############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CellNOptR_1.38.0.tar.gz && rm -rf CellNOptR.buildbin-libdir && mkdir CellNOptR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellNOptR.buildbin-libdir CellNOptR_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CellNOptR_1.38.0.zip && rm CellNOptR_1.38.0.tar.gz CellNOptR_1.38.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 1 1417k 1 14637 0 0 123k 0 0:00:11 --:--:-- 0:00:11 123k 100 1417k 100 1417k 0 0 2431k 0 --:--:-- --:--:-- --:--:-- 2431k install for i386 * installing *source* package 'CellNOptR' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getFit.c -o getFit.o getFit.c: In function 'getFit': getFit.c:47:6: warning: unused variable 'nReacs' [-Wunused-variable] int nReacs = INTEGER(nReacs_in)[0]; ^~~~~~ getFit.c:42:6: warning: unused variable 'selCounter' [-Wunused-variable] int selCounter = 0; ^~~~~~~~~~ getFit.c:41:6: warning: unused variable 'selection' [-Wunused-variable] int selection[40]; ^~~~~~~~~ getFit.c:40:6: warning: unused variable 'or_max' [-Wunused-variable] int or_max = 0; ^~~~~~ getFit.c:39:6: warning: unused variable 'curr_max' [-Wunused-variable] int curr_max = 0; ^~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulatorT1.c -o simulatorT1.o simulatorT1.c: In function 'simulatorT1': simulatorT1.c:502:20: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] if (MA[i][j]<0.95 & MA[i][j]>0.05) // actually we could check if they are exatly 0 or 1 ~~~~~~~~^~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulatorTN.c -o simulatorTN.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CellNOptR.dll tmp.def getFit.o simulatorT1.o simulatorTN.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/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'CellNOptR' finding HTML links ... done CNORbool html CNORwrap html CNOdata html CNOlist-class html CNOlist-methods html CNOlistDREAM html CNOlistToy html CNOlistToy2 html CNOlistToyMMB html CellNOptR-package html DreamModel html ToyModel html ToyModel2 html buildBitString html build_sif_table_from_rule html cSimulator html checkSignals html compressModel html computeScoreT1 html computeScoreTN html createAndRunILP html createILPBitstringAll html create_binaries html crossInhibitedData html crossvalidateBoolean html cutAndPlot html cutAndPlotResultsT1 html cutAndPlotResultsTN html cutCNOlist html cutModel html cutNONC html cutSimList html defaultParameters html exhaustive html expandGates html findNONC html gaBinaryT1 html gaBinaryT2 html gaBinaryTN html getFit html graph2sif html ilpBinaryT1 html ilpBinaryT2 html ilpBinaryTN html indexFinder html internals html invokeCPLEX html makeCNOlist html mapBack html model2igraph html model2sif html normaliseCNOlist html plot-methods html plotCNOlist html plotCNOlist2 html plotCNOlistLarge html plotCNOlistLargePDF html plotCNOlistPDF html plotFit html plotModel html plotOptimResults html plotOptimResultsPDF html plotOptimResultsPan html prep4sim html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/help/prep4Sim.html preprocessing html randomizeCNOlist html readBND html readBNET html readMIDAS html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/help/readMidas.html readSBMLQual html readSIF html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/help/readSIF.html residualError html sif2graph html simulateT1 html simulateTN html simulatorT0 html simulatorT1 html simulatorT2 html simulatorTN html toSBML html writeDot html writeFile html writeMIDAS html writeNetwork html writeObjectiveFunction html writeReport html writeSIF html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/help/writeSif.html writeScaffold html write_bounds html write_constraints 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 'CellNOptR' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getFit.c -o getFit.o getFit.c: In function 'getFit': getFit.c:47:6: warning: unused variable 'nReacs' [-Wunused-variable] int nReacs = INTEGER(nReacs_in)[0]; ^~~~~~ getFit.c:42:6: warning: unused variable 'selCounter' [-Wunused-variable] int selCounter = 0; ^~~~~~~~~~ getFit.c:41:6: warning: unused variable 'selection' [-Wunused-variable] int selection[40]; ^~~~~~~~~ getFit.c:40:6: warning: unused variable 'or_max' [-Wunused-variable] int or_max = 0; ^~~~~~ getFit.c:39:6: warning: unused variable 'curr_max' [-Wunused-variable] int curr_max = 0; ^~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulatorT1.c -o simulatorT1.o simulatorT1.c: In function 'simulatorT1': simulatorT1.c:502:20: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] if (MA[i][j]<0.95 & MA[i][j]>0.05) // actually we could check if they are exatly 0 or 1 ~~~~~~~~^~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulatorTN.c -o simulatorTN.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CellNOptR.dll tmp.def getFit.o simulatorT1.o simulatorTN.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/CellNOptR.buildbin-libdir/CellNOptR/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'CellNOptR' as CellNOptR_1.38.0.zip * DONE (CellNOptR) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'CellNOptR' successfully unpacked and MD5 sums checked