Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 388/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.42.0  (landing page)
Ge Tan
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/CNEr
git_branch: RELEASE_3_20
git_last_commit: d83a1b6
git_last_commit_date: 2024-10-29 09:50:06 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  

INSTALL results for CNEr on palomino8

To the developers/maintainers of the CNEr package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: CNEr
Version: 1.42.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CNEr
StartedAt: 2024-12-19 16:01:14 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 16:03:01 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 107.4 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CNEr
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'CNEr' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_CNEr.c -o R_init_CNEr.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/axt.c -o ucsc/axt.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/base64.c -o ucsc/base64.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/binRange.c -o ucsc/binRange.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/bits.c -o ucsc/bits.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/chain.c -o ucsc/chain.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/common.c -o ucsc/common.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/dlist.c -o ucsc/dlist.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/dystring.c -o ucsc/dystring.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/hash.c -o ucsc/hash.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/https.c -o ucsc/https.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/intExp.c -o ucsc/intExp.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/localmem.c -o ucsc/localmem.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:703:37: 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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/verbose.c -o ucsc/verbose.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ucsc/os.c -o ucsc/os.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -g   -O2 -Wall  -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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/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
* DONE (CNEr)