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This page was generated on 2022-06-24 12:06:42 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

INSTALL results for rtracklayer on palomino3


To the developers/maintainers of the rtracklayer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rtracklayer.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1722/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rtracklayer 1.56.1  (landing page)
Michael Lawrence
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/rtracklayer
git_branch: RELEASE_3_15
git_last_commit: 4c6d220
git_last_commit_date: 2022-06-22 15:10:46 -0400 (Wed, 22 Jun 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  YES
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  YES
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: rtracklayer
Version: 1.56.1
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rtracklayer
StartedAt: 2022-06-23 16:26:32 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 16:29:07 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 155.6 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rtracklayer
###
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* 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)