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Package 341/658HostnameOS / ArchBUILDCHECKBUILD BIN
IRanges 1.17.41
Bioconductor Package Maintainer
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges
Last Changed Rev: 74718 / Revision: 74774
Last Changed Date: 2013-03-22 16:57:24 -0700 (Fri, 22 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: IRanges
Version: 1.17.41
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IRanges_1.17.41.tar.gz
StartedAt: 2013-03-25 03:13:02 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 03:17:29 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 267.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IRanges.Rcheck
Warnings: 3

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/IRanges.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'IRanges/DESCRIPTION' ... OK
* this is package 'IRanges' version '1.17.41'
* 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 'IRanges' can be installed ... [39s/42s] OK
* checking installed package size ... OK
* checking package 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 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 ... WARNING
Found .Internal calls in the following functions:
  'isNotSorted' 'isNotStrictlySorted'
with calls to .Internal functions
  'is.unsorted'

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'as.list.CompressedList' 'as.list.CompressedNormalIRangesList'
  'as.list.Hits' 'as.list.List' 'as.list.Rle' 'as.list.SimpleList'
  'duplicated.AtomicList' 'duplicated.DataTable' 'duplicated.Dups'
  'duplicated.Ranges' 'duplicated.Rle' 'duplicated.XRawList'
  'levels.OverlapEncodings' 'levels.Rle' 'sort.Rle' 'sort.RleList'
  'sort.Vector' 'splitAsList' 'splitAsListReturnedClass'
  'subsetByRanges' 'unique.CompressedRleList' 'unique.DataTable'
  'unique.Rle' 'unique.SimpleRleList' 'unique.Vector'
  'window.DataTable' 'window.GappedRanges' 'window.GroupedIRanges'
  'window.IRanges' 'window.NULL' 'window.Rle' 'window.Vector'
  'window.XVector' 'window.XVectorList' 'window.factor' 'window.vector'
  'window<-.DataTable' 'window<-.RangedData' 'window<-.Vector'
  'window<-.factor' 'window<-.vector'
Undocumented S4 methods:
  generic '<=' and siglist 'XRawList,XRawList'
  generic '==' and siglist 'XRawList,XRawList'
  generic 'Ops' and siglist 'SimpleAtomicList,atomic'
  generic 'Ops' and siglist 'atomic,SimpleAtomicList'
  generic '[[<-' and siglist 'SharedRaw_Pool'
  generic 'coerce' and siglist 'ANY,DataFrame'
  generic 'compare' and siglist 'XRawList,XRawList'
  generic 'duplicated' and siglist 'Rle'
  generic 'duplicated' and siglist 'XRawList'
  generic 'elementLengths' and siglist 'XVectorList'
  generic 'is.unsorted' and siglist 'XRawList'
  generic 'match' and siglist 'XRawList,XRawList'
  generic 'mstack' and siglist 'DataFrame'
  generic 'order' and siglist 'XRawList'
  generic 'rank' and siglist 'XRawList'
  generic 'relist' and siglist 'ANY,PartitioningByEnd'
  generic 'relist' and siglist 'Vector,list'
  generic 'splitAsListReturnedClass' and siglist 'ANY'
  generic 'splitAsListReturnedClass' and siglist 'DataFrame'
  generic 'splitAsListReturnedClass' and siglist 'Hits'
  generic 'splitAsListReturnedClass' and siglist 'data.frame'
  generic 'subsetByRanges' and siglist 'ANY'
  generic 'subsetByRanges' and siglist 'IRanges'
  generic 'subsetByRanges' and siglist 'NULL'
  generic 'subsetByRanges' and siglist 'vector'
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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File '/Users/biocbuild/bbs-2.12-bioc/meat/IRanges.Rcheck/IRanges/libs/i386/IRanges.so':
  Found '___stderrp', possibly from 'stderr' (C)
    Object: 'errabort.o'
  Found '___stdoutp', possibly from 'stdout' (C)
    Objects: 'IntervalTree.o', 'common.o', 'errabort.o'
  Found '_abort', possibly from 'abort' (C)
    Object: 'errabort.o'
  Found '_exit', possibly from 'exit' (C)
    Object: 'errabort.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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [21s/21s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'IRanges_unit_tests.R' [48s/48s]
 [49s/49s] 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.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/IRanges.Rcheck/00check.log'
for details.

IRanges.Rcheck/00install.out:

* installing *source* package 'IRanges' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c AEbufs.c -o AEbufs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c CompressedList_class.c -o CompressedList_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c DataFrame_class.c -o DataFrame_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c GappedRanges_class.c -o GappedRanges_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c Grouping_class.c -o Grouping_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c Hits_class.c -o Hits_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c IRanges_class.c -o IRanges_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c IRanges_constructor.c -o IRanges_constructor.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c IntervalTree.c -o IntervalTree.o
IntervalTree.c: In function '_IntegerIntervalTree_overlap':
IntervalTree.c:131: warning: 'result_inds' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
Ocopy_byteblocks.c: In function '_Ocopy_bytes_from_i1i2_to_complex':
Ocopy_byteblocks.c:492: warning: 'lkup_val.r' may be used uninitialized in this function
Ocopy_byteblocks.c:492: warning: 'lkup_val.i' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c R_init_IRanges.c -o R_init_IRanges.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c RangedData_class.c -o RangedData_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c Ranges_comparison.c -o Ranges_comparison.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c RleViews_utils.c -o RleViews_utils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c Rle_class.c -o Rle_class.o
Rle_class.c: In function 'compute_int_runs':
Rle_class.c:29: warning: 'val0' may be used uninitialized in this function
Rle_class.c: In function 'compute_Rbyte_runs':
Rle_class.c:152: warning: 'val0' may be used uninitialized in this function
Rle_class.c: In function 'compute_CHARSXP_runs':
Rle_class.c:122: warning: 'val0' may be used uninitialized in this function
Rle_class.c: In function 'compute_Rcomplex_runs':
Rle_class.c:88: warning: 'val0.r' may be used uninitialized in this function
Rle_class.c:88: warning: 'val0.i' may be used uninitialized in this function
Rle_class.c: In function 'compute_double_runs':
Rle_class.c:57: warning: 'val0' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c Rle_utils.c -o Rle_utils.o
Rle_utils.c: In function 'Rle_integer_runsum':
Rle_utils.c:97: warning: suggest parentheses around comparison in operand of |
Rle_utils.c: In function 'Rle_integer_runwtsum':
Rle_utils.c:461: warning: suggest parentheses around comparison in operand of |
Rle_utils.c: In function 'Rle_real_runwtsum':
Rle_utils.c:509: warning: unused variable 'm_value'
Rle_utils.c:508: warning: unused variable 'm_length'
Rle_utils.c:507: warning: unused variable 'm_offset'
Rle_utils.c: In function 'Rle_integer_runq':
Rle_utils.c:735: warning: implicit declaration of function 'roundingScale'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c SEXP_utils.c -o SEXP_utils.o
SEXP_utils.c: In function 'address_asSTRSXP':
SEXP_utils.c:19: warning: format '%p' expects type 'void *', but argument 4 has type 'SEXP'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c SharedDouble_class.c -o SharedDouble_class.o
SharedDouble_class.c: In function 'SharedDouble_get_show_string':
SharedDouble_class.c:57: warning: format '%p' expects type 'void *', but argument 5 has type 'double *'
SharedDouble_class.c: In function 'SharedDouble_new':
SharedDouble_class.c:24: warning: 'tag' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c SharedInteger_class.c -o SharedInteger_class.o
SharedInteger_class.c: In function 'SharedInteger_get_show_string':
SharedInteger_class.c:56: warning: format '%p' expects type 'void *', but argument 5 has type 'int *'
SharedInteger_class.c: In function 'SharedInteger_new':
SharedInteger_class.c:24: warning: 'tag' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c: In function 'SharedRaw_new':
SharedRaw_class.c:24: warning: 'tag' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c SharedVector_class.c -o SharedVector_class.o
SharedVector_class.c: In function 'SharedVector_address0':
SharedVector_class.c:185: warning: 'address0' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c SimpleList_class.c -o SimpleList_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c Vector_class.c -o Vector_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c XDoubleViews_utils.c -o XDoubleViews_utils.o
XDoubleViews_utils.c: In function 'get_cachedDoubleSeq_which_max':
XDoubleViews_utils.c:212: warning: 'cur_max' may be used uninitialized in this function
XDoubleViews_utils.c: In function 'XDoubleViews_summary2':
XDoubleViews_utils.c:284: warning: 'fun' may be used uninitialized in this function
XDoubleViews_utils.c: In function 'XDoubleViews_summary1':
XDoubleViews_utils.c:243: warning: 'fun' may be used uninitialized in this function
XDoubleViews_utils.c: In function 'get_cachedDoubleSeq_which_min':
XDoubleViews_utils.c:185: warning: 'cur_min' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c XIntegerViews_utils.c -o XIntegerViews_utils.o
XIntegerViews_utils.c: In function 'get_cachedIntSeq_which_min':
XIntegerViews_utils.c:160: warning: 'cur_min' may be used uninitialized in this function
XIntegerViews_utils.c: In function 'get_cachedIntSeq_which_max':
XIntegerViews_utils.c:183: warning: 'cur_max' may be used uninitialized in this function
XIntegerViews_utils.c: In function 'XIntegerViews_summary2':
XIntegerViews_utils.c:254: warning: 'fun' may be used uninitialized in this function
XIntegerViews_utils.c: In function 'XIntegerViews_summary1':
XIntegerViews_utils.c:214: warning: 'fun' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c XRawList_comparison.c -o XRawList_comparison.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function 'alloc_XVectorList':
XVectorList_class.c:340: warning: 'ans' may be used uninitialized in this function
XVectorList_class.c: In function '_new_XRawList_from_CharAEAE':
XVectorList_class.c:426: warning: 'lkup_length' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c XVector_class.c -o XVector_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c anyMissing.c -o anyMissing.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c common.c -o common.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c compact_bitvector.c -o compact_bitvector.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c coverage_methods.c -o coverage_methods.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c dlist.c -o dlist.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function 'overlap_encoding':
encodeOverlaps_methods.c:95: warning: 'out_nelt0' may be used uninitialized in this function
encodeOverlaps_methods.c:95: note: 'out_nelt0' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c errabort.c -o errabort.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c hash_utils.c -o hash_utils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c int_utils.c -o int_utils.o
int_utils.c: In function 'Integer_tabulate2':
int_utils.c:486: warning: unused variable 'ans_elt'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'reduce_ranges':
inter_range_methods.c:115: warning: 'mapping_elt' may be used uninitialized in this function
inter_range_methods.c:114: warning: 'delta' may be used uninitialized in this function
inter_range_methods.c:114: warning: 'gapwidth' may be used uninitialized in this function
inter_range_methods.c:114: warning: 'max_end' may be used uninitialized in this function
inter_range_methods.c:114: warning: 'append_or_drop' may be used uninitialized in this function
inter_range_methods.c: In function 'Ranges_reduce':
inter_range_methods.c:194: warning: 'ans_inframe_start' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c localmem.c -o localmem.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c memalloc.c -o memalloc.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c rbTree.c -o rbTree.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c safe_arithm.c -o safe_arithm.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c sort_utils.c -o sort_utils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c str_utils.c -o str_utils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c ucsc_handlers.c -o ucsc_handlers.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c vector_copy.c -o vector_copy.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 IRanges.so AEbufs.o CompressedIRangesList_class.o CompressedList_class.o DataFrame_class.o GappedRanges_class.o Grouping_class.o Hits_class.o IRanges_class.o IRanges_constructor.o IntervalTree.o Ocopy_byteblocks.o R_init_IRanges.o RangedData_class.o Ranges_comparison.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o SimpleList_class.o SimpleRangesList_class.o Vector_class.o XDoubleViews_utils.o XIntegerViews_utils.o XRawList_comparison.o XVectorList_class.o XVector_class.o anyMissing.o common.o compact_bitvector.o coverage_methods.o dlist.o encodeOverlaps_methods.o errabort.o hash_utils.o int_utils.o inter_range_methods.o localmem.o memalloc.o rbTree.o safe_arithm.o sort_utils.o str_utils.o ucsc_handlers.o vector_copy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/IRanges.Rcheck/IRanges/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'window' from package 'stats' in package 'IRanges'
Creating a generic function for 'window<-' from package 'stats' in package 'IRanges'
Creating a generic function for 'head' from package 'utils' in package 'IRanges'
Creating a generic function for 'tail' from package 'utils' in package 'IRanges'
Creating a generic function for 'rev' from package 'base' in package 'IRanges'
Creating a generic function for 'subset' from package 'base' in package 'IRanges'
Creating a generic function for '%in%' from package 'base' in package 'IRanges'
in method for 'coerce' with signature '"Vector","double"': no definition for class "double"
Creating a generic function for 'append' from package 'base' in package 'IRanges'
Creating a generic function for 'relist' from package 'utils' in package 'IRanges'
in method for 'relist' with signature '"ANY","PartitioningByEnd"': no definition for class "PartitioningByEnd"
in method for 'relist' with signature '"ANY","List"': no definition for class "List"
Creating a generic function for 'split' from package 'base' in package 'IRanges'
Creating a generic function for 'split<-' from package 'base' in package 'IRanges'
Creating a generic function for 'aggregate' from package 'stats' in package 'IRanges'
Creating a generic function for 'as.list' from package 'base' in package 'IRanges'
Creating a generic function for 'unsplit' from package 'base' in package 'IRanges'
Creating a generic function for 'stack' from package 'utils' in package 'IRanges'
Creating a generic function for 'with' from package 'base' in package 'IRanges'
Creating a generic function for 'within' from package 'base' in package 'IRanges'
Creating a generic function for 'start' from package 'stats' in package 'IRanges'
Creating a generic function for 'end' from package 'stats' in package 'IRanges'
Creating a generic function for 'as.matrix' from package 'base' in package 'IRanges'
Creating a generic function for 'na.omit' from package 'stats' in package 'IRanges'
Creating a generic function for 'na.exclude' from package 'stats' in package 'IRanges'
Creating a generic function for 'complete.cases' from package 'stats' in package 'IRanges'
Creating a generic function for 'merge' from package 'base' in package 'IRanges'
Creating a generic function for 'by' from package 'base' in package 'IRanges'
Creating a generic function for 'mean' from package 'base' in package 'IRanges'
Creating a generic function for 'which.max' from package 'base' in package 'IRanges'
Creating a generic function for 'which.min' from package 'base' in package 'IRanges'
Creating a generic function for 'as.vector' from package 'base' in package 'IRanges'
Creating a generic function for 'as.factor' from package 'base' in package 'IRanges'
Creating a generic function for 'is.unsorted' from package 'base' in package 'IRanges'
Creating a generic function for 'which' from package 'base' in package 'IRanges'
Creating a generic function for 'ifelse' from package 'base' in package 'IRanges'
Creating a generic function for 'diff' from package 'base' in package 'IRanges'
Creating a generic function for 'var' from package 'stats' in package 'IRanges'
Creating a generic function for 'cov' from package 'stats' in package 'IRanges'
Creating a generic function for 'cor' from package 'stats' in package 'IRanges'
Creating a generic function for 'sd' from package 'stats' in package 'IRanges'
Creating a generic function for 'median' from package 'stats' in package 'IRanges'
Creating a generic function for 'quantile' from package 'stats' in package 'IRanges'
Creating a generic function for 'mad' from package 'stats' in package 'IRanges'
Creating a generic function for 'IQR' from package 'stats' in package 'IRanges'
Creating a generic function for 'smoothEnds' from package 'stats' in package 'IRanges'
Creating a generic function for 'runmed' from package 'stats' in package 'IRanges'
Creating a generic function for 'nchar' from package 'base' in package 'IRanges'
Creating a generic function for 'substr' from package 'base' in package 'IRanges'
Creating a generic function for 'substring' from package 'base' in package 'IRanges'
Creating a generic function for 'chartr' from package 'base' in package 'IRanges'
Creating a generic function for 'tolower' from package 'base' in package 'IRanges'
Creating a generic function for 'toupper' from package 'base' in package 'IRanges'
Creating a generic function for 'sub' from package 'base' in package 'IRanges'
Creating a generic function for 'gsub' from package 'base' in package 'IRanges'
Creating a generic function for 'levels' from package 'base' in package 'IRanges'
Creating a generic function for 'drop' from package 'base' in package 'IRanges'
Creating a generic function for 'rownames<-' from package 'base' in package 'IRanges'
Creating a generic function for 'colnames<-' from package 'base' in package 'IRanges'
in method for 'coerce' with signature '"xtabs","DataFrame"': no definition for class "xtabs"
Creating a generic function for 'as.table' from package 'base' in package 'IRanges'
Creating a generic function for 't' from package 'base' in package 'IRanges'
Creating a generic function for 'toString' from package 'base' in package 'IRanges'
** help
*** installing help indices
** building package indices
** installing vignettes
   'IRangesOverview.Rnw' 
   'RleTricks.Rnw' 
** testing if installed package can be loaded
* DONE (IRanges)

IRanges.Rcheck/IRanges-Ex.timings:

nameusersystemelapsed
AtomicList-class0.6200.0720.695
DataFrame-class0.5600.0570.619
DataTable-API0.0110.0070.019
DataTable-stats0.0200.0050.025
FilterRules-class0.0740.0230.097
GappedRanges-class0.2010.0210.222
Grouping-class0.1620.0650.228
Hits-class0.0720.0140.085
IRanges-class2.5940.2382.839
IRanges-constructor0.0610.0240.084
IRanges-utils2.1060.2672.381
IRangesList-class0.0590.0150.074
IntervalTree-class0.0640.0100.074
List-class0.0110.0140.027
MaskCollection-class0.1300.0280.158
OverlapEncodings-class0.0630.0190.082
RDApplyParams-class1.0670.0341.101
RangedData-class1.6880.0691.808
RangedDataList-class0.0610.0080.069
RangedSelection-class0.0320.0070.038
Ranges-class0.0660.0300.096
Ranges-comparison0.0700.0310.101
RangesList-class0.0940.0270.123
Rle-class0.2010.0610.263
RleViews-class0.0530.0110.064
RleViewsList-class0.0650.0140.081
SimpleList-class0.0130.0120.025
Vector-class0.0130.0150.028
Views-class0.3950.0270.422
Views-utils0.0760.0230.100
ViewsList-class0.0040.0080.017
XDoubleViews-class0.0910.0320.124
XIntegerViews-class0.0750.0250.100
XVector-class0.0760.0330.112
classNameForDisplay-methods0.0210.0120.034
compact-methods0.7450.0400.788
coverage-methods0.1610.0250.186
encodeOverlaps-methods0.0560.0270.085
endoapply0.0140.0100.024
expand-methods0.2710.0150.285
findOverlaps-methods0.3540.0550.410
funprog-methods0.1350.0140.150
inter-range-methods1.0880.0881.184
intra-range-methods0.4780.0760.554
isConstant0.0190.0260.046
multisplit0.0330.0040.037
nearest-methods0.0770.0190.097
read.Mask0.0610.0370.098
reverse-methods0.1110.0200.131
runstat0.0700.0140.085
seqapply0.0910.0100.101
setops-methods0.2880.0300.320
strutils0.0070.0100.017