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This page was generated on 2024-05-15 13:46:29 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 378/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.41.0  (landing page)
Ge Tan
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/CNEr
git_branch: devel
git_last_commit: cd329da
git_last_commit_date: 2024-04-30 10:35:00 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

INSTALL results for CNEr on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: CNEr
Version: 1.40.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL CNEr
StartedAt: 2024-05-08 20:23:24 -0000 (Wed, 08 May 2024)
EndedAt: 2024-05-08 20:24:36 -0000 (Wed, 08 May 2024)
EllapsedTime: 71.6 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL CNEr
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘CNEr’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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]
   50 |   int _binNextShift = binNextShift();
      |       ^~~~~~~~~~~~~
utils.c:49:7: warning: unused variable ‘_binFirstShift’ [-Wunused-variable]
   49 |   int _binFirstShift = binFirstShift();
      |       ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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]
   94 |   struct axt *axt=NULL, *curAxt;
      |                          ^~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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]
  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"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/axt.c -o ucsc/axt.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/chain.c -o ucsc/chain.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/common.c -o ucsc/common.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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]
  942 | int pastPoly = 0;
      |     ^~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -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"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/https.c -o ucsc/https.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/intExp.c -o ucsc/intExp.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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]
   49 | long long discardMe = 0;
      |           ^~~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/os.c -o ucsc/os.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-CNEr/00new/CNEr/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CNEr)