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BioC 3.4: INSTALL report for EBImage on moscato1

This page was generated on 2016-09-21 03:41:45 -0700 (Wed, 21 Sep 2016).

Package 350/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBImage 4.15.4
Andrzej Oleś
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EBImage
Last Changed Rev: 119863 / Revision: 121152
Last Changed Date: 2016-08-03 03:06:29 -0700 (Wed, 03 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: EBImage
Version: 4.15.4
Command: rm -rf EBImage.buildbin-libdir && mkdir EBImage.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/EBImage_4.15.4.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=EBImage.buildbin-libdir --merge-multiarch EBImage_4.15.4.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL EBImage_4.15.4.zip && rm EBImage_4.15.4.tar.gz EBImage_4.15.4.zip
StartedAt: 2016-09-19 20:29:59 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 20:31:05 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 65.8 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf EBImage.buildbin-libdir && mkdir EBImage.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/EBImage_4.15.4.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=EBImage.buildbin-libdir --merge-multiarch EBImage_4.15.4.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL EBImage_4.15.4.zip  && rm EBImage_4.15.4.tar.gz EBImage_4.15.4.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1857k  100 1857k    0     0  53.1M      0 --:--:-- --:--:-- --:--:-- 60.4M

install for i386

* installing *source* package 'EBImage' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c EBImage.c -o EBImage.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c distmap.c -o distmap.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c drawCircle.c -o drawCircle.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c floodFill.cpp -o floodFill.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c haralick.c -o haralick.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c medianFilter.c -o medianFilter.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c morphology.c -o morphology.o
morphology.c: In function 'compute_lookup_table_for_line_dilate':
morphology.c:59:7: warning: statement with no effect [-Wunused-value]
       for (i; i < 0; ++i) {
       ^
morphology.c:62:7: warning: statement with no effect [-Wunused-value]
       for (i; i < maxX; ++i) {
       ^
morphology.c:66:7: warning: statement with no effect [-Wunused-value]
       for (i; i < size.x + set->maxXoffset; ++i) {
       ^
morphology.c: In function 'compute_lookup_table_for_line_erode':
morphology.c:90:5: warning: statement with no effect [-Wunused-value]
     for (i; i < 0; ++i) {
     ^
morphology.c:93:5: warning: statement with no effect [-Wunused-value]
     for (i; i < maxX; ++i) {
     ^
morphology.c:97:5: warning: statement with no effect [-Wunused-value]
     for (i; i < size.x + set->maxXoffset; ++i) {
     ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c nativeRaster.c -o nativeRaster.o
nativeRaster.c: In function 'nativeRaster':
nativeRaster.c:38:7: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
   out = INTEGER(res);
       ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c normalize.c -o normalize.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c objects.c -o objects.o
In file included from objects.h:5:0,
                 from objects.c:1:
objects.c: In function 'stackObjects':
D:/biocbld/BBS-3˜1.4-B/R/include/Rdefines.h:148:28: warning: 'dim' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define SET_DIM(x, n)      Rf_setAttrib(x, R_DimSymbol, n)
                            ^
objects.c:171:22: note: 'dim' was declared here
   SEXP res, st=NULL, dim, xys;
                      ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ocontour.c -o ocontour.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c propagate.cpp -o propagate.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c spatial.c -o spatial.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c thresh.c -o thresh.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c tile.c -o tile.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c tools.c -o tools.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c watershed.cpp -o watershed.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o EBImage.dll tmp.def EBImage.o distmap.o drawCircle.o floodFill.o haralick.o medianFilter.o morphology.o nativeRaster.o normalize.o objects.o ocontour.o propagate.o spatial.o thresh.o tile.o tools.o watershed.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/EBImage.buildbin-libdir/EBImage/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'EBImage' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c EBImage.c -o EBImage.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c distmap.c -o distmap.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c drawCircle.c -o drawCircle.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c floodFill.cpp -o floodFill.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c haralick.c -o haralick.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c medianFilter.c -o medianFilter.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c morphology.c -o morphology.o
morphology.c: In function 'compute_lookup_table_for_line_dilate':
morphology.c:59:7: warning: statement with no effect [-Wunused-value]
       for (i; i < 0; ++i) {
       ^
morphology.c:62:7: warning: statement with no effect [-Wunused-value]
       for (i; i < maxX; ++i) {
       ^
morphology.c:66:7: warning: statement with no effect [-Wunused-value]
       for (i; i < size.x + set->maxXoffset; ++i) {
       ^
morphology.c: In function 'compute_lookup_table_for_line_erode':
morphology.c:90:5: warning: statement with no effect [-Wunused-value]
     for (i; i < 0; ++i) {
     ^
morphology.c:93:5: warning: statement with no effect [-Wunused-value]
     for (i; i < maxX; ++i) {
     ^
morphology.c:97:5: warning: statement with no effect [-Wunused-value]
     for (i; i < size.x + set->maxXoffset; ++i) {
     ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c nativeRaster.c -o nativeRaster.o
nativeRaster.c: In function 'nativeRaster':
nativeRaster.c:38:7: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
   out = INTEGER(res);
       ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c normalize.c -o normalize.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c objects.c -o objects.o
In file included from objects.h:5:0,
                 from objects.c:1:
objects.c: In function 'stackObjects':
D:/biocbld/BBS-3˜1.4-B/R/include/Rdefines.h:148:28: warning: 'dim' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define SET_DIM(x, n)      Rf_setAttrib(x, R_DimSymbol, n)
                            ^
objects.c:171:22: note: 'dim' was declared here
   SEXP res, st=NULL, dim, xys;
                      ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ocontour.c -o ocontour.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c propagate.cpp -o propagate.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c spatial.c -o spatial.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c thresh.c -o thresh.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c tile.c -o tile.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c tools.c -o tools.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c watershed.cpp -o watershed.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o EBImage.dll tmp.def EBImage.o distmap.o drawCircle.o floodFill.o haralick.o medianFilter.o morphology.o nativeRaster.o normalize.o objects.o ocontour.o propagate.o spatial.o thresh.o tile.o tools.o watershed.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/EBImage.buildbin-libdir/EBImage/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EBImage' as EBImage_4.15.4.zip
* DONE (EBImage)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'EBImage' successfully unpacked and MD5 sums checked