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Package 247/479HostnameOS / ArchBUILDCHECKBUILD BIN
IRanges 1.11.11
Biocore Team c/o BioC user list
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges
Last Changed Rev: 56456 / Revision: 56603
Last Changed Date: 2011-06-28 16:33:41 -0700 (Tue, 28 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 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: IRanges
Version: 1.11.11
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IRanges_1.11.11.tar.gz
StartedAt: 2011-07-07 03:55:32 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 03:59:38 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 245.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IRanges.Rcheck
Warnings: 4

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* 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 '1.11.11'
* 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:
  'AsIs' '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

IRanges.Rcheck/00install.out:

* installing *source* package 'IRanges' ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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)

IRanges.Rcheck/IRanges-Ex.timings:

nameusersystemelapsed
AtomicList-class0.5760.0070.586
DataFrame-class0.6730.0130.691
DataTable-API0.0020.0000.002
DataTable-stats0.0210.0010.022
FilterRules-class0.0530.0010.055
GappedRanges-class0.2760.0020.279
Grouping-class0.1380.0060.145
IRanges-class2.1800.6122.829
IRanges-constructor0.0900.0070.098
IRanges-setops0.2240.0140.241
IRanges-utils2.2710.6262.938
IRangesList-class0.0690.0010.071
IntervalTree-class0.2320.0090.245
List-class0.0090.0010.009
MaskCollection-class0.2470.0040.253
RDApplyParams-class0.9930.0041.019
RangedData-class2.2610.0272.341
RangedData-utils0.1240.0010.126
RangedDataList-class0.0580.0010.060
RangedSelection-class0.0290.0010.035
Ranges-class0.0900.0030.094
Ranges-comparison0.0330.0020.035
Ranges-utils0.1690.0040.174
RangesList-class0.2510.0040.262
RangesList-utils0.6120.0100.630
RangesMatching-class0.0160.0010.020
Rle-class0.1830.0050.211
RleViews-class0.0770.0020.084
RleViewsList-class0.0940.0020.110
SimpleList-class0.0090.0010.010
Vector-class0.0100.0010.011
Views-class0.4730.0120.490
Views-utils0.0850.0020.089
XDoubleViews-class0.0910.0020.094
XIntegerViews-class0.0640.0020.067
XVector-class0.0650.0050.071
compact0.8240.0220.893
coverage0.1120.0030.124
disjoin0.0240.0000.029
endoapply0.0160.0010.017
isConstant0.0050.0010.006
nearest0.0450.0010.051
read.Mask0.0690.0050.086
reverse0.0990.0020.101
runstat0.0500.0010.051
seqapply0.0910.0010.096
strutils0.0010.0010.002