##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rtracklayer
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'rtracklayer' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readGFF.c -o readGFF.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bbiHelper.c -o bbiHelper.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigWig.c -o bigWig.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigBedHelper.c -o bigBedHelper.o
bigBedHelper.c: In function 'bbNamedFileChunkKey':
bigBedHelper.c:148:3: warning: 'strncpy' destination unchanged after copying no bytes [-Wstringop-truncation]
148 | strncpy(keyBuf,item->name, maxBedNameSize);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigBed.c -o bigBed.o
bigBed.c: In function 'BBDFile_write':
bigBed.c:338:10: warning: variable 'extraIndexListEndOffset' set but not used [-Wunused-but-set-variable]
338 | bits64 extraIndexListEndOffset = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~
bigBed.c: In function 'BBDFile_query':
bigBed.c:226:22: warning: 'typeId' may be used uninitialized in this function [-Wmaybe-uninitialized]
226 | switch(typeId[efIndex]) {
| ^
bigBed.c:236:13: warning: 'lengthIndex' may be used uninitialized in this function [-Wmaybe-uninitialized]
236 | INTEGER(lengthIndex)[efIndex] = index + 1;
| ^~~~~~~~~~~~~~~~~~~~
bigBed.c:218:7: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized]
218 | SET_VECTOR_ELT(blocks, i, new_IRanges("IRanges", bstart, bwidth, R_NilValue));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:209:7: warning: 'itemRgb' may be used uninitialized in this function [-Wmaybe-uninitialized]
209 | SET_STRING_ELT(itemRgb, i, mkChar(rgbBuf));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:204:7: warning: 'thickWidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
204 | INTEGER(thickWidth)[i] = bed->thickEnd - bed->thickStart + 1;
| ^~~~~~~~~~~~~~~~~~~
bigBed.c:205:7: warning: 'thickStart' may be used uninitialized in this function [-Wmaybe-uninitialized]
205 | INTEGER(thickStart)[i] = bed->thickStart;
| ^~~~~~~~~~~~~~~~~~~
bigBed.c:198:7: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized]
198 | INTEGER(score)[i] = bed->score;
| ^~~~~~~~~~~~~~
bigBed.c:257:5: warning: 'name' may be used uninitialized in this function [-Wmaybe-uninitialized]
257 | SET_VECTOR_ELT(ans, index++, name);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chain_io.c -o chain_io.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c twoBit.c -o twoBit.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c handlers.c -o handlers.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memgfx.c -o ucsc/memgfx.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/aliType.c -o ucsc/aliType.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/htmlColor.c -o ucsc/htmlColor.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -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:1041:31: warning: unknown conversion type character 'l' in format [-Wformat=]
1041 | dyStringPrintf(string, "%lld,", array[i]);
| ^
ucsc/sqlList.c:1041:28: warning: too many arguments for format [-Wformat-extra-args]
1041 | dyStringPrintf(string, "%lld,", array[i]);
| ^~~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/tokenizer.c -o ucsc/tokenizer.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/asParse.c -o ucsc/asParse.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/basicBed.c -o ucsc/basicBed.o
ucsc/basicBed.c: In function 'loadAndValidateBedExt':
ucsc/basicBed.c:1619:46: warning: unknown conversion type character 'l' in format [-Wformat=]
1619 | lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name);
| ^
ucsc/basicBed.c:1619:62: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
1619 | lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| char * long long unsigned int
| %I64d
ucsc/basicBed.c:1619:25: warning: too many arguments for format [-Wformat-extra-args]
1619 | lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/basicBed.c: In function 'bedParseRgb':
ucsc/basicBed.c:997:1: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
997 | strncpy(dupe, itemRgb, sizeof(dupe));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bigBed.c -o ucsc/bigBed.o
ucsc/bigBed.c: In function 'extractField':
ucsc/bigBed.c:314:2: warning: '%s' directive argument is null [-Wformat-overflow=]
314 | warn("Not enough fields in extractField of %s", line);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:307:28: warning: unknown conversion type character 'l' in format [-Wformat=]
307 | errAbort("Item index %lld greater than item count %lld in %s",
| ^
ucsc/bPlusTree.c:307:57: warning: unknown conversion type character 'l' in format [-Wformat=]
307 | errAbort("Item index %lld greater than item count %lld in %s",
| ^
ucsc/bPlusTree.c:307:64: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
307 | errAbort("Item index %lld greater than item count %lld in %s",
| ~^
| |
| char *
| %I64d
308 | itemPos, bpt->itemCount, bpt->fileName);
| ~~~~~~~
| |
| long long unsigned int
ucsc/bPlusTree.c:307:14: warning: too many arguments for format [-Wformat-extra-args]
307 | errAbort("Item index %lld greater than item count %lld in %s",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'writeIndexLevel',
inlined from 'bptFileBulkIndexToOpenFile' at ucsc/bPlusTree.c:567:29:
ucsc/bPlusTree.c:461:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
461 | keyBuf[keySize] = 0;
| ~~~~~~~~~~~~~~~~^~~
ucsc/bPlusTree.c: In function 'bptFileBulkIndexToOpenFile':
ucsc/bPlusTree.c:460:6: note: at offset [-9223372036854775808, 9223372036854775807] to an object with size at most 4294967295 declared here
460 | char keyBuf[keySize+1];
| ^~~~~~
In function 'writeLeafLevel',
inlined from 'bptFileBulkIndexToOpenFile' at ucsc/bPlusTree.c:575:1:
ucsc/bPlusTree.c:513:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
513 | keyBuf[keySize] = 0;
| ~~~~~~~~~~~~~~~~^~~
ucsc/bPlusTree.c: In function 'bptFileBulkIndexToOpenFile':
ucsc/bPlusTree.c:512:6: note: at offset [-9223372036854775808, 9223372036854775807] to an object with size at most 4294967295 declared here
512 | char keyBuf[keySize+1];
| ^~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
635 | bzero(summary, summarySize * sizeof(summary[0]));
| ^~~~~
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero'
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/bwgQuery.c:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
187 | char *blockPt, *blockEnd;
| ^~~~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -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:238:50: warning: unknown conversion type character 'l' in format [-Wformat=]
238 | verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
| ^
ucsc/cirTree.c:238:12: warning: too many arguments for format [-Wformat-extra-args]
238 | verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:45: warning: unknown conversion type character 'l' in format [-Wformat=]
319 | verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
| ^
ucsc/cirTree.c:319:16: warning: too many arguments for format [-Wformat-extra-args]
319 | verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c:334:54: warning: unknown conversion type character 'l' in format [-Wformat=]
334 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
| ^
ucsc/cirTree.c:334:62: warning: unknown conversion type character 'l' in format [-Wformat=]
334 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
| ^
ucsc/cirTree.c:334:72: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
334 | 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:334:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
334 | 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:334:18: warning: too many arguments for format [-Wformat-extra-args]
334 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:38: warning: unknown conversion type character 'l' in format [-Wformat=]
505 | verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
| ^
ucsc/cirTree.c:505:42: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
505 | verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
| ~^ ~~~~~~~~~~~~~~~
| | |
| unsigned int long long unsigned int
| %I64u
ucsc/cirTree.c:505:12: warning: too many arguments for format [-Wformat-extra-args]
505 | verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:32: warning: unknown conversion type character 'l' in format [-Wformat=]
585 | verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
| ^
ucsc/cirTree.c:585:47: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
585 | verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
| ~^ ~~~~~~~~~~~~~~~
| | |
| int long long unsigned int
| %I64d
ucsc/cirTree.c:585:12: warning: too many arguments for format [-Wformat-extra-args]
585 | verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -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:2476:31: warning: unknown conversion type character 'l' in format [-Wformat=]
2476 | errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
| ^
ucsc/common.c:2476:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
2476 | errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
| ~^ ~~~~~~~~~~~~~~~
| | |
| | long long int
| char *
| %I64d
ucsc/common.c:2476:14: warning: too many arguments for format [-Wformat-extra-args]
2476 | errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:28: warning: unknown conversion type character 'l' in format [-Wformat=]
2487 | errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
| ^
ucsc/common.c:2487:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
2487 | errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
| ~^ ~~~~~~~~~~~~~~~
| | |
| | long long int
| char *
| %I64d
ucsc/common.c:2487:11: warning: too many arguments for format [-Wformat-extra-args]
2487 | errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2489:34: warning: unknown conversion type character 'l' in format [-Wformat=]
2489 | errAbort("End of file reading %lld bytes", (long long)size);
| ^
ucsc/common.c:2489:11: warning: too many arguments for format [-Wformat-extra-args]
2489 | errAbort("End of file reading %lld bytes", (long long)size);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:30: warning: unknown conversion type character 'l' in format [-Wformat=]
2630 | errnoAbort("Error reading %lld bytes", (long long)size);
| ^
ucsc/common.c:2630:13: warning: too many arguments for format [-Wformat-extra-args]
2630 | errnoAbort("Error reading %lld bytes", (long long)size);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2632:34: warning: unknown conversion type character 'l' in format [-Wformat=]
2632 | errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
| ^
ucsc/common.c:2632:50: warning: unknown conversion type character 'l' in format [-Wformat=]
2632 | errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
| ^
ucsc/common.c:2632:11: warning: too many arguments for format [-Wformat-extra-args]
2632 | errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2647:44: warning: unknown conversion type character 'l' in format [-Wformat=]
2647 | errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
| ^
ucsc/common.c:2647:52: warning: unknown conversion type character 'l' in format [-Wformat=]
2647 | errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
| ^
ucsc/common.c:2647:18: warning: too many arguments for format [-Wformat-extra-args]
2647 | errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2658:29: warning: unknown conversion type character 'l' in format [-Wformat=]
2658 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
| ^
ucsc/common.c:2658:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=]
2658 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
| ~^ ~~~~~~~~~~~~~~~~~
| | |
| char * long long int
| %I64d
ucsc/common.c:2658:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
2658 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
| ~^
| |
| int
| %s
2659 | ((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
2660 | (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2658:16: warning: too many arguments for format [-Wformat-extra-args]
2658 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:60: warning: unknown conversion type character 'l' in format [-Wformat=]
2785 | errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
| ^
ucsc/common.c:2785:65: warning: unknown conversion type character 'l' in format [-Wformat=]
2785 | errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
| ^
ucsc/common.c:2785:18: warning: too many arguments for format [-Wformat-extra-args]
2785 | errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:39: warning: unknown conversion type character 'l' in format [-Wformat=]
3251 | errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
| ^
ucsc/common.c:3251:58: warning: unknown conversion type character 'l' in format [-Wformat=]
3251 | errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
| ^
ucsc/common.c:3251:14: warning: too many arguments for format [-Wformat-extra-args]
3251 | errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:39: warning: unknown conversion type character 'l' in format [-Wformat=]
3260 | errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
| ^
ucsc/common.c:3260:61: warning: unknown conversion type character 'l' in format [-Wformat=]
3260 | errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
| ^
ucsc/common.c:3260:14: warning: too many arguments for format [-Wformat-extra-args]
3260 | errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:39: warning: unknown conversion type character 'l' in format [-Wformat=]
3276 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
| ^
ucsc/common.c:3276:62: warning: unknown conversion type character 'l' in format [-Wformat=]
3276 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
| ^
ucsc/common.c:3276:14: warning: too many arguments for format [-Wformat-extra-args]
3276 | 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:3285:39: warning: unknown conversion type character 'l' in format [-Wformat=]
3285 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
| ^
ucsc/common.c:3285:62: warning: unknown conversion type character 'l' in format [-Wformat=]
3285 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
| ^
ucsc/common.c:3285:14: warning: too many arguments for format [-Wformat-extra-args]
3285 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnautil.c -o ucsc/dnautil.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:34: warning: unknown conversion type character 'l' in format [-Wformat=]
356 | safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid));
| ^
ucsc/errAbort.c:356:31: warning: too many arguments for format [-Wformat-extra-args]
356 | safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid));
| ^~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hash.c -o ucsc/hash.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:56: warning: unknown conversion type character 'l' in format [-Wformat=]
1083 | safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
| ^
ucsc/linefile.c:1083:28: warning: too many arguments for format [-Wformat-extra-args]
1083 | safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
112 | static char * headerBytes(char *fileName, int numbytes)
| ^~~~~~~~~~~
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
35 | static char **getDecompressor(char *fileName)
| ^~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -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-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:51:36: warning: unknown conversion type character 'l' in format [-Wformat=]
51 | errAbort("Couldn't zCompress %lld bytes: %s",
| ^
ucsc/zlibFace.c:51:47: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
51 | errAbort("Couldn't zCompress %lld bytes: %s",
| ~^
| |
| char *
| %I64d
52 | (long long)uncompressedSize, zlibErrorMessage(err));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long int
ucsc/zlibFace.c:51:14: warning: too many arguments for format [-Wformat-extra-args]
51 | errAbort("Couldn't zCompress %lld bytes: %s",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:72:38: warning: unknown conversion type character 'l' in format [-Wformat=]
72 | errAbort("Couldn't zUncompress %lld bytes: %s",
| ^
ucsc/zlibFace.c:72:49: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
72 | errAbort("Couldn't zUncompress %lld bytes: %s",
| ~^
| |
| char *
| %I64d
73 | (long long)compressedSize, zlibErrorMessage(err));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long int
ucsc/zlibFace.c:72:14: warning: too many arguments for format [-Wformat-extra-args]
72 | errAbort("Couldn't zUncompress %lld bytes: %s",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -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:789:30: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' {aka 'long long int'} [-Wformat=]
789 | fprintf(stderr, "# pid=%d: %s\n", pid, line);
| ~^ ~~~
| | |
| int pid_t {aka long long int}
| %lld
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -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:90:50: warning: unknown conversion type character 'l' in format [-Wformat=]
90 | errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
| ^
ucsc/memalloc.c:90:69: warning: unknown conversion type character 'l' in format [-Wformat=]
90 | errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
| ^
ucsc/memalloc.c:90:14: warning: too many arguments for format [-Wformat-extra-args]
90 | errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:93:60: warning: unknown conversion type character 'l' in format [-Wformat=]
93 | errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
| ^
ucsc/memalloc.c:93:78: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
93 | errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
| ~^
| |
| int
| %I64d
94 | (unsigned long long)size, errno);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
93 | errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:113:56: warning: unknown conversion type character 'l' in format [-Wformat=]
113 | errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
| ^
ucsc/memalloc.c:113:75: warning: unknown conversion type character 'l' in format [-Wformat=]
113 | errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
| ^
ucsc/memalloc.c:113:14: warning: too many arguments for format [-Wformat-extra-args]
113 | errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:116:66: warning: unknown conversion type character 'l' in format [-Wformat=]
116 | errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
| ^
ucsc/memalloc.c:116:84: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
116 | errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
| ~^
| |
| int
| %I64d
117 | (unsigned long long)size, errno);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
116 | errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:138:64: warning: unknown conversion type character 'l' in format [-Wformat=]
138 | errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
| ^
ucsc/memalloc.c:138:82: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
138 | errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
| ~^
| |
| int
| %I64d
139 | (unsigned long long)size, errno);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
138 | errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:160:67: warning: unknown conversion type character 'l' in format [-Wformat=]
160 | errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
| ^
ucsc/memalloc.c:160:85: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
160 | errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
| ~^
| |
| int
| %I64d
161 | (unsigned long long)size, errno);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
ucsc/memalloc.c:160:14: warning: too many arguments for format [-Wformat-extra-args]
160 | errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:186:45: warning: unknown conversion type character 'l' in format [-Wformat=]
186 | errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
| ^
ucsc/memalloc.c:186:64: warning: unknown conversion type character 'l' in format [-Wformat=]
186 | errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
| ^
ucsc/memalloc.c:186:14: warning: too many arguments for format [-Wformat-extra-args]
186 | errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:189:55: warning: unknown conversion type character 'l' in format [-Wformat=]
189 | errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
| ^
ucsc/memalloc.c:189:73: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
189 | errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
| ~^
| |
| int
| %I64d
190 | (unsigned long long)size, errno);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
189 | errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:325:45: warning: unknown conversion type character 'l' in format [-Wformat=]
325 | errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
| ^
ucsc/memalloc.c:325:14: warning: too many arguments for format [-Wformat-extra-args]
325 | errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:331:49: warning: unknown conversion type character 'l' in format [-Wformat=]
331 | errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
| ^
ucsc/memalloc.c:331:14: warning: too many arguments for format [-Wformat-extra-args]
331 | errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:376:70: warning: unknown conversion type character 'l' in format [-Wformat=]
376 | safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie,
| ^
ucsc/memalloc.c:376:38: warning: too many arguments for format [-Wformat-extra-args]
376 | safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:383:74: warning: unknown conversion type character 'l' in format [-Wformat=]
383 | safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
| ^
ucsc/memalloc.c:383:38: warning: too many arguments for format [-Wformat-extra-args]
383 | safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hex.c -o ucsc/hex.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/filePath.c -o ucsc/filePath.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/htmlPage.c -o ucsc/htmlPage.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/udc.c -o ucsc/udc.o
In file included from ucsc/udc.c:41:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
|
ucsc/udc.c: In function 'udcReadAndIgnore':
ucsc/udc.c:223:61: warning: unknown conversion type character 'l' in format [-Wformat=]
223 | errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total);
| ^
ucsc/udc.c:223:13: warning: too many arguments for format [-Wformat-extra-args]
223 | errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:228:46: warning: unknown conversion type character 'l' in format [-Wformat=]
228 | errAbort("udcReadAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
| ^
ucsc/udc.c:228:65: warning: unknown conversion type character 'l' in format [-Wformat=]
228 | errAbort("udcReadAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
| ^
ucsc/udc.c:228:14: warning: too many arguments for format [-Wformat-extra-args]
228 | errAbort("udcReadAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:340:49: warning: unknown conversion type character 'l' in format [-Wformat=]
340 | verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
| ^
ucsc/udc.c:340:58: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
340 | verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
| ~^ ~~~~~~
| | |
| char * long long unsigned int
| %I64d
ucsc/udc.c:340:12: warning: too many arguments for format [-Wformat-extra-args]
340 | verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:347:57: warning: unknown conversion type character 'l' in format [-Wformat=]
347 | warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
| ^
ucsc/udc.c:347:10: warning: too many arguments for format [-Wformat-extra-args]
347 | warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:396:54: warning: unknown conversion type character 'l' in format [-Wformat=]
396 | verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
| ^
ucsc/udc.c:396:63: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
396 | verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
| ~^ ~~~~~~
| | |
| char * long long unsigned int
| %I64d
ucsc/udc.c:396:12: warning: too many arguments for format [-Wformat-extra-args]
396 | verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:414:53: warning: unknown conversion type character 'l' in format [-Wformat=]
414 | warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
| ^
ucsc/udc.c:414:7: warning: too many arguments for format [-Wformat-extra-args]
414 | warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:721:42: warning: unknown conversion type character 'l' in format [-Wformat=]
721 | errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
| ^
ucsc/udc.c:721:80: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
721 | errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
| ~^
| |
| int
| %I64d
722 | fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
| ~~~~~~
| |
| long long int
ucsc/udc.c:721:14: warning: too many arguments for format [-Wformat-extra-args]
721 | errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:877:40: warning: unknown conversion type character 'l' in format [-Wformat=]
877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
| ^
ucsc/udc.c:877:48: warning: unknown conversion type character 'l' in format [-Wformat=]
877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
| ^
ucsc/udc.c:877:56: warning: unknown conversion type character 'l' in format [-Wformat=]
877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
| ^
ucsc/udc.c:877:64: warning: unknown conversion type character 'l' in format [-Wformat=]
877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
| ^
ucsc/udc.c:877:71: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
| ~^
| |
| char *
| %I64d
878 | "new version %d\n",
879 | bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
| ~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
ucsc/udc.c:877:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
878 | "new version %d\n",
879 | bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long int
ucsc/udc.c:878:17: note: format string is defined here
878 | "new version %d\n",
| ~^
| |
| int
| %I64d
ucsc/udc.c:877:13: warning: too many arguments for format [-Wformat-extra-args]
877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'djb2_hash':
ucsc/udc.c:1088:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
1088 | while (c = *str++)
| ^
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1446:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
1446 | (unsigned long)file, clearBlock,
| ^
ucsc/udc.c:1445:52: warning: unknown conversion type character 'l' in format [-Wformat=]
1445 | warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
| ^
ucsc/udc.c:1445:58: warning: unknown conversion type character 'l' in format [-Wformat=]
1445 | warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
| ^
ucsc/udc.c:1445:10: warning: too many arguments for format [-Wformat-extra-args]
1445 | warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1470:30: warning: unknown conversion type character 'l' in format [-Wformat=]
1470 | errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
| ^
ucsc/udc.c:1470:45: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
1470 | errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
| ~^
| |
| char *
| %I64d
1471 | readSize, file->url, startPos, actualSize);
| ~~~~~~~~
| |
| long long unsigned int
ucsc/udc.c:1470:50: warning: unknown conversion type character 'l' in format [-Wformat=]
1470 | errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
| ^
ucsc/udc.c:1470:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
1470 | errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
| ~^
| |
| int
| %s
1471 | readSize, file->url, startPos, actualSize);
| ~~~~~~~~~
| |
| char *
ucsc/udc.c:1470:11: warning: too many arguments for format [-Wformat-extra-args]
1470 | errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1713:35: warning: unknown conversion type character 'l' in format [-Wformat=]
1713 | errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
| ^
ucsc/udc.c:1713:50: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
1713 | errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
| ~^ ~~~~
| | |
| char * long long unsigned int
| %I64d
ucsc/udc.c:1713:64: warning: unknown conversion type character 'l' in format [-Wformat=]
1713 | errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
| ^
ucsc/udc.c:1713:14: warning: too many arguments for format [-Wformat-extra-args]
1713 | errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1853:23: warning: unknown conversion type character 'l' in format [-Wformat=]
1853 | errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
| ^
ucsc/udc.c:1853:68: warning: unknown conversion type character 'l' in format [-Wformat=]
1853 | errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
| ^
ucsc/udc.c:1853:14: warning: too many arguments for format [-Wformat-extra-args]
1853 | errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
ucsc/udc.c:211:13: warning: 'udcReadAndIgnore' defined but not used [-Wunused-function]
211 | static void udcReadAndIgnore(struct ioStats *ioStats, int sd, bits64 size)
| ^~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/net.c -o ucsc/net.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bits.c -o ucsc/bits.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/twoBit.c -o ucsc/twoBit.o
In file included from ucsc/twoBit.c:15:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
|
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/internet.c -o ucsc/internet.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/https.c -o ucsc/https.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/base64.c -o ucsc/base64.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/os.c -o ucsc/os.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/aliType.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/hex.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -LF:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lws2_32 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rtracklayer/00new/rtracklayer/libs/x64
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer'
** 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 (rtracklayer)
