Cardinal 2.1.6
Kylie A. Bemis
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Cardinal |
| Branch: master |
| Last Commit: 9c8dd9a |
| Last Changed Date: 2019-02-21 16:21:08 -0400 (Thu, 21 Feb 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | ERROR | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | ERROR | skipped | skipped | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Cardinal_2.1.6.tar.gz && rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Cardinal.buildbin-libdir Cardinal_2.1.6.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Cardinal_2.1.6.zip && rm Cardinal_2.1.6.tar.gz Cardinal_2.1.6.zip
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install for i386
* installing *source* package 'Cardinal' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c DIP.cpp -o DIP.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dynAlign.cpp -o dynAlign.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c imzML.cpp -o imzML.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c localMaxima.cpp -o localMaxima.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-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/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c spatial.cpp -o spatial.o
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = int; T2 = int; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
int k; // center pixel
^
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = int; T2 = double; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = double; T2 = int; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = double; T2 = double; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-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 DIP.o dynAlign.o imzML.o localMaxima.o pugixml.o spatial.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Cardinal.buildbin-libdir/00LOCK-Cardinal/00new/Cardinal/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'filter' in package 'Cardinal'
Creating a new generic function for 'group_by' in package 'Cardinal'
** 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
ImageList-class html
ImagingExperiment-class html
MIAPE-Imaging-class html
MSContinuousImagingExperiment-class html
MSImageData-class html
MSImageProcess-class html
MSImageSet-class html
MSImagingExperiment-class html
MSImagingInfo-class html
MSProcessedImagingExperiment-class html
MassDataFrame-class html
OPLS-methods html
PCA-methods html
PLS-methods html
PositionDataFrame-class html
ResultImagingExperiment-class html
ResultSet-class html
SImageData-class html
SImageSet-class html
SparseImagingExperiment-class html
XDataFrame-class html
batchProcess-methods html
colors-functions html
coregister-methods html
cvApply-methods html
deprecated html
filter-methods html
findNeighbors-methods html
generateSpectrum html
iSet-class html
image-methods html
mz-methods html
normalize-methods html
peakAlign-methods html
peakBin-methods html
peakFilter-methods html
peakPick-methods html
pixelApply-methods html
plot-methods html
process-methods html
readMSIData html
reduceBaseline-methods html
reduceDimension-methods html
reexports html
selectROI-methods html
simulateSpectrum html
smoothSignal-methods.R html
spatialFastmap-methods html
spatialKMeans-methods html
spatialShrunkenCentroids-methods html
standardizeRuns-methods html
topLabels-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:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c DIP.cpp -o DIP.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dynAlign.cpp -o dynAlign.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c imzML.cpp -o imzML.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c localMaxima.cpp -o localMaxima.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-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/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c spatial.cpp -o spatial.o
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = int; T2 = int; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
int k; // center pixel
^
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = int; T2 = double; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = double; T2 = int; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = double; T2 = double; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-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 DIP.o dynAlign.o imzML.o localMaxima.o pugixml.o spatial.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Cardinal.buildbin-libdir/Cardinal/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Cardinal' as Cardinal_2.1.6.zip
* DONE (Cardinal)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Cardinal' successfully unpacked and MD5 sums checked