IRanges 1.11.10
Biocore Team c/o BioC user list
| Snapshot Date: 2011-06-21 19:21:48 -0700 (Tue, 21 Jun 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges | | Last Changed Rev: 56234 / Revision: 56351 | | Last Changed Date: 2011-06-16 12:48:17 -0700 (Thu, 16 Jun 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRanges/DESCRIPTION’ ... OK
* this is package ‘IRanges’ version ‘1.11.10’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
unlist:
function(x, recursive, use.names)
unlist.list.of.XVectorList:
function(classname, x)
See section ‘Generic functions and methods’ of the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'ranges':
‘RangedData-class.Rd’ ‘Views-class.Rd’
Rd files with duplicated alias 'ranges<-':
‘RangedData-class.Rd’ ‘Views-class.Rd’
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object ‘/Users/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck/00_pkg_src/IRanges/man/MaskCollection-class.Rd’:
‘[Biostrings]{reverse}’
Missing link(s) in documentation object ‘/Users/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck/00_pkg_src/IRanges/man/RleViewsList-class.Rd’:
‘ViewsList-class’
See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
‘SimpleViewsList’ ‘ViewsList’
Undocumented S4 methods:
generic '!=' and siglist 'XVector,XVector'
generic '[' and siglist 'Views'
generic 'as.data.frame' and siglist 'Vector'
generic 'as.matrix' and siglist 'Views'
generic 'coerce' and siglist 'Vector,data.frame'
generic 'coerce' and siglist 'Views,IRanges'
generic 'coerce' and siglist 'Views,Ranges'
generic 'elementLengths' and siglist 'Views'
generic 'end' and siglist 'SimpleViewsList'
generic 'end' and siglist 'Views'
generic 'end<-' and siglist 'Views'
generic 'length' and siglist 'Views'
generic 'names' and siglist 'Views'
generic 'names<-' and siglist 'Views'
generic 'narrow' and siglist 'Views'
generic 'ranges' and siglist 'SimpleViewsList'
generic 'reduce' and siglist 'Views'
generic 'shift' and siglist 'Views'
generic 'slice' and siglist 'numeric'
generic 'start' and siglist 'SimpleViewsList'
generic 'start' and siglist 'Views'
generic 'start<-' and siglist 'Views'
generic 'unique' and siglist 'Vector'
generic 'universe' and siglist 'ViewsList'
generic 'universe<-' and siglist 'ViewsList'
generic 'width' and siglist 'SimpleViewsList'
generic 'width' and siglist 'Views'
generic 'width<-' and siglist 'Views'
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 ... NOTE
‘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 sizes of PDF files under ‘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, see
‘/Users/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck/00check.log’
for details
* installing *source* package ‘IRanges’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c AEbufs.c -o AEbufs.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c CompressedList_class.c -o CompressedList_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c DataFrame_class.c -o DataFrame_class.o
DataFrame_class.c: In function ‘set_DataFrame_rownames’:
DataFrame_class.c:11: warning: control reaches end of non-void function
DataFrame_class.c: In function ‘set_DataFrame_nrows’:
DataFrame_class.c:16: warning: control reaches end of non-void function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c GappedRanges_class.c -o GappedRanges_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c Grouping_class.c -o Grouping_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c IRanges_class.c -o IRanges_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c IRanges_constructor.c -o IRanges_constructor.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -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:138: warning: ‘ans_inframe_start’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c IntervalTree.c -o IntervalTree.o
IntervalTree.c: In function ‘_IntegerIntervalTree_overlap’:
IntervalTree.c:125: warning: ‘result_inds’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
Ocopy_byteblocks.c: In function ‘translate_byte’:
Ocopy_byteblocks.c:20: warning: ‘lkup_val’ may be used uninitialized in this function
Ocopy_byteblocks.c: In function ‘_Ocopy_bytes_from_i1i2_to_complex’:
Ocopy_byteblocks.c:466: warning: ‘lkup_val.r’ may be used uninitialized in this function
Ocopy_byteblocks.c:466: warning: ‘lkup_val.i’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c R_init_IRanges.c -o R_init_IRanges.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c RangedData_class.c -o RangedData_class.o
RangedData_class.c: In function ‘set_RangedData_ranges’:
RangedData_class.c:12: warning: control reaches end of non-void function
RangedData_class.c: In function ‘set_RangedData_values’:
RangedData_class.c:17: warning: control reaches end of non-void function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c RleViews_utils.c -o RleViews_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c Rle_class.c -o Rle_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c Rle_utils.c -o Rle_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c SimpleList_class.c -o SimpleList_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -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:423: warning: ‘lkup_length’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c XVector_class.c -o XVector_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c anyMissing.c -o anyMissing.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c common.c -o common.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c compact_bitvector.c -o compact_bitvector.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c coverage.c -o coverage.o
coverage.c: In function ‘IRanges_coverage’:
coverage.c:34: warning: ‘lengths_buf’ may be used uninitialized in this function
coverage.c:34: warning: ‘values_buf’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c dlist.c -o dlist.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c errabort.c -o errabort.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c int_utils.c -o int_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c localmem.c -o localmem.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c memalloc.c -o memalloc.o
memalloc.c: In function ‘carefulAlloc’:
memalloc.c:293: warning: format ‘%d’ expects type ‘int’, but argument 2 has type ‘size_t’
memalloc.c:293: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘size_t’
memalloc.c:289: warning: unused variable ‘allocRequest’
memalloc.c:288: warning: unused variable ‘maxAlloc’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c rbTree.c -o rbTree.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c sort_utils.c -o sort_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c str_utils.c -o str_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c vector_copy.c -o vector_copy.o
gcc-4.2 -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 IRanges_class.o IRanges_constructor.o IRanges_utils.o IntervalTree.o Ocopy_byteblocks.o R_init_IRanges.o RangedData_class.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 XVectorList_class.o XVector_class.o anyMissing.o common.o compact_bitvector.o coverage.o dlist.o errabort.o int_utils.o localmem.o memalloc.o rbTree.o sort_utils.o str_utils.o vector_copy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck/IRanges/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for "NROW" from package "base" in package “IRanges”
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 new generic function for “rep.int” in package “IRanges”
Creating a generic function for "subset" from package "base" in package “IRanges”
Creating a generic function for "unique" from package "base" in package “IRanges”
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 "tapply" from package "base" in package “IRanges”
Creating a generic function for "aggregate" from package "stats" in package “IRanges”
Creating a generic function for "lapply" from package "base" in package “IRanges”
Creating a generic function for "sapply" from package "base" in package “IRanges”
Creating a new generic function for “mapply” in package “IRanges”
Creating a generic function for "as.list" from package "base" in package “IRanges”
Creating a generic function for "stack" from package "utils" in package “IRanges”
Creating a generic function for "relist" from package "utils" in package “IRanges”
Creating a generic function for "Reduce" from package "base" in package “IRanges”
Creating a generic function for "Filter" from package "base" in package “IRanges”
Creating a generic function for "Find" from package "base" in package “IRanges”
Creating a new generic function for “Map” in package “IRanges”
Creating a generic function for "Position" from package "base" in package “IRanges”
Creating a new generic function for “eval” in package “IRanges”
Creating a generic function for "with" 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 "update" from package "stats" in package “IRanges”
Creating a generic function for "as.matrix" from package "base" in package “IRanges”
Creating a generic function for "unlist" from package "base" in package “IRanges”
Creating a generic function for "duplicated" from package "base" in package “IRanges”
Creating a new generic function for “order” in package “IRanges”
Creating a generic function for "sort" from package "base" in package “IRanges”
Creating a generic function for "rank" from package "base" in package “IRanges”
Creating a generic function for "%in%" from package "base" in package “IRanges”
Creating a new generic function for “union” in package “IRanges”
Creating a new generic function for “intersect” in package “IRanges”
Creating a new generic function for “setdiff” in package “IRanges”
Creating a generic function for "NCOL" 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 new generic function for “cbind” in package “IRanges”
Creating a new generic function for “rbind” in package “IRanges”
Creating a generic function for "xtabs" from package "stats" 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 "split" from package "base" in package “IRanges”
Creating a generic function for "summary" from package "base" in package “IRanges”
Creating a new generic function for “table” 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 new generic function for “pmax” in package “IRanges”
Creating a new generic function for “pmin” in package “IRanges”
Creating a new generic function for “pmax.int” in package “IRanges”
Creating a new generic function for “pmin.int” 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 new generic function for “paste” in package “IRanges”
Creating a generic function for "levels" from package "base" in package “IRanges”
Creating a generic function for "nrow" from package "base" in package “IRanges”
Creating a generic function for "ncol" 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 "rownames<-" from package "base" in package “IRanges”
Creating a generic function for "colnames<-" from package "base" in package “IRanges”
Creating a generic function for "merge" from package "base" in package “IRanges”
Creating a generic function for "within" 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 ...
*** tangling vignette sources ...
‘IRangesOverview.Rnw’
‘RleTricks.Rnw’
** testing if installed package can be loaded
* DONE (IRanges)