| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L M N O P Q [R] S T U V W X Y Z |
| Package 486/565 | Hostname | OS / Arch | BUILD | CHECK | BUILD BIN | ||||
| rtracklayer 1.17.9 Michael Lawrence
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | WARNINGS | |||||
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK | |||||
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK | |||||
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
| Package: rtracklayer |
| Version: 1.17.9 |
| Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rtracklayer_1.17.9.tar.gz |
| StartedAt: 2012-06-21 03:27:47 -0700 (Thu, 21 Jun 2012) |
| EndedAt: 2012-06-21 03:33:57 -0700 (Thu, 21 Jun 2012) |
| EllapsedTime: 370.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rtracklayer.Rcheck |
| Warnings: 3 |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/rtracklayer.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'rtracklayer/DESCRIPTION' ... OK
* this is package 'rtracklayer' version '1.17.9'
* 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 whether package 'rtracklayer' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'export' and siglist 'ANY,BamFile,ANY'
generic 'export' and siglist 'GappedAlignments,BamFile,ANY'
generic 'genome' and siglist 'GFFFile'
generic 'import' and siglist 'BamFile,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'BEDFile-class':
\S4method{import}{BEDFile,ANY,ANY}
Code: function(con, format, text, trackLine = TRUE, genome = NA,
asRangedData = TRUE, colnames = NULL, which = NULL,
seqinfo = NULL, extraCols = character())
Docs: function(con, format, text, trackLine = TRUE, genome = NA,
asRangedData = TRUE, colnames = NULL, which = NULL,
seqinfo = NULL)
Argument names in code not in docs:
extraCols
Codoc mismatches from documentation object 'TabixFile-methods':
\S4method{import}{TabixFile,character,ANY}
Code: function(con, format, text, which = if (is.na(genome)) NULL
else as(seqinfoForGenome(genome), "GenomicRanges"),
genome = NA, header = TRUE, ...)
Docs: function(con, format, text, which =
as(seqinfoForGenome(genome), "GenomicRanges"), genome
= NA, header = TRUE, ...)
Mismatches in argument default values:
Name: 'which' Code: if (is.na(genome)) NULL else as(seqinfoForGenome(genome), "GenomicRanges") Docs: as(seqinfoForGenome(genome), "GenomicRanges")
\S4method{import}{TabixFile,missing,ANY}
Code: function(con, format, text, ...)
Docs: function(con, format, text, which =
as(seqinfoForGenome(genome), "GenomicRanges"), genome
= NA, header = TRUE, ...)
Argument names in docs not in code:
which genome header
Mismatches in argument names:
Position: 4 Code: ... Docs: which
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'TwoBitFile-class':
'\S4method{export}{DNAStringSet,character,ANY}'
'\S4method{export}{BSgenome,character,ANY}'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.11-bioc/meat/rtracklayer.Rcheck/rtracklayer/libs/i386/rtracklayer.so':
Found '___stderrp', possibly from 'stderr' (C)
Objects: 'ucsc/errabort.o', 'ucsc/obscure.o', 'ucsc/net.o',
'ucsc/verbose.o', 'ucsc/os.o'
Found '___stdoutp', possibly from 'stdout' (C)
Objects: 'ucsc/common.o', 'ucsc/errabort.o', 'ucsc/net.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: 'ucsc/pipeline.o', 'ucsc/net.o'
Found '_putchar', possibly from 'putchar' (C)
Object: 'ucsc/net.o'
Found '_puts', possibly from 'printf' (C), 'puts' (C)
Object: 'ucsc/pipeline.o'
Compiled code should not call functions 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'rtracklayer_unit_tests.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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 3 warnings.
NOTE: There was 1 note.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/rtracklayer.Rcheck/00check.log'
for details.
rtracklayer.Rcheck/00install.out:
* installing *source* package 'rtracklayer' ... ** libs *** arch - i386 gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c R_init_rtracklayer.c -o R_init_rtracklayer.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c bigWig.c -o bigWig.o bigWig.c: In function 'BWGFile_query': bigWig.c:223: warning: 'ans_score' may be used uninitialized in this function gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c chain_io.c -o chain_io.o chain_io.c: In function 'read_chain_file': chain_io.c:39: warning: 'header_line' may be used uninitialized in this function chain_io.c:36: warning: 'block' may be used uninitialized in this function chain_io.c:35: warning: 'qrc' may be used uninitialized in this function chain_io.c:35: warning: 'trc' may be used uninitialized in this function chain_io.c:34: warning: 'qstart' may be used uninitialized in this function chain_io.c:34: warning: 'tstart' may be used uninitialized in this function gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c twoBit.c -o twoBit.o twoBit.c: In function 'TwoBitFile_read': twoBit.c:111: warning: pointer targets in passing argument 3 of 'Ocopy_bytes_to_i1i2_with_lkup' differ in signedness gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c handlers.c -o handlers.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c utils.c -o utils.o utils.c: In function '_STRSXP_collapse': utils.c:4: warning: unused variable 'ans' gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o ucsc/bPlusTree.c: In function 'bptFileTraverse': ucsc/bPlusTree.c:240: warning: 'return' with a value, in function returning void gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/bbiRead.c -o ucsc/bbiRead.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/cirTree.c -o ucsc/cirTree.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/common.c -o ucsc/common.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/dnaseq.c -o ucsc/dnaseq.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/dnautil.c -o ucsc/dnautil.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/errabort.c -o ucsc/errabort.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/hash.c -o ucsc/hash.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/linefile.c -o ucsc/linefile.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/localmem.c -o ucsc/localmem.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/sqlNum.c -o ucsc/sqlNum.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/zlibFace.c -o ucsc/zlibFace.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/dystring.c -o ucsc/dystring.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/hmmstats.c -o ucsc/hmmstats.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/obscure.c -o ucsc/obscure.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/pipeline.c -o ucsc/pipeline.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/rangeTree.c -o ucsc/rangeTree.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/rbTree.c -o ucsc/rbTree.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/memalloc.c -o ucsc/memalloc.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/dlist.c -o ucsc/dlist.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/udc.c -o ucsc/udc.o ucsc/udc.c: In function 'qDecode': ucsc/udc.c:961: warning: format '%02X' expects type 'unsigned int *', but argument 3 has type 'int *' gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/net.c -o ucsc/net.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/bits.c -o ucsc/bits.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/twoBit.c -o ucsc/twoBit.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o ucsc/_cheapcgi.c: In function 'cgiDecode': ucsc/_cheapcgi.c:20: warning: format '%2x' expects type 'unsigned int *', but argument 3 has type 'int *' gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/internet.c -o ucsc/internet.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/https.c -o ucsc/https.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/base64.c -o ucsc/base64.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/verbose.c -o ucsc/verbose.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/os.c -o ucsc/os.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/wildcmp.c -o ucsc/wildcmp.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -g -fPIC -g -O2 -Wall -pedantic -c ucsc/_portimpl.c -o ucsc/_portimpl.o gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o rtracklayer.so IRanges_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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-2.11-bioc/meat/rtracklayer.Rcheck/rtracklayer/libs/i386 ** 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 'rtracklayer.Rnw' ** testing if installed package can be loaded * DONE (rtracklayer)
rtracklayer.Rcheck/rtracklayer-Ex.timings:
| name | user | system | elapsed | |
| BEDFile-class | 3.943 | 0.527 | 19.974 | |
| BigWigFile | 6.228 | 2.062 | 8.597 | |
| BigWigSelection-class | 0.038 | 0.001 | 0.041 | |
| GFFFile-class | 5.196 | 0.145 | 5.647 | |
| GenomicSelection | 0.110 | 0.003 | 0.118 | |
| Quickload-class | 0.050 | 0.003 | 0.056 | |
| QuickloadGenome-class | 0.235 | 0.007 | 0.286 | |
| RangedData-methods | 0.688 | 0.013 | 0.795 | |
| TwoBitFile-class | 0.288 | 0.003 | 0.314 | |
| UCSCSchema-class | 0 | 0 | 0 | |
| UCSCTableQuery-class | 0.000 | 0.000 | 0.001 | |
| WIGFile-class | 2.282 | 0.023 | 2.642 | |
| asBED | 0.001 | 0.000 | 0.001 | |
| asGFF | 0.000 | 0.000 | 0.001 | |
| browseGenome | 0.001 | 0.000 | 0.001 | |
| browserView-methods | 0 | 0 | 0 | |
| browserViews-methods | 0.001 | 0.000 | 0.000 | |
| cpneTrack | 0.612 | 0.060 | 0.763 | |
| export | 0.217 | 0.008 | 0.293 | |
| layTrack-methods | 0.000 | 0.001 | 0.001 | |
| liftOver | 0 | 0 | 0 | |
| targets | 0.169 | 0.010 | 0.231 | |
| ucscGenomes | 0.143 | 0.005 | 0.235 | |
| ucscTrackModes-methods | 0.020 | 0.000 | 0.044 | |