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BioC 3.3: CHECK report for CNEr on linux2.bioconductor.org

This page was generated on 2015-10-27 12:12:32 -0400 (Tue, 27 Oct 2015).

Package 193/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.7.0
Ge Tan
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CNEr
Last Changed Rev: 109592 / Revision: 109948
Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015)
linux2.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
windows2.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNEr
Version: 1.7.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings CNEr_1.7.0.tar.gz
StartedAt: 2015-10-27 02:43:48 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 02:46:18 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 149.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CNEr.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings CNEr_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/CNEr.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ‘1.7.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CNEr’ can be installed ... [21s/20s] OK
* checking installed package size ... OK
* 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 ... OK
* 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 compiled code ... WARNING
File ‘CNEr/libs/CNEr.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘ucsc/errabort.o’
  Found ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘ucsc/errabort.o’, ‘ucsc/pipeline.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘ucsc/pipeline.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ucsc/obscure.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Objects: ‘ucsc/axt.o’, ‘ucsc/errabort.o’, ‘ucsc/obscure.o’,
      ‘ucsc/verbose.o’, ‘ucsc/os.o’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Objects: ‘ucsc/common.o’, ‘ucsc/errabort.o’, ‘ucsc/verbose.o’,
      ‘ucsc/os.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [6s/6s]
 [6s/6s] 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
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/CNEr.Rcheck/00check.log’
for details.

CNEr.Rcheck/00install.out:

* installing *source* package ‘CNEr’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c R_init_CNEr.c -o R_init_CNEr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c utils.c -o utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ceScan.c -o ceScan.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/axt.c -o ucsc/axt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/base64.c -o ucsc/base64.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/binRange.c -o ucsc/binRange.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/bits.c -o ucsc/bits.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/chain.c -o ucsc/chain.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/common.c -o ucsc/common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/dlist.c -o ucsc/dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/dnautil.c -o ucsc/dnautil.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/dystring.c -o ucsc/dystring.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/errabort.c -o ucsc/errabort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/hash.c -o ucsc/hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/https.c -o ucsc/https.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/intExp.c -o ucsc/intExp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/linefile.c -o ucsc/linefile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/localmem.c -o ucsc/localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/obscure.c -o ucsc/obscure.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/options.c -o ucsc/options.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/verbose.c -o ucsc/verbose.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/os.c -o ucsc/os.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-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-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/CNEr.Rcheck/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)

CNEr.Rcheck/CNEr-Ex.timings:

nameusersystemelapsed
Axt-util0.0410.0040.045
CNE-class0.0010.0000.001
CNEDensity0.3440.0120.357
CNEHg19DanRer70.0170.0000.017
axisTrack0.0040.0000.004
axt-class0.0000.0030.001
axtDanRer7Hg190.0030.0010.006
axtInfo000
binner0.0010.0000.001
blatCNE0.0010.0000.000
ceScan-methods0.0010.0000.000
cneBlatedDanRer7Hg190.0160.0000.016
cneHg19DanRer7_45_500.0030.0000.003
cneMerge0.3720.0110.384
fetchChromSizes0.0250.0041.365
finalCNE0.0030.0000.002
qSizesDanRer70.0050.0000.005
readAxt000
readBed0.0170.0000.017
readCNERangesFromSQLite0.0090.0000.009
reverseCigar0.0020.0000.001
saveCNEToSQLite0.0990.0080.107
subAxt-methods0.0010.0000.000
writeAxt0.0000.0000.001