##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNEr.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CNEr_1.31.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CNEr.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNEr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNEr' version '1.31.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CNEr' can be installed ... WARNING
Found the following significant warnings:
  ucsc/cirTree.c:234:12: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:315:16: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:330:18: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2442:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2453:11: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2455:11: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2596:13: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2598:11: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2618:16: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2745:18: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3211:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3220:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3236:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3245:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:89:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:92:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:112:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:115:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:137:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:159:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:185:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:188:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:316:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:319:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:358:18: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:361:18: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:544:16: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:552:16: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:558:16: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:561:16: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/sqlList.c:1049:28: warning: too many arguments for format [-Wformat-extra-args]
See 'D:/biocbuild/bbs-3.15-bioc/meat/CNEr.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 17.8Mb
  sub-directories of 1Mb or more:
    extdata  15.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'S4Vectors:::make_zero_col_DataFrame'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/CNEr/libs/x64/CNEr.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
makeGRBs        221.67  13.08  234.89
plotCNEWidth      8.78   0.84    9.63
syntenicDotplot   4.41   0.24    6.30
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/CNEr.Rcheck/00check.log'
for details.

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


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CNEr' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c R_init_CNEr.c -o R_init_CNEr.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/axt.c -o ucsc/axt.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/base64.c -o ucsc/base64.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/binRange.c -o ucsc/binRange.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/bits.c -o ucsc/bits.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/chain.c -o ucsc/chain.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c: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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c: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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/dlist.c -o ucsc/dlist.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/dystring.c -o ucsc/dystring.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/hash.c -o ucsc/hash.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/https.c -o ucsc/https.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/intExp.c -o ucsc/intExp.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/kxTok.c -o ucsc/kxTok.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:35: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
                                   ^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c: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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c: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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/pipeline.c -o ucsc/pipeline.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/sqlList.c -o ucsc/sqlList.o
ucsc/sqlList.c: In function 'sqlLongLongArrayToString':
ucsc/sqlList.c: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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/verbose.c -o ucsc/verbose.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/os.c -o ucsc/os.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -g   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/rtools40/mingw64/bin/gcc -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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-CNEr/00new/CNEr/libs/x64
** 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
* DONE (CNEr)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'roar' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CNEr)

> 
> test_check("CNEr")
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 352
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 86 ]

== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
  23.35    1.12   24.43