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BioC 3.1: CHECK report for rtracklayer on zin2

This page was generated on 2015-10-09 09:23:35 -0700 (Fri, 09 Oct 2015).

Package 861/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rtracklayer 1.28.10
Michael Lawrence
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/rtracklayer
Last Changed Rev: 108005 / Revision: 109384
Last Changed Date: 2015-09-01 12:48:52 -0700 (Tue, 01 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: rtracklayer
Version: 1.28.10
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings rtracklayer_1.28.10.tar.gz
StartedAt: 2015-10-09 05:14:45 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 05:17:37 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 171.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: rtracklayer.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings rtracklayer_1.28.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/rtracklayer.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rtracklayer/DESCRIPTION’ ... OK
* this is package ‘rtracklayer’ version ‘1.28.10’
* 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 ... [22s/22s] 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::labeledLine’ ‘BiocGenerics:::testPackage’
  ‘GenomicRanges:::INVALID.GR.COLNAMES’
  ‘S4Vectors:::make_XYZxyz_to_XxYyZz_subscript’
  ‘S4Vectors:::new_SimpleList_from_list’
  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 ... NOTE
import,BEDFile-ANY-ANY : .local: warning in rgb(cols[1, ], cols[2, ],
  cols[3, ], max = 255): partial argument match of 'max' to
  'maxColorValue'
export,GenomicRanges-GFFFile-ANY : .local: no visible global function
  definition for ‘package.version’
getSeq,TwoBitFile : .local: no visible binding for global variable
  ‘con’
intersectTrack<-,UCSCTableQuery : .local: possible error in
  normArgTrack(value, x, TRUE): unused argument (TRUE)
* 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 ‘rtracklayer/libs/rtracklayer.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
    Object: ‘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 ‘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/errAbort.o’, ‘ucsc/obscure.o’, ‘ucsc/pipeline.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, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
BigWigFile 7.164  1.741   8.929
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘rtracklayer_unit_tests.R’ [31s/31s]
 [31s/32s] 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-3.1-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.

rtracklayer.Rcheck/00install.out:

* installing *source* package ‘rtracklayer’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c bigWig.c -o bigWig.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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]
         fgets(linebuf, LINEBUF_SIZE, stream); /* skip empty line */
              ^
chain_io.c:116:24: warning: ‘header_line’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         IntAE_insert_at(&block->length, IntAE_get_nelt(&block->length),
                        ^
chain_io.c:101:54: warning: ‘block’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       IntAE_insert_at(&block->offset, IntAE_get_nelt(&block->offset),
                                                      ^
chain_io.c:110:12: warning: ‘qrc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (qrc)
            ^
chain_io.c:106:12: warning: ‘trc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (trc) /* width already subtracted above */
            ^
chain_io.c:98:14: warning: ‘qstart’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       qstart -= (qrc ? width : 0);
              ^
chain_io.c:97:14: warning: ‘tstart’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       tstart -= (trc ? width : 0);
              ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c twoBit.c -o twoBit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c handlers.c -o handlers.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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]
   SEXP ans;
        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function ‘bptDataStart’:
ucsc/bPlusTree.c:286:12: warning: variable ‘childCount’ set but not used [-Wunused-but-set-variable]
     bits16 childCount;
            ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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:748:34: warning: variable ‘chromEnd’ set but not used [-Wunused-but-set-variable]
      bits32 chromId, chromStart, chromEnd;
                                  ^
ucsc/bbiRead.c:748:22: warning: variable ‘chromStart’ set but not used [-Wunused-but-set-variable]
      bits32 chromId, chromStart, chromEnd;
                      ^
ucsc/bbiRead.c:748:13: warning: variable ‘chromId’ set but not used [-Wunused-but-set-variable]
      bits32 chromId, chromStart, chromEnd;
             ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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:187:18: warning: variable ‘blockEnd’ set but not used [-Wunused-but-set-variable]
  char *blockPt, *blockEnd;
                  ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/common.c -o ucsc/common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function ‘reverseComplementSlashSeparated’:
ucsc/dnautil.c:496:5: warning: implicit declaration of function ‘isAllNt’ [-Wimplicit-function-declaration]
     if (isAllNt(allele, alLen))
     ^
ucsc/dnautil.c: In function ‘findHeadPolyTMaybeMask’:
ucsc/dnautil.c:977:5: warning: variable ‘pastPoly’ set but not used [-Wunused-but-set-variable]
 int pastPoly = 0;
     ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function ‘getThreadVars’:
ucsc/errAbort.c:331:10: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
     write(STDERR_FILENO, errMsg, strlen(errMsg)); 
          ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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:570:8: warning: variable ‘reserved64’ set but not used [-Wunused-but-set-variable]
 bits64 reserved64;
        ^
ucsc/udc.c:569:8: warning: variable ‘reserved32’ set but not used [-Wunused-but-set-variable]
 bits32 reserved32;
        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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:1448:8: warning: variable ‘version’ set but not used [-Wunused-but-set-variable]
  char *version, *code;
        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include"  -g -fpic  -g -O2  -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o rtracklayer.so S4Vectors_stubs.o 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-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/rtracklayer.Rcheck/rtracklayer/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (rtracklayer)

rtracklayer.Rcheck/rtracklayer-Ex.timings:

nameusersystemelapsed
BEDFile-class1.6970.0391.738
BamFile-methods0.1360.0000.137
BigWigFile7.1641.7418.929
BigWigSelection-class0.020.000.02
GFFFile-class1.2910.0001.292
GenomicSelection0.1380.0000.138
Quickload-class0.1360.0230.172
QuickloadGenome-class0.1480.0050.151
RangedData-methods0.1750.0040.179
TwoBitFile-class0.0420.0050.046
UCSCSchema-class0.0010.0000.001
UCSCTableQuery-class0.0010.0000.001
WIGFile-class0.7470.0000.760
asBED000
asGFF0.0010.0000.000
browseGenome0.0000.0000.001
browserView-methods000
browserViews-methods0.0010.0000.001
cpneTrack0.3030.0070.312
export0.0480.0010.048
layTrack-methods0.0010.0000.001
liftOver000
targets0.0620.0030.066
ucscGenomes0.0570.0090.173
ucscTrackModes-methods0.0100.0000.011