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This page was generated on 2022-03-18 11:08:34 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


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? here 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 1683/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rtracklayer 1.55.3  (landing page)
Michael Lawrence
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/rtracklayer
git_branch: master
git_last_commit: 4aa6570
git_last_commit_date: 2021-12-07 16:35:29 -0400 (Tue, 07 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: rtracklayer
Version: 1.55.3
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rtracklayer
StartedAt: 2022-03-17 16:02:02 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 16:04:18 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 135.7 seconds
RetCode: 0
Status:   OK  

Command output

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


* installing to library 'D:/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
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c R_init_rtracklayer.c -o R_init_rtracklayer.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c readGFF.c -o readGFF.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c bbiHelper.c -o bbiHelper.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c bigWig.c -o bigWig.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
   strncpy(keyBuf,item->name, maxBedNameSize);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
   bits64 extraIndexListEndOffset = 0;
          ^~~~~~~~~~~~~~~~~~~~~~~
bigBed.c: In function 'BBDFile_query':
bigBed.c:226:22: warning: 'typeId' may be used uninitialized in this function [-Wmaybe-uninitialized]
         switch(typeId[efIndex]) {
                      ^
bigBed.c:236:13: warning: 'lengthIndex' may be used uninitialized in this function [-Wmaybe-uninitialized]
             INTEGER(lengthIndex)[efIndex] = index + 1;
             ^~~~~~~~~~~~~~~~~~~~
bigBed.c:270:5: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized]
     SET_VECTOR_ELT(ans, index++, blocks);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:267:5: warning: 'itemRgb' may be used uninitialized in this function [-Wmaybe-uninitialized]
     SET_VECTOR_ELT(ans, index++, itemRgb);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:263:5: warning: 'thickWidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
     SET_VECTOR_ELT(ans, index++, new_IRanges("IRanges", thickStart,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                              thickWidth, R_NilValue));
                                              ~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:263:5: warning: 'thickStart' may be used uninitialized in this function [-Wmaybe-uninitialized]
bigBed.c:260:5: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized]
     SET_VECTOR_ELT(ans, index++, score);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:257:5: warning: 'name' may be used uninitialized in this function [-Wmaybe-uninitialized]
     SET_VECTOR_ELT(ans, index++, name);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c chain_io.c -o chain_io.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c twoBit.c -o twoBit.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c handlers.c -o handlers.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c utils.c -o utils.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/memgfx.c -o ucsc/memgfx.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/aliType.c -o ucsc/aliType.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/binRange.c -o ucsc/binRange.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/htmlColor.c -o ucsc/htmlColor.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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=]
     dyStringPrintf(string, "%lld,", array[i]);
                               ^
ucsc/sqlList.c:1041:28: warning: too many arguments for format [-Wformat-extra-args]
     dyStringPrintf(string, "%lld,", array[i]);
                            ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/tokenizer.c -o ucsc/tokenizer.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/asParse.c -o ucsc/asParse.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/basicBed.c -o ucsc/basicBed.o
ucsc/basicBed.c: In function 'lmCloneBed':
ucsc/basicBed.c:769:44: warning: argument to 'sizeof' in 'strncpy' call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess]
 strncpy(newBed->strand, bed->strand, sizeof(bed->strand));
                                            ^
ucsc/basicBed.c: In function 'cloneBed':
ucsc/basicBed.c:805:44: warning: argument to 'sizeof' in 'strncpy' call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess]
 strncpy(newBed->strand, bed->strand, sizeof(bed->strand));
                                            ^
ucsc/basicBed.c: In function 'loadAndValidateBedExt':
ucsc/basicBed.c:1619:46: warning: unknown conversion type character 'l' in format [-Wformat=]
       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=]
       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);
                                                             ~^                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                             %I64d
ucsc/basicBed.c:1619:25: warning: too many arguments for format [-Wformat-extra-args]
       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]
 strncpy(dupe, itemRgb, sizeof(dupe));
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/bigBed.c -o ucsc/bigBed.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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=]
     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=]
     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=]
     errAbort("Item index %lld greater than item count %lld in %s",
                                                               ~^
                                                               %I64d
  itemPos, bpt->itemCount, bpt->fileName);
  ~~~~~~~                                                        
ucsc/bPlusTree.c:307:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Item index %lld greater than item count %lld in %s",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
 bzero(summary, summarySize * sizeof(summary[0]));
 ^~~~~
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero'
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
  char *blockPt, *blockEnd;
                  ^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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=]
 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]
 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=]
     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]
     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=]
         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=]
         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=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                                       ~^           ~~~~~~~~~~~~~~~~
                                                                       %I64d
ucsc/cirTree.c:334:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                                             ~^                       ~~~~~~~~~~~~~~~~~
                                                                             %I64d
ucsc/cirTree.c:334:18: warning: too many arguments for format [-Wformat-extra-args]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:38: warning: unknown conversion type character 'l' in format [-Wformat=]
 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=]
 verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u.  childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
                                         ~^                                      ~~~~~~~~~~~~~~~
                                         %I64u
ucsc/cirTree.c:505:12: warning: too many arguments for format [-Wformat-extra-args]
 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=]
 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=]
 verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
                                              ~^                ~~~~~~~~~~~~~~~
                                              %I64d
ucsc/cirTree.c:585:12: warning: too many arguments for format [-Wformat-extra-args]
 verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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=]
     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=]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
                                         ~^     ~~~~~~~~~~~~~~~
                                         %I64d
ucsc/common.c:2476:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:28: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
                            ^
ucsc/common.c:2487:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
                                      ~^   ~~~~~~~~~~~~~~~
                                      %I64d
ucsc/common.c:2487:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2489:34: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %lld bytes", (long long)size);
                                  ^
ucsc/common.c:2489:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("End of file reading %lld bytes", (long long)size);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:30: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("Error reading %lld bytes", (long long)size);
                              ^
ucsc/common.c:2630:13: warning: too many arguments for format [-Wformat-extra-args]
  errnoAbort("Error reading %lld bytes", (long long)size);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2632:34: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
                                  ^
ucsc/common.c:2632:50: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
                                                  ^
ucsc/common.c:2632:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2647:44: warning: unknown conversion type character 'l' in format [-Wformat=]
         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=]
         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]
         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=]
     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=]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                                 ~^                    ~~~~~~~~~~~~~~~~~
                                 %I64d
ucsc/common.c:2658:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                                     ~^
                                     %s
         ((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2658:16: warning: too many arguments for format [-Wformat-extra-args]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:60: warning: unknown conversion type character 'l' in format [-Wformat=]
         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=]
         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]
         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=]
     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=]
     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]
     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=]
     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=]
     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]
     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=]
     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=]
     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]
     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=]
     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=]
     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]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/dnautil.c -o ucsc/dnautil.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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=]
 safef(pidStr, sizeof(pidStr), "%lld",  ptrToLL(pid));
                                  ^
ucsc/errAbort.c:356:31: warning: too many arguments for format [-Wformat-extra-args]
 safef(pidStr, sizeof(pidStr), "%lld",  ptrToLL(pid));
                               ^~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/hash.c -o ucsc/hash.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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=]
  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]
  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]
 static char * headerBytes(char *fileName, int numbytes)
               ^~~~~~~~~~~
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
 static char **getDecompressor(char *fileName)
               ^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:35: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
                                   ^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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=]
     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=]
     errAbort("Couldn't zCompress %lld bytes: %s",
                                              ~^
                                              %I64d
      (long long)uncompressedSize, zlibErrorMessage(err));
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~               
ucsc/zlibFace.c:51:14: warning: too many arguments for format [-Wformat-extra-args]
     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=]
     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=]
     errAbort("Couldn't zUncompress %lld bytes: %s",
                                                ~^
                                                %I64d
      (long long)compressedSize, zlibErrorMessage(err));
      ~~~~~~~~~~~~~~~~~~~~~~~~~                   
ucsc/zlibFace.c:72:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Couldn't zUncompress %lld bytes: %s",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/dystring.c -o ucsc/dystring.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/hmmstats.c -o ucsc/hmmstats.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                   ^
ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                          ^
ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                                 ^
ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                                        ^
ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                                               ^
ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                   ^
ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                          ^
ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                                 ^
ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                                        ^
ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                                               ^
ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                   ^
ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                          ^
ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                 ^
ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                        ^
ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                   ^
ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                          ^
ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                 ^
ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                        ^
ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                   ^
ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                          ^
ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                                 ^
ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                   ^
ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                          ^
ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                                 ^
ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                   ^
ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                          ^
ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld", thousands, l);
                ^~~~~~~~~~~~~
ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                   ^
ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                          ^
ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld", thousands, l);
                ^~~~~~~~~~~~~
ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
                   ^
ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld", l);
                ^~~~~~
ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
                   ^
ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld", l);
                ^~~~~~
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=]
      fprintf(stderr, "# pid=%d: %s\n", pid, line);
                             ~^         ~~~
                             %I64d
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=]
      fprintf(stderr, "# pid=%d: %s\n", pid, line);
                             ~^         ~~~
                             %I64d
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/pipeline.c -o ucsc/pipeline.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/rangeTree.c -o ucsc/rangeTree.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/rbTree.c -o ucsc/rbTree.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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=]
     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
                                                  ^
ucsc/memalloc.c:90:69: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
                                                                     ^
ucsc/memalloc.c:90:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:93:60: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                            ^
ucsc/memalloc.c:93:78: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                                             ~^
                                                                             %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                         
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:113:56: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
                                                        ^
ucsc/memalloc.c:113:75: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
                                                                           ^
ucsc/memalloc.c:113:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:116:66: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
                                                                  ^
ucsc/memalloc.c:116:84: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
                                                                                   ~^
                                                                                   %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                               
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:138:64: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
                                                                ^
ucsc/memalloc.c:138:82: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
                                                                                 ~^
                                                                                 %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                             
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:160:67: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
                                                                   ^
ucsc/memalloc.c:160:85: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
                                                                                    ~^
                                                                                    %I64d
  (unsigned long long)size, errno);
  ~~~~~~~~~~~~~~~~~~~~~~~~                                                            
ucsc/memalloc.c:160:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:186:45: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
                                             ^
ucsc/memalloc.c:186:64: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
                                                                ^
ucsc/memalloc.c:186:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:189:55: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                       ^
ucsc/memalloc.c:189:73: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                                        ~^
                                                                        %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                    
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:325:45: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
                                             ^
ucsc/memalloc.c:325:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:331:49: warning: unknown conversion type character 'l' in format [-Wformat=]
     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]
     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=]
         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]
         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=]
         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]
         safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/dlist.c -o ucsc/dlist.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/hex.c -o ucsc/hex.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/filePath.c -o ucsc/filePath.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/htmlPage.c -o ucsc/htmlPage.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
 /* 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=]
  errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total);
                                                             ^
ucsc/udc.c:223:13: warning: too many arguments for format [-Wformat-extra-args]
  errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:228:46: warning: unknown conversion type character 'l' in format [-Wformat=]
     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=]
     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]
     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=]
 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=]
 verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
                                                         ~^           ~~~~~~
                                                         %I64d
ucsc/udc.c:340:12: warning: too many arguments for format [-Wformat-extra-args]
 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=]
     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]
     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=]
 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=]
 verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
                                                              ~^           ~~~~~~
                                                              %I64d
ucsc/udc.c:396:12: warning: too many arguments for format [-Wformat-extra-args]
 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=]
  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]
  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=]
     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=]
     errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
                                                                               ~^
                                                                               %I64d
       fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
                                 ~~~~~~                                          
ucsc/udc.c:721:14: warning: too many arguments for format [-Wformat-extra-args]
     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=]
  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=]
  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=]
  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=]
  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=]
  verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
                                                                      ~^
                                                                      %I64d
ucsc/udc.c:879:3:
   bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
   ~~~~~~~~~~~~~~~~~~                                                   
ucsc/udc.c:877:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
  verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:879:23:
   bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:878:17: note: format string is defined here
   "new version %d\n",
                ~^
                %I64d
ucsc/udc.c:877:13: warning: too many arguments for format [-Wformat-extra-args]
  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 'udcCheckCacheBits':
ucsc/udc.c:1411:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
   (unsigned long)file, clearBlock,
   ^
ucsc/udc.c:1410:52: warning: unknown conversion type character 'l' in format [-Wformat=]
     warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
                                                    ^
ucsc/udc.c:1410:58: warning: unknown conversion type character 'l' in format [-Wformat=]
     warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
                                                          ^
ucsc/udc.c:1410:10: warning: too many arguments for format [-Wformat-extra-args]
     warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1435:30: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
                              ^
ucsc/udc.c:1435:45: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
                                            ~^
                                            %I64d
    readSize, file->url, startPos, actualSize);
    ~~~~~~~~                                  
ucsc/udc.c:1435:50: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
                                                  ^
ucsc/udc.c:1435:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
                                                          ~^
                                                          %s
    readSize, file->url, startPos, actualSize);
              ~~~~~~~~~                                     
ucsc/udc.c:1435:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1678:35: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
                                   ^
ucsc/udc.c:1678:50: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
                                                 ~^                  ~~~~
                                                 %I64d
ucsc/udc.c:1678:64: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
                                                                ^
ucsc/udc.c:1678:14: warning: too many arguments for format [-Wformat-extra-args]
     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:1818:23: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
                       ^
ucsc/udc.c:1818:68: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
                                                                    ^
ucsc/udc.c:1818:14: warning: too many arguments for format [-Wformat-extra-args]
     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]
 static void udcReadAndIgnore(struct ioStats *ioStats, int sd, bits64 size)
             ^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/net.c -o ucsc/net.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/bits.c -o ucsc/bits.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
 /* Use byteRange as a work-around alternate method to get file size (content-length).
  
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/internet.c -o ucsc/internet.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/https.c -o ucsc/https.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/base64.c -o ucsc/base64.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/verbose.c -o ucsc/verbose.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/os.c -o ucsc/os.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/rtools40/mingw64/bin/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 -LD:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/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
  converting help for package 'rtracklayer'
    finding HTML links ... done
    BEDFile-class                           html  
    BamFile-methods                         html  
    Bed15TrackLine-class                    html  
    BigBedFile                              html  
    finding level-2 HTML links ... done

    BigBedSelection                         html  
    BigWigFile                              html  
    BigWigSelection-class                   html  
    BrowserViewList-class                   html  
    Chain-class                             html  
    FastaFile-class                         html  
    GFFFile-class                           html  
    GRangesForUCSCGenome                    html  
    GenomicData                             html  
    GenomicSelection                        html  
    IntegerRangesList-methods               html  
    Quickload-class                         html  
    QuickloadGenome-class                   html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rtracklayer/00new/rtracklayer/help/quickload.html
    TabixFile-methods                       html  
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** 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)
Making 'packages.html' ... done