############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GenomicAlignments_1.28.0.tar.gz && rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GenomicAlignments_1.28.0.zip && rm GenomicAlignments_1.28.0.tar.gz GenomicAlignments_1.28.0.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 33 1371k 33 454k 0 0 1209k 0 0:00:01 --:--:-- 0:00:01 1209k 100 1371k 100 1371k 0 0 1753k 0 --:--:-- --:--:-- --:--:-- 1753k install for i386 * installing *source* package 'GenomicAlignments' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cigar_utils.c -o cigar_utils.o cigar_utils.c: In function 'cigar_ranges': cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this function [-Wmaybe-uninitialized] range_buf1 = range_buf2->elts[*f_elt - 1]; ~~~~~~~~~~^~~~~~ In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:42, from GenomicAlignments.h:1, from cigar_utils.c:1: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rinternals.h:1553:20: warning: 'f_levels' may be used uninitialized in this function [-Wmaybe-uninitialized] #define duplicate Rf_duplicate ^~~~~~~~~~~~ cigar_utils.c:587:29: note: 'f_levels' was declared here SEXP ans, ans_breakpoints, f_levels, cigar_elt; ^~~~~~~~ cigar_utils.c:542:4: warning: 'ans_breakpoints' may be used uninitialized in this function [-Wmaybe-uninitialized] new_PartitioningByEnd("PartitioningByEnd", ^~~~~~~~~~~~~~~~~~~~~ cigar_utils.c:587:12: note: 'ans_breakpoints' was declared here SEXP ans, ans_breakpoints, f_levels, cigar_elt; ^~~~~~~~~~~~~~~ cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] f_elt++; ~~~~~^~ cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized] *(breakpoint++) = IntPairAE_get_nelt(range_buf1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized] *(breakpoint++) = IntPairAE_get_nelt(range_buf1); ~~~~~~~~~~~^~~ cigar_utils.c:626:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] if (*flag_elt == NA_INTEGER) { ^~~~~~~~~ cigar_utils.c: In function 'cigar_width': cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] if (*flag_elt == NA_INTEGER) { ^~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.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/GenomicAlignments.buildbin-libdir/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GenomicAlignments' finding HTML links ... done GAlignmentPairs-class html finding level-2 HTML links ... done GAlignments-class html GAlignmentsList-class html GappedReads-class html OverlapEncodings-class html cigar-utils html coordinate-mapping-methods html coverage-methods html encodeOverlaps-methods html findCompatibleOverlaps-methods html findMateAlignment html findOverlaps-methods html findSpliceOverlaps-methods html intra-range-methods html junctions-methods html pileLettersAt html readGAlignments html sequenceLayer html setops-methods html stackStringsFromGAlignments html summarizeOverlaps-methods 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 'GenomicAlignments' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cigar_utils.c -o cigar_utils.o cigar_utils.c: In function 'cigar_ranges': cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] f_elt++; ~~~~~^~ cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized] *(breakpoint++) = IntPairAE_get_nelt(range_buf1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized] *(breakpoint++) = IntPairAE_get_nelt(range_buf1); ~~~~~~~~~~~^~~ cigar_utils.c:626:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] if (*flag_elt == NA_INTEGER) { ^~~~~~~~~ cigar_utils.c: In function 'cigar_width': cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] if (*flag_elt == NA_INTEGER) { ^~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o encodeOverlaps_methods.c: In function 'overlap_encoding': encodeOverlaps_methods.c:180:33: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized] CharAE_set_nelt(out, out_nelt0 + j2 * nrow); ~~~~~~~~~~^~~~~~~~~~~ encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej, ^~~~~~~~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.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/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'GenomicAlignments' as GenomicAlignments_1.28.0.zip * DONE (GenomicAlignments) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'GenomicAlignments' successfully unpacked and MD5 sums checked