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BioC 3.4: CHECK report for CNEr on zin1

This page was generated on 2016-09-21 03:38:47 -0700 (Wed, 21 Sep 2016).

Package 221/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.9.39
Ge Tan
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CNEr
Last Changed Rev: 120860 / Revision: 121152
Last Changed Date: 2016-09-12 07:04:22 -0700 (Mon, 12 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNEr
Version: 1.9.39
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CNEr_1.9.39.tar.gz
StartedAt: 2016-09-20 04:42:05 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:46:19 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 254.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CNEr.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CNEr_1.9.39.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/CNEr.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.9.39’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 18.2Mb
  sub-directories of 1Mb or more:
    extdata  15.9Mb
    libs      1.1Mb
* 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 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 ... 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
makeGRBs       23.004  6.196  29.270
makeCNEDensity 16.340  0.144  16.484
plotCNEWidth   10.396  0.104  10.500
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/CNEr.Rcheck/00check.log’
for details.

CNEr.Rcheck/00install.out:

* installing *source* package ‘CNEr’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c R_init_CNEr.c -o R_init_CNEr.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/axt.c -o ucsc/axt.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/chain.c -o ucsc/chain.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/errabort.c -o ucsc/errabort.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/https.c -o ucsc/https.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/intExp.c -o ucsc/intExp.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/os.c -o ucsc/os.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -shared -L/home/biocbuild/bbs-3.4-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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/CNEr.Rcheck/CNEr/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘CNEr’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNEr)

CNEr.Rcheck/CNEr-Ex.timings:

nameusersystemelapsed
AssemblyStats0.0120.0000.212
Axt-class0.4280.0080.437
Axt-util0.0280.0000.027
CNE-class0.1360.0040.137
CNEDanRer10Hg380.0120.0000.011
CNEDensity0.5800.0000.579
GRangePairs-class0.3400.0000.339
axisTrack0.0040.0000.004
axtChain0.0000.0000.001
axtInfo0.0040.0000.001
binner0.0040.0000.002
blatCNE0.0000.0000.001
ceScan-methods0.4280.0241.051
chainMergeSort0.0000.0000.001
chainNetSyntenic000
chainPreNet0.0000.0000.001
cneFinalListDanRer10Hg380.0280.0000.027
cneMerge0.3680.0000.369
fetchChromSizes000
fixCoordinates0.4040.0040.408
grangesPairsForDotplot0.0040.0000.002
last0.0000.0000.001
lastz000
lavToPsl0.0000.0000.001
makeAncoraFiles0.0360.0000.034
makeCNEDensity16.340 0.14416.484
makeGRBs23.004 6.19629.270
matchDistribution0.2240.0000.222
netToAxt0.0000.0000.001
plotCNEDistribution0.5640.0040.567
plotCNEWidth10.396 0.10410.500
psubAxt0.3360.0040.336
read.rmMask.GRanges0.0280.0000.048
readAncora0.0480.0040.051
readAncoraIntoSQLite0.8680.0080.875
readAxt0.0320.0000.032
readBed0.0120.0000.013
readCNERangesFromSQLite0.0560.0040.063
reverseCigar0.0000.0000.002
saveCNEToSQLite0.1440.0000.141
scoringMatrix0.0000.0000.001
subAxt-methods0.8520.0000.849
syntenicDotplot1.0640.0881.597
writeAxt0.0280.0000.026