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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/CNEr_1.18.1.tar.gz && rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNEr.buildbin-libdir CNEr_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL CNEr_1.18.1.zip && rm CNEr_1.18.1.tar.gz CNEr_1.18.1.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 9012k 100 9012k 0 0 59.0M 0 --:--:-- --:--:-- --:--:-- 60.6M
install for i386
* installing *source* package 'CNEr' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c R_init_CNEr.c -o R_init_CNEr.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c utils.c -o utils.o
utils.c: In function 'bin_ranges_from_coord_range_standard':
utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable]
int _binNextShift = binNextShift();
^
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
int _binFirstShift = binFirstShift();
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c io.c -o io.o
io.c: In function 'myReadAxt':
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
struct axt *axt=NULL, *curAxt;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ceScan.c -o ceScan.o
ceScan.c: In function 'ceScan':
ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable]
char rest, path[PATH_LEN];
^
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
int i, n;
^
ceScan.c: In function 'freeSlThreshold':
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
struct slCNE *CNE, *nextCNE, *el_CNE;
^
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
struct slThreshold *thresholds, *nextThreshold, *el_threshold;
^
ceScan.c: In function 'myCeScan':
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
int nrCNE[nrThresholds], i;
^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable]
int nrCNE[nrThresholds], i;
^
ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable]
struct slCNE *CNE;
^
ceScan.c: In function 'myCeScanFile':
ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
int nrThresholds = GET_LENGTH(winSize);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/axt.c -o ucsc/axt.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/base64.c -o ucsc/base64.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/binRange.c -o ucsc/binRange.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/bits.c -o ucsc/bits.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/chain.c -o ucsc/chain.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
^
ucsc/cirTree.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315:5: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
^
ucsc/cirTree.c:315:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/cirTree.c:330:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:330:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:330:9: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2442:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2442:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2442:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2453:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2453:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2453:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2455:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %lld bytes", (long long)size);
^
ucsc/common.c:2455:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2596:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("Error reading %lld bytes", (long long)size);
^
ucsc/common.c:2596:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2598:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^
ucsc/common.c:2598:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2598:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2620:3: warning: unknown conversion type character 'l' in format [-Wformat=]
(whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
^
ucsc/common.c:2620:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat=]
ucsc/common.c:2620:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
ucsc/common.c:2620:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2745:9: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^
ucsc/common.c:2745:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2745:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3211:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^
ucsc/common.c:3211:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3211:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3220:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^
ucsc/common.c:3220:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3220:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3236:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^
ucsc/common.c:3236:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3236:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3245:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^
ucsc/common.c:3245:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3245:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'byteSwap64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^
ucsc/common.c: In function 'readBits64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^
ucsc/common.c: In function 'fdReadBits64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^
ucsc/common.c: In function 'memReadBits64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^
ucsc/common.c: In function 'byteSwapDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^
ucsc/common.c: In function 'readDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^
ucsc/common.c: In function 'memReadDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/dlist.c -o ucsc/dlist.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/dnaseq.c -o ucsc/dnaseq.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:942:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
int pastPoly = 0;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/dystring.c -o ucsc/dystring.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/errabort.c -o ucsc/errabort.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/hash.c -o ucsc/hash.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/https.c -o ucsc/https.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/intExp.c -o ucsc/intExp.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/kxTok.c -o ucsc/kxTok.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
static char **getDecompressor(char *fileName)
^
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function]
static char * headerBytes(char *fileName, int numbytes)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:90:10: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, (unsigned long long)maxAlloc);
^
ucsc/memalloc.c:90:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:90:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:93:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:93:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:113:10: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, (unsigned long long)maxAlloc);
^
ucsc/memalloc.c:113:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:113:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:116:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:116:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:138:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:138:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:160:2: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:160:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:160:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:186:10: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, (unsigned long long)NEEDMEM_LIMIT);
^
ucsc/memalloc.c:186:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:186:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:189:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:189:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:317:14: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(vpt));
^
ucsc/memalloc.c:317:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:321:14: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(vpt));
^
ucsc/memalloc.c:321:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:359:18: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(cmb+1));
^
ucsc/memalloc.c:359:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:363:18: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(cmb+1));
^
ucsc/memalloc.c:363:18: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:544:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:552:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:558:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:558:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:558:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:561:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:561:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'stringToSlNames':
ucsc/obscure.c:472:8: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((s = skipLeadingSpaces(s)) == NULL)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/options.c -o ucsc/options.o
ucsc/options.c: In function 'validateOption':
ucsc/options.c:49:11: warning: variable 'discardMe' set but not used [-Wunused-but-set-variable]
long long discardMe = 0;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/pipeline.c -o ucsc/pipeline.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/sqlList.c -o ucsc/sqlList.o
ucsc/sqlList.c: In function 'sqlLongLongArrayToString':
ucsc/sqlList.c:1049:5: warning: unknown conversion type character 'l' in format [-Wformat=]
dyStringPrintf(string, "%lld,", array[i]);
^
ucsc/sqlList.c:1049:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/sqlNum.c -o ucsc/sqlNum.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/verbose.c -o ucsc/verbose.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/os.c -o ucsc/os.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o CNEr.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/CNEr.buildbin-libdir/CNEr/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CNEr'
finding HTML links ... done
AssemblyStats html
Axt-class html
Axt-util html
CNE-class html
CNEDanRer10Hg38 html
CNEDensity html
GRangePairs-class html
finding level-2 HTML links ... done
addAncestorGO html
axisTrack html
axtChain html
axtInfo html
binner html
blatCNE html
ceScan-methods html
chainMergeSort html
chainNetSyntenic html
chainPreNet html
cneFinalListDanRer10Hg38 html
cneMerge html
fetchChromSizes html
fixCoordinates html
grangesPairsForDotplot html
last html
lastz html
lavToPsl html
makeAncoraFiles html
makeAxtTracks html
makeCNEDensity html
makeGRBs html
matchDistribution html
netToAxt html
orgKEGGIds2EntrezIDs html
plotCNEDistribution html
plotCNEWidth html
psubAxt html
queryCNEData html
read.rmMask.GRanges html
read.rmskFasta html
readAncora html
readAncoraIntoSQLite html
readAxt html
readBed html
readCNERangesFromSQLite html
reverseCigar html
saveCNEToSQLite html
scoringMatrix html
subAxt-methods html
syntenicDotplot html
writeAxt html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'CNEr' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c R_init_CNEr.c -o R_init_CNEr.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c utils.c -o utils.o
utils.c: In function 'bin_ranges_from_coord_range_standard':
utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable]
int _binNextShift = binNextShift();
^
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
int _binFirstShift = binFirstShift();
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c io.c -o io.o
io.c: In function 'myReadAxt':
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
struct axt *axt=NULL, *curAxt;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ceScan.c -o ceScan.o
ceScan.c: In function 'ceScan':
ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable]
char rest, path[PATH_LEN];
^
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
int i, n;
^
ceScan.c: In function 'freeSlThreshold':
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
struct slCNE *CNE, *nextCNE, *el_CNE;
^
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
struct slThreshold *thresholds, *nextThreshold, *el_threshold;
^
ceScan.c: In function 'myCeScan':
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
int nrCNE[nrThresholds], i;
^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable]
int nrCNE[nrThresholds], i;
^
ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable]
struct slCNE *CNE;
^
ceScan.c: In function 'myCeScanFile':
ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
int nrThresholds = GET_LENGTH(winSize);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/axt.c -o ucsc/axt.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/base64.c -o ucsc/base64.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/binRange.c -o ucsc/binRange.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/bits.c -o ucsc/bits.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/chain.c -o ucsc/chain.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
^
ucsc/cirTree.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315:5: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
^
ucsc/cirTree.c:315:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/cirTree.c:330:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:330:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:330:9: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2442:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2442:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2442:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2453:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2453:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2453:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2455:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %lld bytes", (long long)size);
^
ucsc/common.c:2455:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2596:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("Error reading %lld bytes", (long long)size);
^
ucsc/common.c:2596:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2598:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^
ucsc/common.c:2598:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2598:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2620:3: warning: unknown conversion type character 'l' in format [-Wformat=]
(whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
^
ucsc/common.c:2620:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat=]
ucsc/common.c:2620:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
ucsc/common.c:2620:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2745:9: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^
ucsc/common.c:2745:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2745:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3211:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^
ucsc/common.c:3211:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3211:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3220:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^
ucsc/common.c:3220:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3220:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3236:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^
ucsc/common.c:3236:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3236:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3245:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^
ucsc/common.c:3245:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3245:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'byteSwap64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^
ucsc/common.c: In function 'byteSwapDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/dlist.c -o ucsc/dlist.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/dnaseq.c -o ucsc/dnaseq.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:942:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
int pastPoly = 0;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/dystring.c -o ucsc/dystring.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/errabort.c -o ucsc/errabort.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/hash.c -o ucsc/hash.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/https.c -o ucsc/https.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/intExp.c -o ucsc/intExp.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/kxTok.c -o ucsc/kxTok.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
static char **getDecompressor(char *fileName)
^
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function]
static char * headerBytes(char *fileName, int numbytes)
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:90:10: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, (unsigned long long)maxAlloc);
^
ucsc/memalloc.c:90:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:90:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:93:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:93:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:113:10: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, (unsigned long long)maxAlloc);
^
ucsc/memalloc.c:113:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:113:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:116:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:116:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:138:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:138:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:160:2: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:160:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:160:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:186:10: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, (unsigned long long)NEEDMEM_LIMIT);
^
ucsc/memalloc.c:186:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:186:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:189:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:189:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:317:14: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(vpt));
^
ucsc/memalloc.c:317:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:321:14: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(vpt));
^
ucsc/memalloc.c:321:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:359:18: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(cmb+1));
^
ucsc/memalloc.c:359:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:363:18: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(cmb+1));
^
ucsc/memalloc.c:363:18: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:544:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:552:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:558:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:558:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:558:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:561:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:561:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:703:6: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' [-Wformat=]
fprintf(stderr, "# pid=%d: %s\n", pid, line);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/options.c -o ucsc/options.o
ucsc/options.c: In function 'validateOption':
ucsc/options.c:49:11: warning: variable 'discardMe' set but not used [-Wunused-but-set-variable]
long long discardMe = 0;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/pipeline.c -o ucsc/pipeline.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/sqlList.c -o ucsc/sqlList.o
ucsc/sqlList.c: In function 'sqlLongLongArrayToString':
ucsc/sqlList.c:1049:5: warning: unknown conversion type character 'l' in format [-Wformat=]
dyStringPrintf(string, "%lld,", array[i]);
^
ucsc/sqlList.c:1049:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/sqlNum.c -o ucsc/sqlNum.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/verbose.c -o ucsc/verbose.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/os.c -o ucsc/os.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o CNEr.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/CNEr.buildbin-libdir/CNEr/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNEr' as CNEr_1.18.1.zip
* DONE (CNEr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'CNEr' successfully unpacked and MD5 sums checked
In R CMD INSTALL
