BioC 3.4: CHECK report for rtracklayer on tokay1

Package: rtracklayer

Version: 1.34.2

Command: rm -rf rtracklayer.buildbin-libdir rtracklayer.Rcheck && mkdir rtracklayer.buildbin-libdir rtracklayer.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rtracklayer.buildbin-libdir rtracklayer_1.34.2.tar.gz >rtracklayer.Rcheck\00install.out 2>&1 && cp rtracklayer.Rcheck\00install.out rtracklayer-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=rtracklayer.buildbin-libdir --install="check:rtracklayer-install.out" --force-multiarch --no-vignettes --timings rtracklayer_1.34.2.tar.gz

StartedAt: 2017-04-15 00:40:52 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:46:37 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 344.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: rtracklayer.Rcheck

Warnings: 3

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###
### Running command:
###
###   rm -rf rtracklayer.buildbin-libdir rtracklayer.Rcheck && mkdir rtracklayer.buildbin-libdir rtracklayer.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rtracklayer.buildbin-libdir rtracklayer_1.34.2.tar.gz >rtracklayer.Rcheck\00install.out 2>&1 && cp rtracklayer.Rcheck\00install.out rtracklayer-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=rtracklayer.buildbin-libdir --install="check:rtracklayer-install.out" --force-multiarch --no-vignettes --timings rtracklayer_1.34.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/rtracklayer.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rtracklayer/DESCRIPTION' ... OK
* this is package 'rtracklayer' version '1.34.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'rtracklayer' can be installed ... WARNING
Found the following significant warnings:
  ucsc/bPlusTree.c:310:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:238:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:319:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:334:9: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:505:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:585:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2476:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2487:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2489:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2630:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2632:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2648:6: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2660:3: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2785:9: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3251:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3260:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3276:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3285:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/errAbort.c:356:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/linefile.c:1083:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/zlibFace.c:52:6: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/zlibFace.c:73:6: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:547:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:557:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:565:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:571:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:574:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:326:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:333:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:377:18: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:385:18: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:138:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:143:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:241:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:290:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:516:7: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:670:3: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1114:3: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1138:4: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1363:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1499:6: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1113:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'C:/Users/biocbuild/bbs-3.4-bioc/meat/rtracklayer.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  Artistic-2.0 + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::testPackage' 'GenomicRanges:::INVALID.GR.COLNAMES'
  'S4Vectors:::labeledLine'
  'S4Vectors:::make_XYZxyz_to_XxYyZz_subscript'
  'S4Vectors:::new_SimpleList_from_list' 'XVector:::open_input_files'
  'XVector:::rewind_filexp'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
import,BEDFile-ANY-ANY: warning in rgb(cols[1, ], cols[2, ], cols[3, ],
  max = 255): partial argument match of 'max' to 'maxColorValue'
asGTF,GRangesList : processFeatures: no visible binding for global
  variable 'tx_id'
asGTF,GRangesList: no visible global function definition for
  'pmapFromTranscripts'
asGTF,GRangesList: no visible global function definition for
  'rectifyDataFrame'
export,GAlignmentPairs-BamFile-ANY : getMateAttribute: no visible
  global function definition for 'last'
export,GenomicRanges-GFFFile-ANY: no visible global function definition
  for 'package.version'
getSeq,TwoBitFile: no visible binding for global variable 'con'
import,BEDPEFile-ANY-ANY: no visible binding for global variable
  'chrom2'
import,BEDPEFile-ANY-ANY: no visible binding for global variable
  'start2'
import,BEDPEFile-ANY-ANY: no visible binding for global variable 'end2'
import,BEDPEFile-ANY-ANY: no visible binding for global variable
  'strand2'
import,BamFile-ANY-ANY: no visible global function definition for
  'readGAlignmentPairs'
intersectTrack<-,UCSCTableQuery: possible error in normArgTrack(value,
  x, TRUE): unused argument (TRUE)
Undefined global functions or variables:
  chrom2 con end2 last package.version pmapFromTranscripts
  readGAlignmentPairs rectifyDataFrame start2 strand2 tx_id
* checking Rd files ... NOTE
prepare_Rd: readGFF.Rd:52-53: Dropping empty section \details
prepare_Rd: readGFF.Rd:55-56: Dropping empty section \value
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'cleanupBigWigCache' 'readGFFAsGRanges' 'readGFFPragmas'
  'sniffGFFVersion'
Undocumented S4 classes:
  'RTLFileList'
Undocumented S4 methods:
  generic '[' and siglist 'UCSCTrackModes,ANY,ANY,ANY'
  generic 'as.character' and siglist 'RTLFile'
  generic 'export' and siglist 'ANY,BEDPEFile,ANY'
  generic 'export' and siglist 'GRangesList,GTFFile,ANY'
  generic 'export' and siglist 'Pairs,BEDPEFile,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars.in
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.4-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/i386/rtracklayer.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
File 'rtracklayer/libs/i386/rtracklayer.dll':
  Found non-API call to R: 'getConnection'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'rtracklayer_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'rtracklayer_unit_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/rtracklayer.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'rtracklayer' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c readGFF.c -o readGFF.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c bigWig.c -o bigWig.o
bigWig.c: In function 'BWGFile_query':
bigWig.c:289:9: warning: 'numericListEls' may be used uninitialized in this function [-Wmaybe-uninitialized]
         SET_VECTOR_ELT(numericListEls, elt_len, ans_numeric);
         ^
bigWig.c:321:7: warning: 'dataFrameListEls' may be used uninitialized in this function [-Wmaybe-uninitialized]
       SET_VECTOR_ELT(dataFrameListEls, i,
       ^
bigWig.c:319:7: warning: 'rangesListEls' may be used uninitialized in this function [-Wmaybe-uninitialized]
       SET_VECTOR_ELT(rangesListEls, i,
       ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c chain_io.c -o chain_io.o
chain_io.c: In function 'read_chain_file':
chain_io.c:116:9: warning: 'header_line' may be used uninitialized in this function [-Wmaybe-uninitialized]
         IntAE_insert_at(block->length, IntAE_get_nelt(block->length),
         ^
chain_io.c:116:60: warning: 'block' may be used uninitialized in this function [-Wmaybe-uninitialized]
         IntAE_insert_at(block->length, IntAE_get_nelt(block->length),
                                                            ^
chain_io.c:110:12: warning: 'qrc' may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (qrc)
            ^
chain_io.c:106:12: warning: 'trc' may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (trc) /* width already subtracted above */
            ^
chain_io.c:98:14: warning: 'qstart' may be used uninitialized in this function [-Wmaybe-uninitialized]
       qstart -= (qrc ? width : 0);
              ^
chain_io.c:97:14: warning: 'tstart' may be used uninitialized in this function [-Wmaybe-uninitialized]
       tstart -= (trc ? width : 0);
              ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c twoBit.c -o twoBit.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c handlers.c -o handlers.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function '_STRSXP_collapse':
utils.c:4:8: warning: unused variable 'ans' [-Wunused-variable]
   SEXP ans;
        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataStart':
ucsc/bPlusTree.c:286:12: warning: variable 'childCount' set but not used [-Wunused-but-set-variable]
     bits16 childCount;
            ^
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:310:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  itemPos, bpt->itemCount, bpt->fileName);
  ^
ucsc/bPlusTree.c:310:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/bPlusTree.c:310:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/bPlusTree.c:310:2: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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'
ucsc/bbiRead.c: In function 'bbiTotalSummary':
ucsc/bbiRead.c:748:34: warning: variable 'chromEnd' set but not used [-Wunused-but-set-variable]
      bits32 chromId, chromStart, chromEnd;
                                  ^
ucsc/bbiRead.c:748:22: warning: variable 'chromStart' set but not used [-Wunused-but-set-variable]
      bits32 chromId, chromStart, chromEnd;
                      ^
ucsc/bbiRead.c:748:13: warning: variable 'chromId' set but not used [-Wunused-but-set-variable]
      bits32 chromId, chromStart, chromEnd;
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:238:1: 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:238:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:5: 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:319:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:334:9: 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:334:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:1: 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:505:1: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:505:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:1: 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:585:1: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:585:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2476:5: 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:2476:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2476:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
  ^
ucsc/common.c:2487:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2487:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2489:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %lld bytes", (long long)size);
  ^
ucsc/common.c:2489:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("Error reading %lld bytes", (long long)size);
  ^
ucsc/common.c:2630:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2632:2: 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:2632:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2632:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)result, (long long)size);
      ^
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2648:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2660:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
   ^
ucsc/common.c:2660:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat=]
ucsc/common.c:2660:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
ucsc/common.c:2660:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
         ^
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2785:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:5: 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:3251:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3251:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:5: 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:3260:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3260:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:5: 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:3276:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3276:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:5: 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:3285:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3285:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'reverseComplementSlashSeparated':
ucsc/dnautil.c:496:5: warning: implicit declaration of function 'isAllNt' [-Wimplicit-function-declaration]
     if (isAllNt(allele, alLen))
     ^
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:977:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
 int pastPoly = 0;
     ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 safef(pidStr, sizeof(pidStr), "%lld",  ptrToLL(pid));
 ^
ucsc/errAbort.c:356:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:2: 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:1083:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/linefile.c: At top level:
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
 static char **getDecompressor(char *fileName)
               ^
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
 static char * headerBytes(char *fileName, int numbytes)
               ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
     ^
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:52:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)uncompressedSize, zlibErrorMessage(err));
      ^
ucsc/zlibFace.c:52:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:52:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:73:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)compressedSize, zlibErrorMessage(err));
      ^
ucsc/zlibFace.c:73:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:73:6: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
     ^
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
     ^
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
     ^
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
     ^
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:571:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:574:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
     ^
ucsc/obscure.c:574:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'stringToSlNames':
ucsc/obscure.c:473:8: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if ((s = skipLeadingSpaces(s)) == NULL)
        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rbTree.c -o ucsc/rbTree.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:94:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:94:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:117:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:117:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:139:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:139:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:161:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  (unsigned long long)size, errno);
  ^
ucsc/memalloc.c:161:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)NEEDMEM_LIMIT);
          ^
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:190:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:190:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:326:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              ptrToLL(vpt));
              ^
ucsc/memalloc.c:326:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:333:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              ptrToLL(vpt));
              ^
ucsc/memalloc.c:333:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:377:18: warning: unknown conversion type character 'l' in format [-Wformat=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:377:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:385:18: warning: unknown conversion type character 'l' in format [-Wformat=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:385:18: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:138:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
  ^
ucsc/udc.c:138:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
     ^
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:143:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
 ^
ucsc/udc.c:234:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:241:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
     ^
ucsc/udc.c:241:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:290:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
 ^
ucsc/udc.c:290:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:290:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
  ^
ucsc/udc.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:516:7: warning: unknown conversion type character 'l' in format [-Wformat=]
       fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
       ^
ucsc/udc.c:516:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
ucsc/udc.c:516:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcBitmapOpen':
ucsc/udc.c:570:8: warning: variable 'reserved64' set but not used [-Wunused-but-set-variable]
 bits64 reserved64;
        ^
ucsc/udc.c:569:8: warning: variable 'reserved32' set but not used [-Wunused-but-set-variable]
 bits32 reserved32;
        ^
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   file->sparseFileName, version);
   ^
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:670:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:670:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
ucsc/udc.c:670:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1114:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   ((long long)clearBlock * udcBlockSize), (((long long)clearBlock+1) * udcBlockSize));
   ^
ucsc/udc.c:1114:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1114:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1138:4: warning: unknown conversion type character 'l' in format [-Wformat=]
    readSize, file->url, startPos, actualSize);
    ^
ucsc/udc.c:1138:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1138:4: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1138:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
ucsc/udc.c:1138:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1363:5: 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:1363:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1363:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1363:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1499:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      url, (long long)size, (long long)maxSize);
      ^
ucsc/udc.c:1499:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1499:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:126:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
 static void readAndIgnore(int sd, bits64 size)
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/net.c -o ucsc/net.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/twoBit.c -o ucsc/twoBit.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/internet.c -o ucsc/internet.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/Rtools/mingw_32/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 bigWig.o chain_io.o twoBit.o handlers.o utils.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/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 -LC:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lws2_32 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer'
Creating a generic function from function 'uri' in package 'rtracklayer'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'rtracklayer' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c readGFF.c -o readGFF.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bigWig.c -o bigWig.o
bigWig.c: In function 'BWGFile_query':
bigWig.c:289:9: warning: 'numericListEls' may be used uninitialized in this function [-Wmaybe-uninitialized]
         SET_VECTOR_ELT(numericListEls, elt_len, ans_numeric);
         ^
bigWig.c:321:7: warning: 'dataFrameListEls' may be used uninitialized in this function [-Wmaybe-uninitialized]
       SET_VECTOR_ELT(dataFrameListEls, i,
       ^
bigWig.c:319:7: warning: 'rangesListEls' may be used uninitialized in this function [-Wmaybe-uninitialized]
       SET_VECTOR_ELT(rangesListEls, i,
       ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c chain_io.c -o chain_io.o
chain_io.c: In function 'read_chain_file':
chain_io.c:116:9: warning: 'header_line' may be used uninitialized in this function [-Wmaybe-uninitialized]
         IntAE_insert_at(block->length, IntAE_get_nelt(block->length),
         ^
chain_io.c:116:60: warning: 'block' may be used uninitialized in this function [-Wmaybe-uninitialized]
         IntAE_insert_at(block->length, IntAE_get_nelt(block->length),
                                                            ^
chain_io.c:110:12: warning: 'qrc' may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (qrc)
            ^
chain_io.c:106:12: warning: 'trc' may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (trc) /* width already subtracted above */
            ^
chain_io.c:98:14: warning: 'qstart' may be used uninitialized in this function [-Wmaybe-uninitialized]
       qstart -= (qrc ? width : 0);
              ^
chain_io.c:97:14: warning: 'tstart' may be used uninitialized in this function [-Wmaybe-uninitialized]
       tstart -= (trc ? width : 0);
              ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c twoBit.c -o twoBit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c handlers.c -o handlers.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function '_STRSXP_collapse':
utils.c:4:8: warning: unused variable 'ans' [-Wunused-variable]
   SEXP ans;
        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataStart':
ucsc/bPlusTree.c:286:12: warning: variable 'childCount' set but not used [-Wunused-but-set-variable]
     bits16 childCount;
            ^
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:310:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  itemPos, bpt->itemCount, bpt->fileName);
  ^
ucsc/bPlusTree.c:310:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/bPlusTree.c:310:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/bPlusTree.c:310:2: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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'
ucsc/bbiRead.c: In function 'bbiTotalSummary':
ucsc/bbiRead.c:748:34: warning: variable 'chromEnd' set but not used [-Wunused-but-set-variable]
      bits32 chromId, chromStart, chromEnd;
                                  ^
ucsc/bbiRead.c:748:22: warning: variable 'chromStart' set but not used [-Wunused-but-set-variable]
      bits32 chromId, chromStart, chromEnd;
                      ^
ucsc/bbiRead.c:748:13: warning: variable 'chromId' set but not used [-Wunused-but-set-variable]
      bits32 chromId, chromStart, chromEnd;
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:238:1: 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:238:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:5: 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:319:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:334:9: 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:334:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:1: 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:505:1: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:505:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:1: 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:585:1: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:585:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2476:5: 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:2476:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2476:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
  ^
ucsc/common.c:2487:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2487:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2489:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %lld bytes", (long long)size);
  ^
ucsc/common.c:2489:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("Error reading %lld bytes", (long long)size);
  ^
ucsc/common.c:2630:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2632:2: 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:2632:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2632:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)result, (long long)size);
      ^
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2648:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2660:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
   ^
ucsc/common.c:2660:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat=]
ucsc/common.c:2660:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
ucsc/common.c:2660:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
         ^
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2785:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:5: 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:3251:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3251:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:5: 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:3260:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3260:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:5: 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:3276:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3276:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:5: 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:3285:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3285:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'reverseComplementSlashSeparated':
ucsc/dnautil.c:496:5: warning: implicit declaration of function 'isAllNt' [-Wimplicit-function-declaration]
     if (isAllNt(allele, alLen))
     ^
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:977:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
 int pastPoly = 0;
     ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 safef(pidStr, sizeof(pidStr), "%lld",  ptrToLL(pid));
 ^
ucsc/errAbort.c:356:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:2: 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:1083:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/linefile.c: At top level:
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
 static char **getDecompressor(char *fileName)
               ^
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
 static char * headerBytes(char *fileName, int numbytes)
               ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
     ^
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:52:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)uncompressedSize, zlibErrorMessage(err));
      ^
ucsc/zlibFace.c:52:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:52:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:73:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)compressedSize, zlibErrorMessage(err));
      ^
ucsc/zlibFace.c:73:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:73:6: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
     ^
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
     ^
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
     ^
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
     ^
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:571:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:574:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
     ^
ucsc/obscure.c:574:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:789:6: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' [-Wformat=]
      fprintf(stderr, "# pid=%d: %s\n", pid, line);
      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rbTree.c -o ucsc/rbTree.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:94:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:94:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:117:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:117:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:139:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:139:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:161:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  (unsigned long long)size, errno);
  ^
ucsc/memalloc.c:161:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)NEEDMEM_LIMIT);
          ^
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:190:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:190:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:326:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              ptrToLL(vpt));
              ^
ucsc/memalloc.c:326:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:333:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              ptrToLL(vpt));
              ^
ucsc/memalloc.c:333:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:377:18: warning: unknown conversion type character 'l' in format [-Wformat=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:377:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:385:18: warning: unknown conversion type character 'l' in format [-Wformat=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:385:18: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:138:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
  ^
ucsc/udc.c:138:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
     ^
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:143:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
 ^
ucsc/udc.c:234:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:241:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
     ^
ucsc/udc.c:241:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:290:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
 ^
ucsc/udc.c:290:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:290:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
  ^
ucsc/udc.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:516:7: warning: unknown conversion type character 'l' in format [-Wformat=]
       fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
       ^
ucsc/udc.c:516:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
ucsc/udc.c:516:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcBitmapOpen':
ucsc/udc.c:570:8: warning: variable 'reserved64' set but not used [-Wunused-but-set-variable]
 bits64 reserved64;
        ^
ucsc/udc.c:569:8: warning: variable 'reserved32' set but not used [-Wunused-but-set-variable]
 bits32 reserved32;
        ^
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   file->sparseFileName, version);
   ^
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:670:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:670:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'time_t' [-Wformat=]
ucsc/udc.c:670:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1113:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
   (unsigned long)file, clearBlock,
   ^
ucsc/udc.c:1114:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   ((long long)clearBlock * udcBlockSize), (((long long)clearBlock+1) * udcBlockSize));
   ^
ucsc/udc.c:1114:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1114:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1138:4: warning: unknown conversion type character 'l' in format [-Wformat=]
    readSize, file->url, startPos, actualSize);
    ^
ucsc/udc.c:1138:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1138:4: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1138:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
ucsc/udc.c:1138:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1363:5: 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:1363:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1363:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1363:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1499:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      url, (long long)size, (long long)maxSize);
      ^
ucsc/udc.c:1499:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1499:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:126:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
 static void readAndIgnore(int sd, bits64 size)
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/net.c -o ucsc/net.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/twoBit.c -o ucsc/twoBit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/internet.c -o ucsc/internet.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/Rtools/mingw_64/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 bigWig.o chain_io.o twoBit.o handlers.o utils.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/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 -LC:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lws2_32 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rtracklayer' as rtracklayer_1.34.2.zip
* DONE (rtracklayer)

name	user	system	elapsed
BEDFile-class	2.14	0.39	2.54
BamFile-methods	0.14	0.03	0.23
BigWigFile	0	0	0
BigWigSelection-class	0.03	0.00	0.04
GFFFile-class	1.26	0.02	1.28
GenomicData	0.18	0.00	0.17
GenomicSelection	0.17	0.00	0.17
Quickload-class	0.24	0.04	0.45
QuickloadGenome-class	0.14	0.00	0.14
TwoBitFile-class	0.04	0.00	0.05
UCSCSchema-class	0	0	0
UCSCTableQuery-class	0	0	0
WIGFile-class	0.59	0.02	0.63
asBED	0	0	0
asGFF	0	0	0
browseGenome	0	0	0
browserView-methods	0	0	0
browserViews-methods	0	0	0
cpneTrack	0.47	0.01	0.48
export	0.05	0.02	0.06
layTrack-methods	0	0	0
liftOver	0	0	0
readGFF	0.34	0.00	0.35
targets	0.07	0.00	0.06
ucscGenomes	0.17	0.00	0.45
ucscTrackModes-methods	0.01	0.00	0.02

name	user	system	elapsed
BEDFile-class	2.50	0.28	2.78
BamFile-methods	0.10	0.02	0.13
BigWigFile	0.02	0.00	0.01
BigWigSelection-class	0.02	0.00	0.02
GFFFile-class	1.28	0.00	1.28
GenomicData	0.16	0.00	0.15
GenomicSelection	0.16	0.00	0.16
Quickload-class	0.31	0.07	0.55
QuickloadGenome-class	0.15	0.02	0.17
TwoBitFile-class	0.07	0.00	0.06
UCSCSchema-class	0	0	0
UCSCTableQuery-class	0	0	0
WIGFile-class	0.79	0.01	0.81
asBED	0	0	0
asGFF	0	0	0
browseGenome	0	0	0
browserView-methods	0	0	0
browserViews-methods	0	0	0
cpneTrack	0.76	0.00	0.76
export	0.1	0.0	0.1
layTrack-methods	0	0	0
liftOver	0	0	0
readGFF	1.56	0.00	1.56
targets	0.08	0.00	0.08
ucscGenomes	0.23	0.02	0.51
ucscTrackModes-methods	0.02	0.00	0.02