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###
### Running command:
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### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL CNEr
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'CNEr' ...
** using staged installation
** libs
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_CNEr.c -o R_init_CNEr.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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]
50 | int _binNextShift = binNextShift();
| ^~~~~~~~~~~~~
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
49 | int _binFirstShift = binFirstShift();
| ^~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o
io.c: In function 'myReadAxt':
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
94 | struct axt *axt=NULL, *curAxt;
| ^~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ceScan.c -o ceScan.o
ceScan.c: In function 'ceScan':
ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable]
615 | char rest, path[PATH_LEN];
| ^~~~
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
613 | int i, n;
| ^
ceScan.c: In function 'freeSlThreshold':
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
674 | struct slCNE *CNE, *nextCNE, *el_CNE;
| ^~~
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
673 | struct slThreshold *thresholds, *nextThreshold, *el_threshold;
| ^~~~~~~~~~
ceScan.c: In function 'myCeScan':
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
868 | int nrCNE[nrThresholds], i;
| ^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable]
868 | int nrCNE[nrThresholds], i;
| ^~~~~
ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable]
865 | struct slCNE *CNE;
| ^~~
ceScan.c: In function 'myCeScanFile':
ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
898 | int nrThresholds = GET_LENGTH(winSize);
| ^~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/axt.c -o ucsc/axt.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/base64.c -o ucsc/base64.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bits.c -o ucsc/bits.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/chain.c -o ucsc/chain.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:237:50: warning: unknown conversion type character 'l' in format [-Wformat=]
237 | verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
| ^
ucsc/cirTree.c:237:12: warning: too many arguments for format [-Wformat-extra-args]
237 | verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:318:45: warning: unknown conversion type character 'l' in format [-Wformat=]
318 | verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
| ^
ucsc/cirTree.c:318:16: warning: too many arguments for format [-Wformat-extra-args]
318 | verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c:333:54: warning: unknown conversion type character 'l' in format [-Wformat=]
333 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
| ^
ucsc/cirTree.c:333:62: warning: unknown conversion type character 'l' in format [-Wformat=]
333 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
| ^
ucsc/cirTree.c:333:72: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
333 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
| ~^ ~~~~~~~~~~~~~~~~
| | |
| int long long unsigned int
| %I64d
ucsc/cirTree.c:333:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
333 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
| ~^ ~~~~~~~~~~~~~~~~~
| | |
| char * long long unsigned int
| %I64d
ucsc/cirTree.c:333:18: warning: too many arguments for format [-Wformat-extra-args]
333 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2442:31: warning: unknown conversion type character 'l' in format [-Wformat=]
2442 | errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
| ^
ucsc/common.c:2442:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
2442 | errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
| ~^ ~~~~~~~~~~~~~~~
| | |
| | long long int
| char *
| %I64d
ucsc/common.c:2442:14: warning: too many arguments for format [-Wformat-extra-args]
2442 | errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2453:28: warning: unknown conversion type character 'l' in format [-Wformat=]
2453 | errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
| ^
ucsc/common.c:2453:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
2453 | errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
| ~^ ~~~~~~~~~~~~~~~
| | |
| | long long int
| char *
| %I64d
ucsc/common.c:2453:11: warning: too many arguments for format [-Wformat-extra-args]
2453 | errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2455:34: warning: unknown conversion type character 'l' in format [-Wformat=]
2455 | errAbort("End of file reading %lld bytes", (long long)size);
| ^
ucsc/common.c:2455:11: warning: too many arguments for format [-Wformat-extra-args]
2455 | errAbort("End of file reading %lld bytes", (long long)size);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2596:30: warning: unknown conversion type character 'l' in format [-Wformat=]
2596 | errnoAbort("Error reading %lld bytes", (long long)size);
| ^
ucsc/common.c:2596:13: warning: too many arguments for format [-Wformat-extra-args]
2596 | errnoAbort("Error reading %lld bytes", (long long)size);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2598:34: warning: unknown conversion type character 'l' in format [-Wformat=]
2598 | errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
| ^
ucsc/common.c:2598:50: warning: unknown conversion type character 'l' in format [-Wformat=]
2598 | errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
| ^
ucsc/common.c:2598:11: warning: too many arguments for format [-Wformat-extra-args]
2598 | errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2618:29: warning: unknown conversion type character 'l' in format [-Wformat=]
2618 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
| ^
ucsc/common.c:2618:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=]
2618 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
| ~^ ~~~~~~~~~~~~~~~~~
| | |
| char * long long int
| %I64d
ucsc/common.c:2618:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
2618 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
| ~^
| |
| int
| %s
2619 | ((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
2620 | (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2618:16: warning: too many arguments for format [-Wformat-extra-args]
2618 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2745:60: warning: unknown conversion type character 'l' in format [-Wformat=]
2745 | errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
| ^
ucsc/common.c:2745:65: warning: unknown conversion type character 'l' in format [-Wformat=]
2745 | errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
| ^
ucsc/common.c:2745:18: warning: too many arguments for format [-Wformat-extra-args]
2745 | errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3211:39: warning: unknown conversion type character 'l' in format [-Wformat=]
3211 | errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
| ^
ucsc/common.c:3211:58: warning: unknown conversion type character 'l' in format [-Wformat=]
3211 | errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
| ^
ucsc/common.c:3211:14: warning: too many arguments for format [-Wformat-extra-args]
3211 | errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3220:39: warning: unknown conversion type character 'l' in format [-Wformat=]
3220 | errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
| ^
ucsc/common.c:3220:61: warning: unknown conversion type character 'l' in format [-Wformat=]
3220 | errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
| ^
ucsc/common.c:3220:14: warning: too many arguments for format [-Wformat-extra-args]
3220 | errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecat':
ucsc/common.c:3236:39: warning: unknown conversion type character 'l' in format [-Wformat=]
3236 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
| ^
ucsc/common.c:3236:62: warning: unknown conversion type character 'l' in format [-Wformat=]
3236 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
| ^
ucsc/common.c:3236:14: warning: too many arguments for format [-Wformat-extra-args]
3236 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencat':
ucsc/common.c:3245:39: warning: unknown conversion type character 'l' in format [-Wformat=]
3245 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
| ^
ucsc/common.c:3245:62: warning: unknown conversion type character 'l' in format [-Wformat=]
3245 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
| ^
ucsc/common.c:3245:14: warning: too many arguments for format [-Wformat-extra-args]
3245 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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]
942 | int pastPoly = 0;
| ^~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/errabort.c -o ucsc/errabort.o
ucsc/errabort.c:30:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
30 | static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $";
| ^~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hash.c -o ucsc/hash.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/https.c -o ucsc/https.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/intExp.c -o ucsc/intExp.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function]
100 | static char * headerBytes(char *fileName, int numbytes)
| ^~~~~~~~~~~
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
32 | static char **getDecompressor(char *fileName)
| ^~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:35: warning: unknown conversion type character 'l' in format [-Wformat=]
38 | errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
| ^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
38 | errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:89:50: warning: unknown conversion type character 'l' in format [-Wformat=]
89 | errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
| ^
ucsc/memalloc.c:89:69: warning: unknown conversion type character 'l' in format [-Wformat=]
89 | errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
| ^
ucsc/memalloc.c:89:14: warning: too many arguments for format [-Wformat-extra-args]
89 | errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:92:60: warning: unknown conversion type character 'l' in format [-Wformat=]
92 | errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
| ^
ucsc/memalloc.c:92:78: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
92 | errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
| ~^
| |
| int
| %I64d
93 | (unsigned long long)size, errno);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
ucsc/memalloc.c:92:14: warning: too many arguments for format [-Wformat-extra-args]
92 | errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:112:56: warning: unknown conversion type character 'l' in format [-Wformat=]
112 | errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
| ^
ucsc/memalloc.c:112:75: warning: unknown conversion type character 'l' in format [-Wformat=]
112 | errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
| ^
ucsc/memalloc.c:112:14: warning: too many arguments for format [-Wformat-extra-args]
112 | errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:115:66: warning: unknown conversion type character 'l' in format [-Wformat=]
115 | errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
| ^
ucsc/memalloc.c:115:84: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
115 | errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
| ~^
| |
| int
| %I64d
116 | (unsigned long long)size, errno);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
ucsc/memalloc.c:115:14: warning: too many arguments for format [-Wformat-extra-args]
115 | errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:137:64: warning: unknown conversion type character 'l' in format [-Wformat=]
137 | errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
| ^
ucsc/memalloc.c:137:82: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
137 | errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
| ~^
| |
| int
| %I64d
138 | (unsigned long long)size, errno);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
ucsc/memalloc.c:137:14: warning: too many arguments for format [-Wformat-extra-args]
137 | errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:159:67: warning: unknown conversion type character 'l' in format [-Wformat=]
159 | errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
| ^
ucsc/memalloc.c:159:85: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
159 | errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
| ~^
| |
| int
| %I64d
160 | (unsigned long long)size, errno);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
ucsc/memalloc.c:159:14: warning: too many arguments for format [-Wformat-extra-args]
159 | errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:185:45: warning: unknown conversion type character 'l' in format [-Wformat=]
185 | errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
| ^
ucsc/memalloc.c:185:64: warning: unknown conversion type character 'l' in format [-Wformat=]
185 | errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
| ^
ucsc/memalloc.c:185:14: warning: too many arguments for format [-Wformat-extra-args]
185 | errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:188:55: warning: unknown conversion type character 'l' in format [-Wformat=]
188 | errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
| ^
ucsc/memalloc.c:188:73: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
188 | errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
| ~^
| |
| int
| %I64d
189 | (unsigned long long)size, errno);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
ucsc/memalloc.c:188:14: warning: too many arguments for format [-Wformat-extra-args]
188 | errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:316:45: warning: unknown conversion type character 'l' in format [-Wformat=]
316 | errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
| ^
ucsc/memalloc.c:316:14: warning: too many arguments for format [-Wformat-extra-args]
316 | errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:319:49: warning: unknown conversion type character 'l' in format [-Wformat=]
319 | errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
| ^
ucsc/memalloc.c:319:14: warning: too many arguments for format [-Wformat-extra-args]
319 | errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:358:50: warning: unknown conversion type character 'l' in format [-Wformat=]
358 | errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie,
| ^
ucsc/memalloc.c:358:18: warning: too many arguments for format [-Wformat-extra-args]
358 | errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:361:54: warning: unknown conversion type character 'l' in format [-Wformat=]
361 | errAbort("Bad end cookie %x%x%x%x checking %llx\n",
| ^
ucsc/memalloc.c:361:18: warning: too many arguments for format [-Wformat-extra-args]
361 | errAbort("Bad end cookie %x%x%x%x checking %llx\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:703:30: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' {aka 'long long int'} [-Wformat=]
703 | fprintf(stderr, "# pid=%d: %s\n", pid, line);
| ~^ ~~~
| | |
| int pid_t {aka long long int}
| %lld
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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]
49 | long long discardMe = 0;
| ^~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlList.c -o ucsc/sqlList.o
ucsc/sqlList.c: In function 'sqlLongLongArrayToString':
ucsc/sqlList.c:1049:31: warning: unknown conversion type character 'l' in format [-Wformat=]
1049 | dyStringPrintf(string, "%lld,", array[i]);
| ^
ucsc/sqlList.c:1049:28: warning: too many arguments for format [-Wformat-extra-args]
1049 | dyStringPrintf(string, "%lld,", array[i]);
| ^~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/os.c -o ucsc/os.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/wildcmp.c -o ucsc/wildcmp.o
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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-CNEr/00new/CNEr/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (CNEr)
