IRanges 1.16.6
Bioconductor Package Maintainer
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/IRanges | | Last Changed Rev: 73672 / Revision: 74773 | | Last Changed Date: 2013-02-21 11:23:00 -0800 (Thu, 21 Feb 2013) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/IRanges.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.16.6'
* 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 'IRanges' 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 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 ... WARNING
Foreign function call with 'PACKAGE' argument in a base package:
.Call("R_Tabulate", ..., PACKAGE = "base")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* checking R code for possible problems ... NOTE
as.data.frame,RangesList: warning in factor(rep.int(seq_len(length(x)),
elementLengths(x)), level = spaceLevels, labels = spaceLabels):
partial argument match of 'level' to 'levels'
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:
'splitAsList' 'splitAsListReturnedClass'
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 'compare' and siglist 'XRawList,XRawList'
generic 'duplicated' and siglist 'XRawList'
generic 'is.unsorted' and siglist 'XRawList'
generic 'match' and siglist 'XRawList,XRawList'
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'
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 ... WARNING
Objects in \usage without \alias in documentation object 'Ranges-comparison':
'\S4method{!=}{Ranges,Ranges}' '\S4method{>=}{Ranges,Ranges}'
'\S4method{<}{Ranges,Ranges}' '\S4method{>}{Ranges,Ranges}'
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 ... WARNING
'library' or 'require' call not declared from: 'BSgenome.Celegans.UCSC.ce2'
* 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 ... NOTE
File '/Users/biocbuild/bbs-2.11-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 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 'IRanges_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 4 warnings.
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/IRanges.Rcheck/00check.log'
for details.
* 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 IRanges_utils.c -o IRanges_utils.o
IRanges_utils.c: In function '_reduce_ranges':
IRanges_utils.c:77: warning: 'delta' may be used uninitialized in this function
IRanges_utils.c:77: warning: 'gapwidth' may be used uninitialized in this function
IRanges_utils.c:77: warning: 'max_end' may be used uninitialized in this function
IRanges_utils.c:77: warning: 'append_or_drop' may be used uninitialized in this function
IRanges_utils.c: In function 'IRanges_reduce':
IRanges_utils.c:137: 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 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_utils.c -o SharedDouble_utils.o
SharedDouble_utils.c: In function 'SharedDouble_get_show_string':
SharedDouble_utils.c:57: warning: format '%p' expects type 'void *', but argument 5 has type 'double *'
SharedDouble_utils.c: In function 'SharedDouble_new':
SharedDouble_utils.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_utils.c -o SharedInteger_utils.o
SharedInteger_utils.c: In function 'SharedInteger_get_show_string':
SharedInteger_utils.c:56: warning: format '%p' expects type 'void *', but argument 5 has type 'int *'
SharedInteger_utils.c: In function 'SharedInteger_new':
SharedInteger_utils.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_utils.c -o SharedRaw_utils.o
SharedRaw_utils.c: In function 'SharedRaw_new':
SharedRaw_utils.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
Vector_class.c: In function 'vector_seqselect':
Vector_class.c:95: warning: implicit declaration of function 'UNIMPLEMENTED_TYPE'
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.c -o coverage.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 encode_overlaps.c -o encode_overlaps.o
encode_overlaps.c: In function 'overlap_encoding':
encode_overlaps.c:95: warning: 'out_nelt0' may be used uninitialized in this function
encode_overlaps.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 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 IRanges_utils.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_utils.o SharedInteger_utils.o SharedRaw_utils.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.o dlist.o encode_overlaps.o errabort.o hash_utils.o int_utils.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-2.11-bioc/meat/IRanges.Rcheck/IRanges/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nlevels' from package 'base' in package 'IRanges'
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 'sort' 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 'as.data.frame' from package 'base' in package 'IRanges'
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 'unlist' 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 'rank' 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 '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 'match' 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'
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)