Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-11 11:06:25 -0400 (Thu, 11 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4375
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4159
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4165
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for CNEr on palomino4


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

raw results

Package 354/2139HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.33.0  (landing page)
Ge Tan
Snapshot Date: 2022-08-10 14:00:02 -0400 (Wed, 10 Aug 2022)
git_url: https://git.bioconductor.org/packages/CNEr
git_branch: master
git_last_commit: a9829eb
git_last_commit_date: 2022-04-26 11:17:50 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CNEr
Version: 1.33.0
Command: rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNEr.buildbin-libdir CNEr_1.33.0.tar.gz
StartedAt: 2022-08-11 07:39:23 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 07:40:48 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 84.9 seconds
RetCode: 0
Status:   OK  
PackageFile: CNEr_1.33.0.zip
PackageFileSize: 10.07 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNEr.buildbin-libdir CNEr_1.33.0.tar.gz
###
##############################################################################
##############################################################################


only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'CNEr' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_CNEr.c -o R_init_CNEr.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
   50 |   int _binNextShift = binNextShift();
      |       ^~~~~~~~~~~~~
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
   49 |   int _binFirstShift = binFirstShift();
      |       ^~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
   94 |   struct axt *axt=NULL, *curAxt;
      |                          ^~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  615 |   char rest, path[PATH_LEN];
      |        ^~~~
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
  613 |   int i, n;
      |          ^
ceScan.c: In function 'freeSlThreshold':
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
  674 |   struct slCNE *CNE, *nextCNE, *el_CNE;
      |                 ^~~
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
  673 |   struct slThreshold *thresholds, *nextThreshold, *el_threshold;
      |                       ^~~~~~~~~~
ceScan.c: In function 'myCeScan':
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
  868 |   int nrCNE[nrThresholds], i;
      |                            ^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable]
  868 |   int nrCNE[nrThresholds], i;
      |       ^~~~~
ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable]
  865 |   struct slCNE *CNE;
      |                 ^~~
ceScan.c: In function 'myCeScanFile':
ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
  898 |   int nrThresholds = GET_LENGTH(winSize);
      |       ^~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/axt.c -o ucsc/axt.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/base64.c -o ucsc/base64.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/binRange.c -o ucsc/binRange.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/bits.c -o ucsc/bits.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/chain.c -o ucsc/chain.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
  234 | 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]
  234 | 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=]
  315 |     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]
  315 |     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=]
  330 |         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=]
  330 |         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=]
  330 |         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
      |                                                                       ~^           ~~~~~~~~~~~~~~~~
      |                                                                        |           |
      |                                                                        int         long long unsigned int
      |                                                                       %I64d
ucsc/cirTree.c:330:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
  330 |         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
      |                                                                             ~^                       ~~~~~~~~~~~~~~~~~
      |                                                                              |                                   |
      |                                                                              char *                              long long unsigned int
      |                                                                             %I64d
ucsc/cirTree.c:330:18: warning: too many arguments for format [-Wformat-extra-args]
  330 |         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
 2442 |     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=]
 2442 |     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
      |                                         ~^     ~~~~~~~~~~~~~~~
      |                                          |     |
      |                                          |     long long int
      |                                          char *
      |                                         %I64d
ucsc/common.c:2442:14: warning: too many arguments for format [-Wformat-extra-args]
 2442 |     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=]
 2453 |  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=]
 2453 |  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
      |                                      ~^   ~~~~~~~~~~~~~~~
      |                                       |   |
      |                                       |   long long int
      |                                       char *
      |                                      %I64d
ucsc/common.c:2453:11: warning: too many arguments for format [-Wformat-extra-args]
 2453 |  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=]
 2455 |  errAbort("End of file reading %lld bytes", (long long)size);
      |                                  ^
ucsc/common.c:2455:11: warning: too many arguments for format [-Wformat-extra-args]
 2455 |  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=]
 2596 |  errnoAbort("Error reading %lld bytes", (long long)size);
      |                              ^
ucsc/common.c:2596:13: warning: too many arguments for format [-Wformat-extra-args]
 2596 |  errnoAbort("Error reading %lld bytes", (long long)size);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2598:34: warning: unknown conversion type character 'l' in format [-Wformat=]
 2598 |  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=]
 2598 |  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]
 2598 |  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=]
 2618 |     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=]
 2618 |     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
      |                                 ~^                    ~~~~~~~~~~~~~~~~~
      |                                  |                    |
      |                                  char *               long long int
      |                                 %I64d
ucsc/common.c:2618:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
 2618 |     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
      |                                     ~^
      |                                      |
      |                                      int
      |                                     %s
 2619 |         ((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            char *
 2620 |   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2618:16: warning: too many arguments for format [-Wformat-extra-args]
 2618 |     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=]
 2745 |         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=]
 2745 |         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]
 2745 |         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=]
 3211 |     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=]
 3211 |     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]
 3211 |     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=]
 3220 |     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=]
 3220 |     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]
 3220 |     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=]
 3236 |     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=]
 3236 |     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]
 3236 |     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=]
 3245 |     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=]
 3245 |     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]
 3245 |     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'byteSwap64':
ucsc/common.c:2846:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2846 | v.bytes[4] = u.bytes[3];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2847:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2847 | v.bytes[5] = u.bytes[2];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2848:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2848 | v.bytes[6] = u.bytes[1];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2849:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2849 | v.bytes[7] = u.bytes[0];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c: In function 'readBits64':
ucsc/common.c:2846:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2846 | v.bytes[4] = u.bytes[3];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2847:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2847 | v.bytes[5] = u.bytes[2];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2848:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2848 | v.bytes[6] = u.bytes[1];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2849:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2849 | v.bytes[7] = u.bytes[0];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c: In function 'fdReadBits64':
ucsc/common.c:2846:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2846 | v.bytes[4] = u.bytes[3];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2847:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2847 | v.bytes[5] = u.bytes[2];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2848:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2848 | v.bytes[6] = u.bytes[1];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2849:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2849 | v.bytes[7] = u.bytes[0];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c: In function 'memReadBits64':
ucsc/common.c:2846:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2846 | v.bytes[4] = u.bytes[3];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2847:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2847 | v.bytes[5] = u.bytes[2];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2848:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2848 | v.bytes[6] = u.bytes[1];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2849:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2849 | v.bytes[7] = u.bytes[0];
      | ~~~~~~~^~~
ucsc/common.c:2840:28: note: while referencing 'bytes'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2840:41: note: defined here 'v'
 2840 | union {bits64 whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c: In function 'byteSwapDouble':
ucsc/common.c:2980:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2980 | v.bytes[4] = u.bytes[3];
      | ~~~~~~~^~~
ucsc/common.c:2974:28: note: while referencing 'bytes'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2974:41: note: defined here 'v'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2981:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2981 | v.bytes[5] = u.bytes[2];
      | ~~~~~~~^~~
ucsc/common.c:2974:28: note: while referencing 'bytes'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2974:41: note: defined here 'v'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2982:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2982 | v.bytes[6] = u.bytes[1];
      | ~~~~~~~^~~
ucsc/common.c:2974:28: note: while referencing 'bytes'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2974:41: note: defined here 'v'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2983:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2983 | v.bytes[7] = u.bytes[0];
      | ~~~~~~~^~~
ucsc/common.c:2974:28: note: while referencing 'bytes'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2974:41: note: defined here 'v'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c: In function 'readDouble':
ucsc/common.c:2980:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2980 | v.bytes[4] = u.bytes[3];
      | ~~~~~~~^~~
ucsc/common.c:2974:28: note: while referencing 'bytes'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2974:41: note: defined here 'v'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2981:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2981 | v.bytes[5] = u.bytes[2];
      | ~~~~~~~^~~
ucsc/common.c:2974:28: note: while referencing 'bytes'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2974:41: note: defined here 'v'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2982:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2982 | v.bytes[6] = u.bytes[1];
      | ~~~~~~~^~~
ucsc/common.c:2974:28: note: while referencing 'bytes'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2974:41: note: defined here 'v'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2983:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2983 | v.bytes[7] = u.bytes[0];
      | ~~~~~~~^~~
ucsc/common.c:2974:28: note: while referencing 'bytes'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2974:41: note: defined here 'v'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c: In function 'memReadDouble':
ucsc/common.c:2980:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2980 | v.bytes[4] = u.bytes[3];
      | ~~~~~~~^~~
ucsc/common.c:2974:28: note: while referencing 'bytes'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2974:41: note: defined here 'v'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2981:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2981 | v.bytes[5] = u.bytes[2];
      | ~~~~~~~^~~
ucsc/common.c:2974:28: note: while referencing 'bytes'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2974:41: note: defined here 'v'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2982:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2982 | v.bytes[6] = u.bytes[1];
      | ~~~~~~~^~~
ucsc/common.c:2974:28: note: while referencing 'bytes'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2974:41: note: defined here 'v'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                                         ^
ucsc/common.c:2983:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
 2983 | v.bytes[7] = u.bytes[0];
      | ~~~~~~~^~~
ucsc/common.c:2974:28: note: while referencing 'bytes'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                            ^~~~~
ucsc/common.c:2974:41: note: defined here 'v'
 2974 | union {double whole; UBYTE bytes[4];} u,v;
      |                                         ^
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/dlist.c -o ucsc/dlist.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  942 | int pastPoly = 0;
      |     ^~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/dystring.c -o ucsc/dystring.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
   30 | static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $";
      |                   ^~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/hash.c -o ucsc/hash.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/https.c -o ucsc/https.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/intExp.c -o ucsc/intExp.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  100 | static char * headerBytes(char *fileName, int numbytes)
      |               ^~~~~~~~~~~
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
   32 | static char **getDecompressor(char *fileName)
      |               ^~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
   38 |     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
      |                                   ^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
   38 |     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
   89 |     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
      |                                                  ^
ucsc/memalloc.c:89:69: warning: unknown conversion type character 'l' in format [-Wformat=]
   89 |     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
      |                                                                     ^
ucsc/memalloc.c:89:14: warning: too many arguments for format [-Wformat-extra-args]
   89 |     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:92:60: warning: unknown conversion type character 'l' in format [-Wformat=]
   92 |     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=]
   92 |     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
      |                                                                             ~^
      |                                                                              |
      |                                                                              int
      |                                                                             %I64d
   93 |              (unsigned long long)size, errno);
      |              ~~~~~~~~~~~~~~~~~~~~~~~~                                         
      |              |
      |              long long unsigned int
ucsc/memalloc.c:92:14: warning: too many arguments for format [-Wformat-extra-args]
   92 |     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=]
  112 |     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
      |                                                        ^
ucsc/memalloc.c:112:75: warning: unknown conversion type character 'l' in format [-Wformat=]
  112 |     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
      |                                                                           ^
ucsc/memalloc.c:112:14: warning: too many arguments for format [-Wformat-extra-args]
  112 |     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:115:66: warning: unknown conversion type character 'l' in format [-Wformat=]
  115 |     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=]
  115 |     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
      |                                                                                   ~^
      |                                                                                    |
      |                                                                                    int
      |                                                                                   %I64d
  116 |              (unsigned long long)size, errno);
      |              ~~~~~~~~~~~~~~~~~~~~~~~~                                               
      |              |
      |              long long unsigned int
ucsc/memalloc.c:115:14: warning: too many arguments for format [-Wformat-extra-args]
  115 |     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=]
  137 |     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=]
  137 |     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
      |                                                                                 ~^
      |                                                                                  |
      |                                                                                  int
      |                                                                                 %I64d
  138 |              (unsigned long long)size, errno);
      |              ~~~~~~~~~~~~~~~~~~~~~~~~                                             
      |              |
      |              long long unsigned int
ucsc/memalloc.c:137:14: warning: too many arguments for format [-Wformat-extra-args]
  137 |     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=]
  159 |     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=]
  159 |     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
      |                                                                                    ~^
      |                                                                                     |
      |                                                                                     int
      |                                                                                    %I64d
  160 |  (unsigned long long)size, errno);
      |  ~~~~~~~~~~~~~~~~~~~~~~~~                                                            
      |  |
      |  long long unsigned int
ucsc/memalloc.c:159:14: warning: too many arguments for format [-Wformat-extra-args]
  159 |     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=]
  185 |     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
      |                                             ^
ucsc/memalloc.c:185:64: warning: unknown conversion type character 'l' in format [-Wformat=]
  185 |     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
      |                                                                ^
ucsc/memalloc.c:185:14: warning: too many arguments for format [-Wformat-extra-args]
  185 |     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:188:55: warning: unknown conversion type character 'l' in format [-Wformat=]
  188 |     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=]
  188 |     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
      |                                                                        ~^
      |                                                                         |
      |                                                                         int
      |                                                                        %I64d
  189 |              (unsigned long long)size, errno);
      |              ~~~~~~~~~~~~~~~~~~~~~~~~                                    
      |              |
      |              long long unsigned int
ucsc/memalloc.c:188:14: warning: too many arguments for format [-Wformat-extra-args]
  188 |     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=]
  316 |     errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
      |                                             ^
ucsc/memalloc.c:316:14: warning: too many arguments for format [-Wformat-extra-args]
  316 |     errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:319:49: warning: unknown conversion type character 'l' in format [-Wformat=]
  319 |     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]
  319 |     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=]
  358 |         errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie,
      |                                                  ^
ucsc/memalloc.c:358:18: warning: too many arguments for format [-Wformat-extra-args]
  358 |         errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie,
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:361:54: warning: unknown conversion type character 'l' in format [-Wformat=]
  361 |         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]
  361 |         errAbort("Bad end cookie %x%x%x%x checking %llx\n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:703:30: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' {aka 'long long int'} [-Wformat=]
  703 |      fprintf(stderr, "# pid=%d: %s\n", pid, line);
      |                             ~^         ~~~
      |                              |         |
      |                              int       pid_t {aka long long int}
      |                             %lld
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
   49 | long long discardMe = 0;
      |           ^~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
 1049 |     dyStringPrintf(string, "%lld,", array[i]);
      |                               ^
ucsc/sqlList.c:1049:28: warning: too many arguments for format [-Wformat-extra-args]
 1049 |     dyStringPrintf(string, "%lld,", array[i]);
      |                            ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/verbose.c -o ucsc/verbose.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/os.c -o ucsc/os.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/CNEr.buildbin-libdir/00LOCK-CNEr/00new/CNEr/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'CNEr' as CNEr_1.33.0.zip
* DONE (CNEr)