                      html  
    peakPick-methods                        html  
    pixelApply-methods                      html  
    pixelData-methods                       html  
    pixelNames-methods                      html  
    pixels-methods                          html  
    plot-methods                            html  
    processingData-methods                  html  
    readMSIData                             html  
    reduceBaseline-methods                  html  
    reduceDimension-methods                 html  
    select-methods                          html  
    smoothSignal-methods.R                  html  
    spatialKMeans-methods                   html  
    spatialShrunkenCentroids-methods        html  
    standardizeSamples-methods              html  
    topLabels-methods                       html  
    writeMSIData                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Cardinal' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dynamicAlign.c -o dynamicAlign.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c fastmap.c -o fastmap.o
fastmap.c: In function 'choose_distant_objects':
fastmap.c:59:24: warning: 'o_b' may be used uninitialized in this function [-Wmaybe-uninitialized]
  pivot_objects->b[col] = o_b;
                        ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c imzML.cpp -o imzML.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c localMaxima.c -o localMaxima.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pugixml.cpp -o pugixml.o
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)
                  ^
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: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)
                ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c smooth.c -o smooth.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c spatial.c -o spatial.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Cardinal.dll tmp.def dynamicAlign.o fastmap.o imzML.o localMaxima.o pugixml.o smooth.o spatial.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Cardinal.buildbin-libdir/Cardinal/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Cardinal' as Cardinal_1.12.1.zip
* DONE (Cardinal)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Cardinal' successfully unpacked and MD5 sums checked
In R CMD INSTALL