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BioC 3.6: CHECK report for CNEr on veracruz1

This page was generated on 2017-08-16 13:44:57 -0400 (Wed, 16 Aug 2017).

Package 247/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.13.2
Ge Tan
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CNEr
Last Changed Rev: 131131 / Revision: 131943
Last Changed Date: 2017-07-12 08:57:21 -0400 (Wed, 12 Jul 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CNEr
Version: 1.13.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNEr_1.13.2.tar.gz
StartedAt: 2017-08-16 01:21:11 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:33:18 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 726.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CNEr.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNEr_1.13.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CNEr.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.13.2’
* 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 17.8Mb
  sub-directories of 1Mb or more:
    extdata  15.9Mb
* 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 ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘ucsc/axt.o’, ‘ucsc/errabort.o’, ‘ucsc/obscure.o’,
      ‘ucsc/verbose.o’, ‘ucsc/os.o’
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Objects: ‘ucsc/common.o’, ‘ucsc/errabort.o’, ‘ucsc/verbose.o’,
      ‘ucsc/os.o’
  Found ‘_abort’, possibly from ‘abort’ (C)
    Object: ‘ucsc/errabort.o’
  Found ‘_exit’, possibly from ‘exit’ (C)
    Objects: ‘ucsc/errabort.o’, ‘ucsc/pipeline.o’
  Found ‘_printf’, possibly from ‘printf’ (C)
    Objects: ‘ceScan.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’

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     363.207 10.172 393.562
plotCNEWidth   7.991  0.301   8.526
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/CNEr.Rcheck/00check.log’
for details.


CNEr.Rcheck/00install.out:

* installing *source* package ‘CNEr’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c R_init_CNEr.c -o R_init_CNEr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c utils.c -o utils.o
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();
      ^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c io.c -o io.o
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
  struct axt *axt=NULL, *curAxt;
                         ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ceScan.c -o ceScan.o
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:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
  struct slThreshold *thresholds, *nextThreshold, *el_threshold;
                      ^
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
  struct slCNE *CNE, *nextCNE, *el_CNE;
                ^
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:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
  int nrThresholds = GET_LENGTH(winSize);
      ^
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/axt.c -o ucsc/axt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/base64.c -o ucsc/base64.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/binRange.c -o ucsc/binRange.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/bits.c -o ucsc/bits.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/chain.c -o ucsc/chain.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c:472:16: warning: unused function 'cirTreeOverlaps' [-Wunused-function]
INLINE boolean cirTreeOverlaps(int qChrom, int qStart, int qEnd, 
               ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/common.c -o ucsc/common.o
ucsc/common.c:1982:18: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        if ((*in == '"'))
             ˜˜˜˜^˜˜˜˜˜
ucsc/common.c:1982:18: note: remove extraneous parentheses around the comparison to silence this warning
        if ((*in == '"'))
            ˜    ^     ˜
ucsc/common.c:1982:18: note: use '=' to turn this equality comparison into an assignment
        if ((*in == '"'))
                 ^˜
                 =
ucsc/common.c:2842:14: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[0] = u.bytes[7];
             ^       ˜
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2843:14: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[1] = u.bytes[6];
             ^       ˜
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2844:14: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[2] = u.bytes[5];
             ^       ˜
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2845:14: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[3] = u.bytes[4];
             ^       ˜
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2846:1: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^       ˜
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2847:1: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^       ˜
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2848:1: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^       ˜
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2849:1: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^       ˜
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2976:14: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[0] = u.bytes[7];
             ^       ˜
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2977:14: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[1] = u.bytes[6];
             ^       ˜
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2978:14: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[2] = u.bytes[5];
             ^       ˜
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2979:14: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[3] = u.bytes[4];
             ^       ˜
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2980:1: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^       ˜
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2981:1: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^       ˜
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2982:1: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^       ˜
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2983:1: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^       ˜
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
17 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/dlist.c -o ucsc/dlist.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/dnautil.c -o ucsc/dnautil.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/dystring.c -o ucsc/dystring.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/errabort.c -o ucsc/errabort.o
ucsc/errabort.c:30:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $";
                  ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/hash.c -o ucsc/hash.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/https.c -o ucsc/https.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/intExp.c -o ucsc/intExp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/kxTok.c -o ucsc/kxTok.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/linefile.c -o ucsc/linefile.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/localmem.c -o ucsc/localmem.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/memalloc.c -o ucsc/memalloc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/obscure.c -o ucsc/obscure.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/options.c -o ucsc/options.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/pipeline.c -o ucsc/pipeline.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/sqlList.c -o ucsc/sqlList.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/verbose.c -o ucsc/verbose.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/os.c -o ucsc/os.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-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
AssemblyStats0.0120.0220.059
Axt-class1.6750.0141.770
Axt-util0.0350.0000.043
CNE-class0.2850.0050.297
CNEDanRer10Hg380.0150.0030.017
CNEDensity1.1610.0131.190
GRangePairs-class0.5500.0090.578
addAncestorGO0.0010.0000.000
axisTrack0.0050.0020.007
axtChain0.0010.0000.001
axtInfo0.0020.0000.003
binner0.0040.0000.004
blatCNE0.0010.0000.001
ceScan-methods0.9700.0301.831
chainMergeSort0.0010.0000.001
chainNetSyntenic0.0010.0000.001
chainPreNet0.0010.0010.001
cneFinalListDanRer10Hg380.0230.0040.030
cneMerge0.6420.0070.665
fetchChromSizes0.0010.0000.000
fixCoordinates0.5770.0060.593
grangesPairsForDotplot0.0020.0040.005
last0.0010.0000.001
lastz0.0010.0010.001
lavToPsl0.0010.0000.001
makeAncoraFiles0.0490.0040.053
makeAxtTracks0.3260.0050.337
makeCNEDensity0.0010.0000.002
makeGRBs363.207 10.172393.562
matchDistribution1.0270.0031.067
netToAxt0.0010.0000.001
orgKEGGIds2EntrezIDs0.0000.0000.001
plotCNEDistribution1.6010.0261.671
plotCNEWidth7.9910.3018.526
psubAxt0.3520.0070.375
read.rmMask.GRanges0.0200.0010.022
read.rmskFasta0.0520.0000.054
readAncora0.0730.0000.073
readAncoraIntoSQLite1.3200.0291.418
readAxt0.0340.0040.038
readBed0.0170.0010.019
readCNERangesFromSQLite0.0740.0050.078
reverseCigar0.0020.0000.002
saveCNEToSQLite0.1250.0050.157
scoringMatrix0.0000.0010.000
subAxt-methods1.0040.0181.033
syntenicDotplot1.8180.1242.761
writeAxt0.0650.0010.067