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BUILD BIN report for CNEr on tokay2

This page was generated on 2020-10-17 11:56:20 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CNEr PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 329/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.24.0
Ge Tan
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CNEr
Branch: RELEASE_3_11
Last Commit: 4d2a728
Last Changed Date: 2020-04-27 14:38:24 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNEr
Version: 1.24.0
Command: rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNEr.buildbin-libdir CNEr_1.24.0.tar.gz
StartedAt: 2020-10-17 10:09:02 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 10:11:18 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 136.2 seconds
RetCode: 0
Status:  OK  
PackageFile: CNEr_1.24.0.zip
PackageFileSize: 10.2 MiB

Command output

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###
### Running command:
###
###   rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNEr.buildbin-libdir CNEr_1.24.0.tar.gz
###
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install for i386

* installing *source* package 'CNEr' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_CNEr.c -o R_init_CNEr.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
utils.c: In function 'bin_ranges_from_coord_range_standard':
utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable]
   int _binNextShift = binNextShift();
       ^~~~~~~~~~~~~
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
   int _binFirstShift = binFirstShift();
       ^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o
io.c: In function 'myReadAxt':
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
   struct axt *axt=NULL, *curAxt;
                          ^~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ceScan.c -o ceScan.o
ceScan.c: In function 'ceScan':
ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable]
   char rest, path[PATH_LEN];
        ^~~~
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
   int i, n;
          ^
ceScan.c: In function 'freeSlThreshold':
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
   struct slCNE *CNE, *nextCNE, *el_CNE;
                 ^~~
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
   struct slThreshold *thresholds, *nextThreshold, *el_threshold;
                       ^~~~~~~~~~
ceScan.c: In function 'myCeScan':
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
   int nrCNE[nrThresholds], i;
                            ^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable]
   int nrCNE[nrThresholds], i;
       ^~~~~
ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable]
   struct slCNE *CNE;
                 ^~~
ceScan.c: In function 'myCeScanFile':
ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
   int nrThresholds = GET_LENGTH(winSize);
       ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/axt.c -o ucsc/axt.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/base64.c -o ucsc/base64.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/binRange.c -o ucsc/binRange.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bits.c -o ucsc/bits.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/chain.c -o ucsc/chain.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:234:50: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
                                                  ^
ucsc/cirTree.c:234:12: warning: too many arguments for format [-Wformat-extra-args]
 verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315:45: warning: unknown conversion type character 'l' in format [-Wformat=]
     verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
                                             ^
ucsc/cirTree.c:315:16: warning: too many arguments for format [-Wformat-extra-args]
     verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c:330:54: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                      ^
ucsc/cirTree.c:330:62: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                              ^
ucsc/cirTree.c:330:72: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                                       ~^           ~~~~~~~~~~~~~~~~
                                                                       %I64d
ucsc/cirTree.c:330:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                                             ~^                       ~~~~~~~~~~~~~~~~~
                                                                             %I64d
ucsc/cirTree.c:330:18: warning: too many arguments for format [-Wformat-extra-args]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2442:31: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
                               ^
ucsc/common.c:2442:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
                                         ~^     ~~~~~~~~~~~~~~~
                                         %I64d
ucsc/common.c:2442:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2453:28: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
                            ^
ucsc/common.c:2453:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
                                      ~^   ~~~~~~~~~~~~~~~
                                      %I64d
ucsc/common.c:2453:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2455:34: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %lld bytes", (long long)size);
                                  ^
ucsc/common.c:2455:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("End of file reading %lld bytes", (long long)size);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2596:30: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("Error reading %lld bytes", (long long)size);
                              ^
ucsc/common.c:2596:13: warning: too many arguments for format [-Wformat-extra-args]
  errnoAbort("Error reading %lld bytes", (long long)size);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2598:34: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
                                  ^
ucsc/common.c:2598:50: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
                                                  ^
ucsc/common.c:2598:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2618:29: warning: unknown conversion type character 'l' in format [-Wformat=]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                             ^
ucsc/common.c:2618:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                                 ~^                    ~~~~~~~~~~~~~~~~~
                                 %I64d
ucsc/common.c:2618:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                                     ~^
                                     %s
         ((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2618:16: warning: too many arguments for format [-Wformat-extra-args]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2745:60: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
                                                            ^
ucsc/common.c:2745:65: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
                                                                 ^
ucsc/common.c:2745:18: warning: too many arguments for format [-Wformat-extra-args]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3211:39: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
                                       ^
ucsc/common.c:3211:58: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
                                                          ^
ucsc/common.c:3211:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3220:39: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
                                       ^
ucsc/common.c:3220:61: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
                                                             ^
ucsc/common.c:3220:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecat':
ucsc/common.c:3236:39: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
                                       ^
ucsc/common.c:3236:62: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
                                                              ^
ucsc/common.c:3236:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencat':
ucsc/common.c:3245:39: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
                                       ^
ucsc/common.c:3245:62: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
                                                              ^
ucsc/common.c:3245:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dlist.c -o ucsc/dlist.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnaseq.c -o ucsc/dnaseq.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:942:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
 int pastPoly = 0;
     ^~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dystring.c -o ucsc/dystring.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/errabort.c -o ucsc/errabort.o
ucsc/errabort.c:30:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
 static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $";
                   ^~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hash.c -o ucsc/hash.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/https.c -o ucsc/https.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/intExp.c -o ucsc/intExp.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/kxTok.c -o ucsc/kxTok.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function]
 static char * headerBytes(char *fileName, int numbytes)
               ^~~~~~~~~~~
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
 static char **getDecompressor(char *fileName)
               ^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:35: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
                                   ^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:89:50: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
                                                  ^
ucsc/memalloc.c:89:69: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
                                                                     ^
ucsc/memalloc.c:89:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:92:60: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                            ^
ucsc/memalloc.c:92:78: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                                             ~^
                                                                             %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                         
ucsc/memalloc.c:92:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:112:56: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
                                                        ^
ucsc/memalloc.c:112:75: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
                                                                           ^
ucsc/memalloc.c:112:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:115:66: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
                                                                  ^
ucsc/memalloc.c:115:84: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
                                                                                   ~^
                                                                                   %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                               
ucsc/memalloc.c:115:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:137:64: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
                                                                ^
ucsc/memalloc.c:137:82: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
                                                                                 ~^
                                                                                 %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                             
ucsc/memalloc.c:137:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:159:67: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
                                                                   ^
ucsc/memalloc.c:159:85: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
                                                                                    ~^
                                                                                    %I64d
  (unsigned long long)size, errno);
  ~~~~~~~~~~~~~~~~~~~~~~~~                                                            
ucsc/memalloc.c:159:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:185:45: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
                                             ^
ucsc/memalloc.c:185:64: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
                                                                ^
ucsc/memalloc.c:185:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:188:55: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                       ^
ucsc/memalloc.c:188:73: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                                        ~^
                                                                        %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                    
ucsc/memalloc.c:188:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:316:45: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
                                             ^
ucsc/memalloc.c:316:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:319:49: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
                                                 ^
ucsc/memalloc.c:319:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:358:50: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie,
                                                  ^
ucsc/memalloc.c:358:18: warning: too many arguments for format [-Wformat-extra-args]
         errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie,
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:361:54: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Bad end cookie %x%x%x%x checking %llx\n",
                                                      ^
ucsc/memalloc.c:361:18: warning: too many arguments for format [-Wformat-extra-args]
         errAbort("Bad end cookie %x%x%x%x checking %llx\n",
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:544:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                   ^
ucsc/obscure.c:544:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                          ^
ucsc/obscure.c:544:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                 ^
ucsc/obscure.c:544:40: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                        ^
ucsc/obscure.c:544:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:544:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                   ^
ucsc/obscure.c:544:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                          ^
ucsc/obscure.c:544:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                 ^
ucsc/obscure.c:544:40: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                        ^
ucsc/obscure.c:544:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:552:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                   ^
ucsc/obscure.c:552:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                          ^
ucsc/obscure.c:552:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                                 ^
ucsc/obscure.c:552:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:552:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                   ^
ucsc/obscure.c:552:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                          ^
ucsc/obscure.c:552:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                                 ^
ucsc/obscure.c:552:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:558:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                   ^
ucsc/obscure.c:558:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                          ^
ucsc/obscure.c:558:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld", thousands, l);
                ^~~~~~~~~~~~~
ucsc/obscure.c:558:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                   ^
ucsc/obscure.c:558:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                          ^
ucsc/obscure.c:558:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld", thousands, l);
                ^~~~~~~~~~~~~
ucsc/obscure.c:561:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
                   ^
ucsc/obscure.c:561:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld", l);
                ^~~~~~
ucsc/obscure.c:561:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
                   ^
ucsc/obscure.c:561:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld", l);
                ^~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/options.c -o ucsc/options.o
ucsc/options.c: In function 'validateOption':
ucsc/options.c:49:11: warning: variable 'discardMe' set but not used [-Wunused-but-set-variable]
 long long discardMe = 0;
           ^~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/pipeline.c -o ucsc/pipeline.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_portimpl.c -o ucsc/_portimpl.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlList.c -o ucsc/sqlList.o
ucsc/sqlList.c: In function 'sqlLongLongArrayToString':
ucsc/sqlList.c:1049:31: warning: unknown conversion type character 'l' in format [-Wformat=]
     dyStringPrintf(string, "%lld,", array[i]);
                               ^
ucsc/sqlList.c:1049:28: warning: too many arguments for format [-Wformat-extra-args]
     dyStringPrintf(string, "%lld,", array[i]);
                            ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlNum.c -o ucsc/sqlNum.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/verbose.c -o ucsc/verbose.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/os.c -o ucsc/os.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CNEr.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CNEr.buildbin-libdir/00LOCK-CNEr/00new/CNEr/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CNEr'
    finding HTML links ... done
    AssemblyStats                           html  
    Axt-class                               html  
    Axt-util                                html  
    CNE-class                               html  
    CNEDanRer10Hg38                         html  
    CNEDensity                              html  
    GRangePairs-class                       html  
    finding level-2 HTML links ... done

    addAncestorGO                           html  
    axisTrack                               html  
    axtChain                                html  
    axtInfo                                 html  
    binner                                  html  
    blatCNE                                 html  
    ceScan-methods                          html  
    chainMergeSort                          html  
    chainNetSyntenic                        html  
    chainPreNet                             html  
    cneFinalListDanRer10Hg38                html  
    cneMerge                                html  
    fetchChromSizes                         html  
    fixCoordinates                          html  
    grangesPairsForDotplot                  html  
    last                                    html  
    lastz                                   html  
    lavToPsl                                html  
    makeAncoraFiles                         html  
    makeAxtTracks                           html  
    makeCNEDensity                          html  
    makeGRBs                                html  
    matchDistribution                       html  
    netToAxt                                html  
    orgKEGGIds2EntrezIDs                    html  
    plotCNEDistribution                     html  
    plotCNEWidth                            html  
    psubAxt                                 html  
    queryCNEData                            html  
    read.rmMask.GRanges                     html  
    read.rmskFasta                          html  
    readAncora                              html  
    readAncoraIntoSQLite                    html  
    readAxt                                 html  
    readBed                                 html  
    readCNERangesFromSQLite                 html  
    reverseCigar                            html  
    saveCNEToSQLite                         html  
    scoringMatrix                           html  
    subAxt-methods                          html  
    syntenicDotplot                         html  
    writeAxt                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CNEr' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_CNEr.c -o R_init_CNEr.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
utils.c: In function 'bin_ranges_from_coord_range_standard':
utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable]
   int _binNextShift = binNextShift();
       ^~~~~~~~~~~~~
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
   int _binFirstShift = binFirstShift();
       ^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o
io.c: In function 'myReadAxt':
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
   struct axt *axt=NULL, *curAxt;
                          ^~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ceScan.c -o ceScan.o
ceScan.c: In function 'ceScan':
ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable]
   char rest, path[PATH_LEN];
        ^~~~
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
   int i, n;
          ^
ceScan.c: In function 'freeSlThreshold':
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
   struct slCNE *CNE, *nextCNE, *el_CNE;
                 ^~~
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
   struct slThreshold *thresholds, *nextThreshold, *el_threshold;
                       ^~~~~~~~~~
ceScan.c: In function 'myCeScan':
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
   int nrCNE[nrThresholds], i;
                            ^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable]
   int nrCNE[nrThresholds], i;
       ^~~~~
ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable]
   struct slCNE *CNE;
                 ^~~
ceScan.c: In function 'myCeScanFile':
ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
   int nrThresholds = GET_LENGTH(winSize);
       ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/axt.c -o ucsc/axt.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/base64.c -o ucsc/base64.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/binRange.c -o ucsc/binRange.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bits.c -o ucsc/bits.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/chain.c -o ucsc/chain.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:234:50: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
                                                  ^
ucsc/cirTree.c:234:12: warning: too many arguments for format [-Wformat-extra-args]
 verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315:45: warning: unknown conversion type character 'l' in format [-Wformat=]
     verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
                                             ^
ucsc/cirTree.c:315:16: warning: too many arguments for format [-Wformat-extra-args]
     verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c:330:54: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                      ^
ucsc/cirTree.c:330:62: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                              ^
ucsc/cirTree.c:330:72: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                                       ~^           ~~~~~~~~~~~~~~~~
                                                                       %I64d
ucsc/cirTree.c:330:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                                             ~^                       ~~~~~~~~~~~~~~~~~
                                                                             %I64d
ucsc/cirTree.c:330:18: warning: too many arguments for format [-Wformat-extra-args]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2442:31: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
                               ^
ucsc/common.c:2442:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
                                         ~^     ~~~~~~~~~~~~~~~
                                         %I64d
ucsc/common.c:2442:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2453:28: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
                            ^
ucsc/common.c:2453:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
                                      ~^   ~~~~~~~~~~~~~~~
                                      %I64d
ucsc/common.c:2453:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2455:34: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %lld bytes", (long long)size);
                                  ^
ucsc/common.c:2455:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("End of file reading %lld bytes", (long long)size);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2596:30: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("Error reading %lld bytes", (long long)size);
                              ^
ucsc/common.c:2596:13: warning: too many arguments for format [-Wformat-extra-args]
  errnoAbort("Error reading %lld bytes", (long long)size);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2598:34: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
                                  ^
ucsc/common.c:2598:50: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
                                                  ^
ucsc/common.c:2598:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2618:29: warning: unknown conversion type character 'l' in format [-Wformat=]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                             ^
ucsc/common.c:2618:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                                 ~^                    ~~~~~~~~~~~~~~~~~
                                 %I64d
ucsc/common.c:2618:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                                     ~^
                                     %s
         ((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2618:16: warning: too many arguments for format [-Wformat-extra-args]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2745:60: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
                                                            ^
ucsc/common.c:2745:65: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
                                                                 ^
ucsc/common.c:2745:18: warning: too many arguments for format [-Wformat-extra-args]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3211:39: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
                                       ^
ucsc/common.c:3211:58: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
                                                          ^
ucsc/common.c:3211:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3220:39: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
                                       ^
ucsc/common.c:3220:61: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
                                                             ^
ucsc/common.c:3220:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecat':
ucsc/common.c:3236:39: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
                                       ^
ucsc/common.c:3236:62: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
                                                              ^
ucsc/common.c:3236:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencat':
ucsc/common.c:3245:39: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
                                       ^
ucsc/common.c:3245:62: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
                                                              ^
ucsc/common.c:3245:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dlist.c -o ucsc/dlist.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnaseq.c -o ucsc/dnaseq.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:942:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
 int pastPoly = 0;
     ^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dystring.c -o ucsc/dystring.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/errabort.c -o ucsc/errabort.o
ucsc/errabort.c:30:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=]
 static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $";
                   ^~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hash.c -o ucsc/hash.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/https.c -o ucsc/https.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/intExp.c -o ucsc/intExp.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/kxTok.c -o ucsc/kxTok.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function]
 static char * headerBytes(char *fileName, int numbytes)
               ^~~~~~~~~~~
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
 static char **getDecompressor(char *fileName)
               ^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:35: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
                                   ^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:89:50: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
                                                  ^
ucsc/memalloc.c:89:69: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
                                                                     ^
ucsc/memalloc.c:89:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:92:60: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                            ^
ucsc/memalloc.c:92:78: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                                             ~^
                                                                             %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                         
ucsc/memalloc.c:92:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:112:56: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
                                                        ^
ucsc/memalloc.c:112:75: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
                                                                           ^
ucsc/memalloc.c:112:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:115:66: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
                                                                  ^
ucsc/memalloc.c:115:84: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
                                                                                   ~^
                                                                                   %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                               
ucsc/memalloc.c:115:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:137:64: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
                                                                ^
ucsc/memalloc.c:137:82: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
                                                                                 ~^
                                                                                 %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                             
ucsc/memalloc.c:137:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:159:67: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
                                                                   ^
ucsc/memalloc.c:159:85: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
                                                                                    ~^
                                                                                    %I64d
  (unsigned long long)size, errno);
  ~~~~~~~~~~~~~~~~~~~~~~~~                                                            
ucsc/memalloc.c:159:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:185:45: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
                                             ^
ucsc/memalloc.c:185:64: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
                                                                ^
ucsc/memalloc.c:185:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:188:55: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                       ^
ucsc/memalloc.c:188:73: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                                        ~^
                                                                        %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                    
ucsc/memalloc.c:188:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:316:45: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
                                             ^
ucsc/memalloc.c:316:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:319:49: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
                                                 ^
ucsc/memalloc.c:319:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:358:50: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie,
                                                  ^
ucsc/memalloc.c:358:18: warning: too many arguments for format [-Wformat-extra-args]
         errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie,
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:361:54: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Bad end cookie %x%x%x%x checking %llx\n",
                                                      ^
ucsc/memalloc.c:361:18: warning: too many arguments for format [-Wformat-extra-args]
         errAbort("Bad end cookie %x%x%x%x checking %llx\n",
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:544:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                   ^
ucsc/obscure.c:544:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                          ^
ucsc/obscure.c:544:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                 ^
ucsc/obscure.c:544:40: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                        ^
ucsc/obscure.c:544:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:544:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                   ^
ucsc/obscure.c:544:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                          ^
ucsc/obscure.c:544:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                 ^
ucsc/obscure.c:544:40: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                        ^
ucsc/obscure.c:544:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:552:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                   ^
ucsc/obscure.c:552:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                          ^
ucsc/obscure.c:552:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                                 ^
ucsc/obscure.c:552:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:552:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                   ^
ucsc/obscure.c:552:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                          ^
ucsc/obscure.c:552:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                                 ^
ucsc/obscure.c:552:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:558:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                   ^
ucsc/obscure.c:558:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                          ^
ucsc/obscure.c:558:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld", thousands, l);
                ^~~~~~~~~~~~~
ucsc/obscure.c:558:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                   ^
ucsc/obscure.c:558:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                          ^
ucsc/obscure.c:558:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld", thousands, l);
                ^~~~~~~~~~~~~
ucsc/obscure.c:561:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
                   ^
ucsc/obscure.c:561:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld", l);
                ^~~~~~
ucsc/obscure.c:561:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
                   ^
ucsc/obscure.c:561:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld", l);
                ^~~~~~
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:703:30: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' {aka 'long long int'} [-Wformat=]
      fprintf(stderr, "# pid=%d: %s\n", pid, line);
                             ~^         ~~~
                             %I64d
ucsc/obscure.c:703:30: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' {aka 'long long int'} [-Wformat=]
      fprintf(stderr, "# pid=%d: %s\n", pid, line);
                             ~^         ~~~
                             %I64d
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/options.c -o ucsc/options.o
ucsc/options.c: In function 'validateOption':
ucsc/options.c:49:11: warning: variable 'discardMe' set but not used [-Wunused-but-set-variable]
 long long discardMe = 0;
           ^~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/pipeline.c -o ucsc/pipeline.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_portimpl.c -o ucsc/_portimpl.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlList.c -o ucsc/sqlList.o
ucsc/sqlList.c: In function 'sqlLongLongArrayToString':
ucsc/sqlList.c:1049:31: warning: unknown conversion type character 'l' in format [-Wformat=]
     dyStringPrintf(string, "%lld,", array[i]);
                               ^
ucsc/sqlList.c:1049:28: warning: too many arguments for format [-Wformat-extra-args]
     dyStringPrintf(string, "%lld,", array[i]);
                            ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlNum.c -o ucsc/sqlNum.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/verbose.c -o ucsc/verbose.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/os.c -o ucsc/os.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CNEr.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CNEr.buildbin-libdir/CNEr/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNEr' as CNEr_1.24.0.zip
* DONE (CNEr)