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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:CNEr.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings CNEr_1.48.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/CNEr.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-29 02:55:53 UTC
* checking for file ‘CNEr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNEr’ version ‘1.48.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CNEr’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is 13.0Mb
  sub-directories of 1Mb or more:
    extdata  11.1Mb
* 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 code 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 loading without being on the library search path ... 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 ... WARNING
checkRd: (5) GRangePairs-class.Rd:58-62: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:69-72: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:73-76: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:77-85: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:86-93: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:94-98: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:99-102: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:103-106: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:115-119: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:127-133: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:141-156: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:157-160: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:161-164: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:172-175: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:176-179: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:180-187: \item in \describe must have non-empty label
checkRd: (-1) lavToPsl.Rd:22: Lost braces
    22 |     code{character}(n): file names of output \emph{psl} files. 
       |         ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GRangePairs-class.Rd: GRanges, GRangesList
  readBed.Rd: import.bed
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.23-bioc/R/site-library/CNEr/libs/CNEr.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 nor [v]sprintf. 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     296.963  9.075 307.623
plotCNEWidth   5.355  0.018   5.373
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/CNEr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL CNEr
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘CNEr’ ...
** this is package ‘CNEr’ version ‘1.48.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c R_init_CNEr.c -o R_init_CNEr.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/axt.c -o ucsc/axt.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/base64.c -o ucsc/base64.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/binRange.c -o ucsc/binRange.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bits.c -o ucsc/bits.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/chain.c -o ucsc/chain.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/common.c -o ucsc/common.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/dlist.c -o ucsc/dlist.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/dystring.c -o ucsc/dystring.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/hash.c -o ucsc/hash.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/https.c -o ucsc/https.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/intExp.c -o ucsc/intExp.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/linefile.c -o ucsc/linefile.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/localmem.c -o ucsc/localmem.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/obscure.c -o ucsc/obscure.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/verbose.c -o ucsc/verbose.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/os.c -o ucsc/os.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include   -g -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-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-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/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)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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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 6 | SKIP 1 | PASS 86 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_GRBs.R:1:1'

[ FAIL 0 | WARN 6 | SKIP 1 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
 22.219   1.045  23.239