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BioC 2.13: CHECK report for rtracklayer on zin1

This page was generated on 2014-04-05 09:47:38 -0700 (Sat, 05 Apr 2014).

Package 634/750HostnameOS / ArchBUILDCHECKBUILD BIN
rtracklayer 1.22.7
Michael Lawrence
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/rtracklayer
Last Changed Rev: 88096 / Revision: 88450
Last Changed Date: 2014-03-28 10:08:23 -0700 (Fri, 28 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: rtracklayer
Version: 1.22.7
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings rtracklayer_1.22.7.tar.gz
StartedAt: 2014-04-05 03:48:04 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:52:18 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 253.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: rtracklayer.Rcheck
Warnings: 1

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/rtracklayer.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rtracklayer/DESCRIPTION’ ... OK
* this is package ‘rtracklayer’ version ‘1.22.7’
* 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 ‘rtracklayer’ can be installed ... [24s/26s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicRanges’
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: ‘XVector’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ‘:::’ calls:
  ‘BiocGenerics:::labeledLine’ ‘BiocGenerics:::testPackage’
  ‘GenomicRanges:::INVALID.GR.COLNAMES’ ‘IRanges:::newList’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File ‘/home/biocbuild/bbs-2.13-bioc/meat/rtracklayer.Rcheck/rtracklayer/libs/rtracklayer.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 ‘putchar’, possibly from ‘putchar’ (C)
    Object: ‘ucsc/net.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘ucsc/pipeline.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Objects: ‘ucsc/errabort.o’, ‘ucsc/obscure.o’, ‘ucsc/net.o’,
      ‘ucsc/verbose.o’, ‘ucsc/os.o’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Objects: ‘ucsc/common.o’, ‘ucsc/errabort.o’, ‘ucsc/net.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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘rtracklayer.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [21s/27s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
BigWigFile    4.536  0.896   5.454
BEDFile-class 2.452  0.132   7.571
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘rtracklayer_unit_tests.R’ [62s/66s]
 [62s/66s] 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.

rtracklayer.Rcheck/00install.out:

* installing *source* package ‘rtracklayer’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c bigWig.c -o bigWig.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c chain_io.c -o chain_io.o
chain_io.c: In function ‘read_chain_file’:
chain_io.c:119:14: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
chain_io.c:116:24: warning: ‘header_line’ may be used uninitialized in this function [-Wuninitialized]
chain_io.c:101:54: warning: ‘block’ may be used uninitialized in this function [-Wuninitialized]
chain_io.c:110:12: warning: ‘qrc’ may be used uninitialized in this function [-Wuninitialized]
chain_io.c:106:12: warning: ‘trc’ may be used uninitialized in this function [-Wuninitialized]
chain_io.c:98:14: warning: ‘qstart’ may be used uninitialized in this function [-Wuninitialized]
chain_io.c:97:14: warning: ‘tstart’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c twoBit.c -o twoBit.o
twoBit.c: In function ‘TwoBitFile_read’:
twoBit.c:111:37: warning: pointer targets in passing argument 3 of ‘Ocopy_bytes_to_i1i2_with_lkup’ differ in signedness [-Wpointer-sign]
/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include/XVector_interface.h:81:6: note: expected ‘char *’ but argument is of type ‘Rbyte *’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c handlers.c -o handlers.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘_STRSXP_collapse’:
utils.c:4:8: warning: unused variable ‘ans’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function ‘bbiTotalSummary’:
ucsc/bbiRead.c:703:34: warning: variable ‘chromEnd’ set but not used [-Wunused-but-set-variable]
ucsc/bbiRead.c:703:22: warning: variable ‘chromStart’ set but not used [-Wunused-but-set-variable]
ucsc/bbiRead.c:703:13: warning: variable ‘chromId’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function ‘bigWigIntervalQuery’:
ucsc/bwgQuery.c:186:18: warning: variable ‘blockEnd’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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:2765:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2766:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2767:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2768:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2769:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2770:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2771:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2772:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function ‘byteSwapDouble’:
ucsc/common.c:2899:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2900:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2901:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2902:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2903:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2904:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2905:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2906:8: warning: array subscript is above array bounds [-Warray-bounds]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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:943:5: warning: variable ‘pastPoly’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/errabort.c -o ucsc/errabort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function ‘udcBitmapOpen’:
ucsc/udc.c:550:8: warning: variable ‘reserved64’ set but not used [-Wunused-but-set-variable]
ucsc/udc.c:549:8: warning: variable ‘reserved32’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/net.c -o ucsc/net.o
ucsc/net.c: In function ‘netSkipHttpHeaderLinesWithRedirect’:
ucsc/net.c:1332:8: warning: variable ‘version’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/internet.c -o ucsc/internet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/https.c -o ucsc/https.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/os.c -o ucsc/os.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -std=gnu99 -shared -L/usr/local/lib -o rtracklayer.so IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errabort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/rtracklayer.Rcheck/rtracklayer/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
Creating a generic function from function ‘uri’ in package ‘rtracklayer’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rtracklayer)

rtracklayer.Rcheck/rtracklayer-Ex.timings:

nameusersystemelapsed
BEDFile-class2.4520.1327.571
BamFile-methods0.1960.0040.200
BigWigFile4.5360.8965.454
BigWigSelection-class0.0280.0040.030
GFFFile-class2.2170.1042.781
GenomicSelection0.0920.0080.099
Quickload-class0.0360.0000.036
QuickloadGenome-class0.2040.0040.210
RangedData-methods0.4960.0120.530
TwoBitFile-class0.1280.0000.141
UCSCSchema-class0.0000.0040.002
UCSCTableQuery-class0.0000.0080.008
WIGFile-class2.0320.0042.103
asBED0.0000.0000.001
asGFF0.0000.0000.001
browseGenome0.0040.0000.001
browserView-methods0.0000.0000.001
browserViews-methods0.0000.0000.001
cpneTrack0.3640.0160.379
export0.2800.0040.286
layTrack-methods0.0000.0040.002
liftOver0.0000.0040.002
targets0.060.000.06
ucscGenomes0.1120.0000.211
ucscTrackModes-methods0.0240.0000.023