############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/geneXtendeR_1.20.0.tar.gz && rm -rf geneXtendeR.buildbin-libdir && mkdir geneXtendeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geneXtendeR.buildbin-libdir geneXtendeR_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL geneXtendeR_1.20.0.zip && rm geneXtendeR_1.20.0.tar.gz geneXtendeR_1.20.0.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 11.7M 1 122k 0 0 356k 0 0:00:33 --:--:-- 0:00:33 356k 9 11.7M 9 1179k 0 0 879k 0 0:00:13 0:00:01 0:00:12 879k 26 11.7M 26 3162k 0 0 1345k 0 0:00:08 0:00:02 0:00:06 1345k 49 11.7M 49 5981k 0 0 1784k 0 0:00:06 0:00:03 0:00:03 1784k 81 11.7M 81 9783k 0 0 2250k 0 0:00:05 0:00:04 0:00:01 2250k 100 11.7M 100 11.7M 0 0 2491k 0 0:00:04 0:00:04 --:--:-- 2654k install for i386 * installing *source* package 'geneXtendeR' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c annotate.c -o annotate.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c extract_number.c -o extract_number.o extract_number.c: In function 'extractnumber': extract_number.c:72:10: warning: variable 'n_1' set but not used [-Wunused-but-set-variable] long n_1; ^~~ extract_number.c:66:10: warning: variable 'j_1' set but not used [-Wunused-but-set-variable] long j_1; ^~~ extract_number.c:54:12: warning: variable 'pvcfcol5_5' set but not used [-Wunused-but-set-variable] char * pvcfcol5_5; ^~~~~~~~~~ extract_number.c:53:12: warning: variable 'pvcfcol4_4' set but not used [-Wunused-but-set-variable] char * pvcfcol4_4; ^~~~~~~~~~ extract_number.c:52:12: warning: variable 'pvcfcol3_3' set but not used [-Wunused-but-set-variable] char * pvcfcol3_3; ^~~~~~~~~~ extract_number.c:51:12: warning: variable 'pvcfcol2_2' set but not used [-Wunused-but-set-variable] char * pvcfcol2_2; ^~~~~~~~~~ extract_number.c:50:12: warning: variable 'pvcfcol1_1' set but not used [-Wunused-but-set-variable] char * pvcfcol1_1; ^~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c extract_peaks.c -o extract_peaks.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o geneXtendeR.dll tmp.def annotate.o extract_number.o extract_peaks.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/geneXtendeR.buildbin-libdir/00LOCK-geneXtendeR/00new/geneXtendeR/libs/i386 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'geneXtendeR' finding HTML links ... done allPeakLengths html annotate html annotate_n html barChart html cumlinePlot html diffGO html distinct html dot-geneXtender html gene_annotate html gene_lookup html hotspotPlot html linePlot html makeNetwork html makeWordCloud html meanPeakLength html meanPeakLengthPlot html peakLengthBoxplot html peaksInput html peaksMerge html plotWordFreq html rat html samplepeaksinput 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 'geneXtendeR' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c annotate.c -o annotate.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c extract_number.c -o extract_number.o extract_number.c: In function 'extractnumber': extract_number.c:72:10: warning: variable 'n_1' set but not used [-Wunused-but-set-variable] long n_1; ^~~ extract_number.c:66:10: warning: variable 'j_1' set but not used [-Wunused-but-set-variable] long j_1; ^~~ extract_number.c:54:12: warning: variable 'pvcfcol5_5' set but not used [-Wunused-but-set-variable] char * pvcfcol5_5; ^~~~~~~~~~ extract_number.c:53:12: warning: variable 'pvcfcol4_4' set but not used [-Wunused-but-set-variable] char * pvcfcol4_4; ^~~~~~~~~~ extract_number.c:52:12: warning: variable 'pvcfcol3_3' set but not used [-Wunused-but-set-variable] char * pvcfcol3_3; ^~~~~~~~~~ extract_number.c:51:12: warning: variable 'pvcfcol2_2' set but not used [-Wunused-but-set-variable] char * pvcfcol2_2; ^~~~~~~~~~ extract_number.c:50:12: warning: variable 'pvcfcol1_1' set but not used [-Wunused-but-set-variable] char * pvcfcol1_1; ^~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c extract_peaks.c -o extract_peaks.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o geneXtendeR.dll tmp.def annotate.o extract_number.o extract_peaks.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/geneXtendeR.buildbin-libdir/geneXtendeR/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'geneXtendeR' as geneXtendeR_1.20.0.zip * DONE (geneXtendeR) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'geneXtendeR' successfully unpacked and MD5 sums checked