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

CHECK 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: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNEr.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CNEr_1.33.0.tar.gz
StartedAt: 2022-08-11 00:27:15 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 00:36:02 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 527.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CNEr.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNEr.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CNEr_1.33.0.tar.gz
###
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##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/CNEr.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CNEr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNEr' version '1.33.0'
* 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/common.c:2846:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
  ucsc/common.c:2847:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
  ucsc/common.c:2848:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
  ucsc/common.c:2849:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
  ucsc/common.c:2980:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
  ucsc/common.c:2981:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
  ucsc/common.c:2982:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
  ucsc/common.c:2983:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds]
  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/sqlList.c:1049:28: warning: too many arguments for format [-Wformat-extra-args]
See 'F:/biocbuild/bbs-3.16-bioc/meat/CNEr.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 17.5Mb
  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 'F:/biocbuild/bbs-3.16-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 '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     211.05   2.16  213.45
plotCNEWidth   7.72   0.48    8.21
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/CNEr.Rcheck/00check.log'
for details.



Installation output

CNEr.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/CNEr_1.33.0.tar.gz && 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 && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL CNEr_1.33.0.zip && rm CNEr_1.33.0.tar.gz CNEr_1.33.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 84 9022k   84 7607k    0     0  10.1M      0 --:--:-- --:--:-- --:--:-- 10.1M
100 9022k  100 9022k    0     0  10.5M      0 --:--:-- --:--:-- --:--:-- 10.6M
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)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'CNEr' successfully unpacked and MD5 sums checked

Tests output

CNEr.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> 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 
  24.60    1.15   25.93 

Example timings

CNEr.Rcheck/CNEr-Ex.timings

nameusersystemelapsed
AssemblyStats0.000.030.13
Axt-class0.830.030.87
Axt-util0.070.020.09
CNE-class0.190.010.20
CNEDanRer10Hg380.020.000.02
CNEDensity0.580.020.67
GRangePairs-class0.610.040.67
addAncestorGO000
axisTrack0.010.000.02
axtChain000
axtInfo000
binner000
blatCNE000
ceScan-methods1.720.181.89
chainMergeSort000
chainNetSyntenic000
chainPreNet000
cneFinalListDanRer10Hg380.020.010.03
cneMerge0.680.000.69
fetchChromSizes000
fixCoordinates0.710.000.70
grangesPairsForDotplot000
last000
lastz000
lavToPsl000
makeAncoraFiles0.060.000.06
makeAxtTracks1.330.031.36
makeCNEDensity000
makeGRBs211.05 2.16213.45
matchDistribution0.310.030.47
netToAxt000
orgKEGGIds2EntrezIDs000
plotCNEDistribution0.740.020.80
plotCNEWidth7.720.488.21
psubAxt0.390.020.42
read.rmMask.GRanges0.050.000.05
read.rmskFasta0.030.000.03
readAncora0.080.000.09
readAncoraIntoSQLite1.120.041.20
readAxt0.110.000.11
readBed0.090.000.11
readCNERangesFromSQLite0.110.000.11
reverseCigar000
saveCNEToSQLite0.130.020.17
scoringMatrix000
subAxt-methods0.890.030.92
syntenicDotplot4.200.134.74
writeAxt0.060.000.06