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###
### Running command:
###
### rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNEr.buildbin-libdir CNEr_1.24.0.tar.gz
###
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install for i386
* installing *source* package 'CNEr' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_CNEr.c -o R_init_CNEr.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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]
int _binNextShift = binNextShift();
^~~~~~~~~~~~~
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
int _binFirstShift = binFirstShift();
^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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]
struct axt *axt=NULL, *curAxt;
^~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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]
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:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/axt.c -o ucsc/axt.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/base64.c -o ucsc/base64.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/binRange.c -o ucsc/binRange.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bits.c -o ucsc/bits.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/chain.c -o ucsc/chain.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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:234:50: 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:234:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315:45: 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:315:16: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c:330:54: 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:330:62: 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:330:72: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
~^ ~~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:330:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
~^ ~~~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:330:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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=]
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=]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2442:14: warning: too many arguments for format [-Wformat-extra-args]
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=]
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=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2453:11: warning: too many arguments for format [-Wformat-extra-args]
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=]
errAbort("End of file reading %lld bytes", (long long)size);
^
ucsc/common.c:2455:11: warning: too many arguments for format [-Wformat-extra-args]
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=]
errnoAbort("Error reading %lld bytes", (long long)size);
^
ucsc/common.c:2596:13: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("Error reading %lld bytes", (long long)size);
^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2598:34: 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:2598:50: 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:2598:11: warning: too many arguments for format [-Wformat-extra-args]
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=]
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=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
~^ ~~~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2618:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
~^
%s
((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2618:16: warning: too many arguments for format [-Wformat-extra-args]
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=]
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=]
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]
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=]
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=]
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]
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=]
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=]
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]
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=]
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=]
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]
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=]
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=]
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]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dlist.c -o ucsc/dlist.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnaseq.c -o ucsc/dnaseq.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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]
int pastPoly = 0;
^~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dystring.c -o ucsc/dystring.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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=]
static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $";
^~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hash.c -o ucsc/hash.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/https.c -o ucsc/https.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/intExp.c -o ucsc/intExp.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/kxTok.c -o ucsc/kxTok.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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]
static char * headerBytes(char *fileName, int numbytes)
^~~~~~~~~~~
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
static char **getDecompressor(char *fileName)
^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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=]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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=]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:89:69: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:89:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:92:60: warning: unknown conversion type character 'l' in format [-Wformat=]
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=]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:92:14: warning: too many arguments for format [-Wformat-extra-args]
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=]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:112:75: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:112:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:115:66: warning: unknown conversion type character 'l' in format [-Wformat=]
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=]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:115:14: warning: too many arguments for format [-Wformat-extra-args]
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=]
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=]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:137:14: warning: too many arguments for format [-Wformat-extra-args]
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=]
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=]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:159:14: warning: too many arguments for format [-Wformat-extra-args]
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=]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:185:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:185:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:188:55: warning: unknown conversion type character 'l' in format [-Wformat=]
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=]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:188:14: warning: too many arguments for format [-Wformat-extra-args]
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=]
errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
^
ucsc/memalloc.c:316:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:319:49: warning: unknown conversion type character 'l' in format [-Wformat=]
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]
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=]
errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie,
^
ucsc/memalloc.c:358:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:361:54: warning: unknown conversion type character 'l' in format [-Wformat=]
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]
errAbort("Bad end cookie %x%x%x%x checking %llx\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:544:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:544:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:552:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:552:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:558:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:558:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:558:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld", thousands, l);
^~~~~~~~~~~~~
ucsc/obscure.c:558:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:558:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:558:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld", thousands, l);
^~~~~~~~~~~~~
ucsc/obscure.c:561:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:561:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld", l);
^~~~~~
ucsc/obscure.c:561:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:561:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld", l);
^~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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]
long long discardMe = 0;
^~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/pipeline.c -o ucsc/pipeline.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_portimpl.c -o ucsc/_portimpl.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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=]
dyStringPrintf(string, "%lld,", array[i]);
^
ucsc/sqlList.c:1049:28: warning: too many arguments for format [-Wformat-extra-args]
dyStringPrintf(string, "%lld,", array[i]);
^~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlNum.c -o ucsc/sqlNum.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/verbose.c -o ucsc/verbose.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/os.c -o ucsc/os.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/rtools40/mingw32/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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CNEr.buildbin-libdir/00LOCK-CNEr/00new/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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CNEr' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_CNEr.c -o R_init_CNEr.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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]
int _binNextShift = binNextShift();
^~~~~~~~~~~~~
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
int _binFirstShift = binFirstShift();
^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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]
struct axt *axt=NULL, *curAxt;
^~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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]
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:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/axt.c -o ucsc/axt.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/base64.c -o ucsc/base64.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/binRange.c -o ucsc/binRange.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bits.c -o ucsc/bits.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/chain.c -o ucsc/chain.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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:234:50: 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:234:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315:45: 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:315:16: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c:330:54: 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:330:62: 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:330:72: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
~^ ~~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:330:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
~^ ~~~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:330:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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=]
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=]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2442:14: warning: too many arguments for format [-Wformat-extra-args]
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=]
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=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2453:11: warning: too many arguments for format [-Wformat-extra-args]
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=]
errAbort("End of file reading %lld bytes", (long long)size);
^
ucsc/common.c:2455:11: warning: too many arguments for format [-Wformat-extra-args]
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=]
errnoAbort("Error reading %lld bytes", (long long)size);
^
ucsc/common.c:2596:13: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("Error reading %lld bytes", (long long)size);
^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2598:34: 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:2598:50: 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:2598:11: warning: too many arguments for format [-Wformat-extra-args]
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=]
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=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
~^ ~~~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2618:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
~^
%s
((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2618:16: warning: too many arguments for format [-Wformat-extra-args]
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=]
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=]
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]
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=]
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=]
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]
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=]
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=]
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]
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=]
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=]
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]
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=]
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=]
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]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dlist.c -o ucsc/dlist.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnaseq.c -o ucsc/dnaseq.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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]
int pastPoly = 0;
^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dystring.c -o ucsc/dystring.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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=]
static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $";
^~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hash.c -o ucsc/hash.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/https.c -o ucsc/https.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/intExp.c -o ucsc/intExp.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/kxTok.c -o ucsc/kxTok.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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]
static char * headerBytes(char *fileName, int numbytes)
^~~~~~~~~~~
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
static char **getDecompressor(char *fileName)
^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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=]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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=]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:89:69: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:89:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:92:60: warning: unknown conversion type character 'l' in format [-Wformat=]
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=]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:92:14: warning: too many arguments for format [-Wformat-extra-args]
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=]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:112:75: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:112:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:115:66: warning: unknown conversion type character 'l' in format [-Wformat=]
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=]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:115:14: warning: too many arguments for format [-Wformat-extra-args]
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=]
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=]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:137:14: warning: too many arguments for format [-Wformat-extra-args]
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=]
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=]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:159:14: warning: too many arguments for format [-Wformat-extra-args]
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=]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:185:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:185:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:188:55: warning: unknown conversion type character 'l' in format [-Wformat=]
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=]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:188:14: warning: too many arguments for format [-Wformat-extra-args]
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=]
errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
^
ucsc/memalloc.c:316:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:319:49: warning: unknown conversion type character 'l' in format [-Wformat=]
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]
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=]
errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie,
^
ucsc/memalloc.c:358:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:361:54: warning: unknown conversion type character 'l' in format [-Wformat=]
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]
errAbort("Bad end cookie %x%x%x%x checking %llx\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:544:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:544:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:544:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:552:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:552:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:552:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:558:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:558:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:558:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld", thousands, l);
^~~~~~~~~~~~~
ucsc/obscure.c:558:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:558:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:558:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld", thousands, l);
^~~~~~~~~~~~~
ucsc/obscure.c:561:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:561:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld", l);
^~~~~~
ucsc/obscure.c:561:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:561:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld", l);
^~~~~~
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=]
fprintf(stderr, "# pid=%d: %s\n", pid, line);
~^ ~~~
%I64d
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=]
fprintf(stderr, "# pid=%d: %s\n", pid, line);
~^ ~~~
%I64d
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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]
long long discardMe = 0;
^~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/pipeline.c -o ucsc/pipeline.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_portimpl.c -o ucsc/_portimpl.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/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=]
dyStringPrintf(string, "%lld,", array[i]);
^
ucsc/sqlList.c:1049:28: warning: too many arguments for format [-Wformat-extra-args]
dyStringPrintf(string, "%lld,", array[i]);
^~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlNum.c -o ucsc/sqlNum.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/verbose.c -o ucsc/verbose.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/os.c -o ucsc/os.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/rtools40/mingw64/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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CNEr.buildbin-libdir/CNEr/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNEr' as CNEr_1.24.0.zip
* DONE (CNEr)
