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BioC 3.5: INSTALL report for CNEr on malbec2

This page was generated on 2017-10-18 14:15:41 -0400 (Wed, 18 Oct 2017).

Package 244/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.12.1
Ge Tan
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/CNEr
Branch: RELEASE_3_5
Last Commit: 90d611f
Last Changed Date: 2017-07-09 14:57:38 -0400 (Sun, 09 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64 [ OK ] OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNEr
Version: 1.12.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD INSTALL CNEr
StartedAt: 2017-10-17 18:06:10 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 18:06:45 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 34.7 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD INSTALL CNEr
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.5-bioc/R/library’
* installing *source* package ‘CNEr’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c R_init_CNEr.c -o R_init_CNEr.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -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();
       ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -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;
                          ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -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);
       ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/axt.c -o ucsc/axt.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/chain.c -o ucsc/chain.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function ‘byteSwap64’:
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[0] = u.bytes[7];
                     ^
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[1] = u.bytes[6];
                     ^
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[2] = u.bytes[5];
                     ^
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[3] = u.bytes[4];
                     ^
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[4] = u.bytes[3];
        ^
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[5] = u.bytes[2];
        ^
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[6] = u.bytes[1];
        ^
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[7] = u.bytes[0];
        ^
ucsc/common.c: In function ‘byteSwapDouble’:
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[0] = u.bytes[7];
                     ^
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[1] = u.bytes[6];
                     ^
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[2] = u.bytes[5];
                     ^
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[3] = u.bytes[4];
                     ^
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[4] = u.bytes[3];
        ^
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[5] = u.bytes[2];
        ^
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[6] = u.bytes[1];
        ^
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[7] = u.bytes[0];
        ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -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;
     ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/errabort.c -o ucsc/errabort.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/https.c -o ucsc/https.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/intExp.c -o ucsc/intExp.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -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;
           ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/os.c -o ucsc/os.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o CNEr.so 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 -lz -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/R/library/CNEr/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNEr)