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Package 154/319HostnameOS / ArchBUILDCHECKBUILD BIN
IRanges 1.2.3
Biocore Team c/o BioC user list
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/IRanges
Last Changed Rev: 40046 / Revision: 42512
Last Changed Date: 2009-06-09 11:52:32 -0700 (Tue, 09 Jun 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: IRanges
Version: 1.2.3
Command: /home/biocbuild/bbs-2.4-bioc/R/bin/R CMD check --no-vignettes IRanges_1.2.3.tar.gz
StartedAt: 2009-10-20 16:39:35 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 16:41:29 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 113.7 seconds
RetCode: 0
Status: OK
CheckDir: IRanges.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.4-bioc/meat/IRanges.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IRanges/DESCRIPTION' ... OK
* this is package 'IRanges' version '1.2.3'
* 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 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 name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
  Running 'runalltests.R'
  Comparing 'runalltests.Rout' to 'runalltests.Rout.save' ... OK
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

IRanges.Rcheck/00install.out:

* Installing *source* package 'IRanges' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c AEbufs.c -o AEbufs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c IRangesList_class.c -o IRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c IRanges_utils.c -o IRanges_utils.o
IRanges_utils.c: In function 'IRanges_reduce':
IRanges_utils.c:117: warning: 'ans_inframe_start' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c IntegerPtr_utils.c -o IntegerPtr_utils.o
IntegerPtr_utils.c: In function 'IntegerPtr_new':
IntegerPtr_utils.c:24: warning: 'tag' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c IntervalTree.c -o IntervalTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c NumericPtr_utils.c -o NumericPtr_utils.o
NumericPtr_utils.c: In function 'NumericPtr_new':
NumericPtr_utils.c:24: warning: 'tag' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c RawPtr_utils.c -o RawPtr_utils.o
RawPtr_utils.c: In function 'RawPtr_new':
RawPtr_utils.c:24: warning: 'tag' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c RleViews_utils.c -o RleViews_utils.o
RleViews_utils.c: In function 'RleViews_viewWhichMaxs':
RleViews_utils.c:424: warning: 'curr' may be used uninitialized in this function
RleViews_utils.c: In function 'RleViews_viewWhichMins':
RleViews_utils.c:327: warning: 'curr' may be used uninitialized in this function
RleViews_utils.c: In function 'RleViews_viewMaxs':
RleViews_utils.c:106: warning: 'ans' may be used uninitialized in this function
RleViews_utils.c: In function 'RleViews_viewMins':
RleViews_utils.c:15: warning: 'ans' may be used uninitialized in this function
RleViews_utils.c: In function 'RleViews_viewSums':
RleViews_utils.c:197: warning: 'ans' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Rle_class.c -o Rle_class.o
Rle_class.c: In function 'Rle_constructor':
Rle_class.c:436: warning: 'ans' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c SEXP_utils.c -o SEXP_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c SequencePtr_class.c -o SequencePtr_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Sequence_class.c -o Sequence_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c XIntegerViews_class.c -o XIntegerViews_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c XIntegerViews_utils.c -o XIntegerViews_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c XNumericViews_class.c -o XNumericViews_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c XRleIntegerViews_class.c -o XRleIntegerViews_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c XRleIntegerViews_utils.c -o XRleIntegerViews_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c XRleInteger_class.c -o XRleInteger_class.o
XRleInteger_class.c: In function 'XRleInteger_Arith':
XRleInteger_class.c:30: warning: 'fun' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c XSequence_class.c -o XSequence_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c chain_io.c -o chain_io.o
chain_io.c: In function 'read_chain_file':
chain_io.c:38: warning: 'header_line' may be used uninitialized in this function
chain_io.c:35: warning: 'block' may be used uninitialized in this function
chain_io.c:34: warning: 'qrc' may be used uninitialized in this function
chain_io.c:34: warning: 'trc' may be used uninitialized in this function
chain_io.c:33: warning: 'qstart' may be used uninitialized in this function
chain_io.c:33: warning: 'tstart' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c common.c -o common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c coverage.c -o coverage.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c dlist.c -o dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c errabort.c -o errabort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c hash.c -o hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c localmem.c -o localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c memcpy_utils.c -o memcpy_utils.o
memcpy_utils.c: In function '_IRanges_memcpy_from_i1i2_to_complex':
memcpy_utils.c:474: warning: 'lkup_val.r' may be used uninitialized in this function
memcpy_utils.c:474: warning: 'lkup_val.i' may be used uninitialized in this function
memcpy_utils.c: In function '_IRanges_reverse_charcpy_from_i1i2_with_lkup':
memcpy_utils.c:430: warning: 'lkup_val' may be used uninitialized in this function
memcpy_utils.c: In function '_IRanges_charcpy_to_subset_with_lkup':
memcpy_utils.c:349: warning: 'lkup_val' may be used uninitialized in this function
memcpy_utils.c: In function '_IRanges_charcpy_to_i1i2_with_lkup':
memcpy_utils.c:308: warning: 'lkup_val' may be used uninitialized in this function
memcpy_utils.c: In function '_IRanges_charcpy_from_subset_with_lkup':
memcpy_utils.c:268: warning: 'lkup_val' may be used uninitialized in this function
memcpy_utils.c: In function '_IRanges_charcpy_from_i1i2_with_lkup':
memcpy_utils.c:227: warning: 'lkup_val' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rbTree.c -o rbTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c sort_utils.c -o sort_utils.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o IRanges.so AEbufs.o IRangesList_class.o IRanges_class.o IRanges_constructor.o IRanges_utils.o IntegerPtr_utils.o IntervalTree.o NumericPtr_utils.o R_init_IRanges.o RawPtr_utils.o RleViews_utils.o Rle_class.o SEXP_utils.o SequencePtr_class.o Sequence_class.o XIntegerViews_class.o XIntegerViews_utils.o XNumericViews_class.o XRleIntegerViews_class.o XRleIntegerViews_utils.o XRleInteger_class.o XSequence_class.o chain_io.o common.o coverage.o dlist.o errabort.o hash.o localmem.o memalloc.o memcpy_utils.o rbTree.o sort_utils.o -L/home/biocbuild/bbs-2.4-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
Creating a new generic function for "lapply" in "IRanges"
Creating a generic for "sapply" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (X), (X, FUN, simplify, USE.NAMES))
Creating a new generic function for "as.list" in "IRanges"
Creating a new generic function for "start" in "IRanges"
Creating a new generic function for "end" in "IRanges"
Creating a new generic function for "as.matrix" in "IRanges"
Creating a new generic function for "as.data.frame" in "IRanges"
Creating a new generic function for "%in%" in "IRanges"
Creating a generic for "duplicated" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (x), (x, incomparables))
Creating a generic for "unique" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (x), (x, incomparables))
Creating a generic for "order" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (...), (na.last, decreasing))
Creating a generic for "sort" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (x), (x, decreasing))
Creating a generic for "rank" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (x), (x, na.last, ties.method))
Creating a new generic function for "update" in "IRanges"
Creating a new generic function for "union" in "IRanges"
Creating a new generic function for "intersect" in "IRanges"
Creating a new generic function for "setdiff" in "IRanges"
Creating a new generic function for "toString" in "IRanges"
Creating a new generic function for "as.vector" in "IRanges"
Creating a new generic function for "as.factor" in "IRanges"
Creating a new generic function for "aggregate" in "IRanges"
Creating a new generic function for "head" in "IRanges"
Creating a generic for "rep.int" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Formal arguments differ: (x, ...), (x, times))
Creating a new generic function for "rev" in "IRanges"
Creating a new generic function for "summary" in "IRanges"
Creating a generic for "table" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Formal arguments differ: (...), (..., exclude, useNA, dnn, deparse.level))
Creating a new generic function for "tail" in "IRanges"
Creating a new generic function for "window" in "IRanges"
Creating a new generic function for "which" in "IRanges"
Creating a new generic function for "diff" in "IRanges"
Creating a generic for "pmax" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (...), (na.rm))
Creating a generic for "pmin" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (...), (na.rm))
Creating a generic for "pmax.int" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (...), (na.rm))
Creating a generic for "pmin.int" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (...), (na.rm))
Creating a new generic function for "mean" in "IRanges"
Creating a new generic function for "var" in "IRanges"
Creating a new generic function for "cov" in "IRanges"
Creating a new generic function for "cor" in "IRanges"
Creating a new generic function for "sd" in "IRanges"
Creating a new generic function for "median" in "IRanges"
Creating a new generic function for "quantile" in "IRanges"
Creating a new generic function for "mad" in "IRanges"
Creating a new generic function for "nchar" in "IRanges"
Creating a new generic function for "substr" in "IRanges"
Creating a new generic function for "substring" in "IRanges"
Creating a new generic function for "chartr" in "IRanges"
Creating a new generic function for "tolower" in "IRanges"
Creating a new generic function for "toupper" in "IRanges"
Creating a new generic function for "sub" in "IRanges"
Creating a new generic function for "gsub" in "IRanges"
Creating a new generic function for "append" in "IRanges"
Creating a new generic function for "unlist" in "IRanges"
Warning in .completeClassSlots(ClassDef, where) :
  undefined slot classes in definition of "AnnotatedList": elementMetadata(class "XDataFrameORNULL")
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "elementMetadata<-" no definition for class: "XDataFrameORNULL"
Warning in .completeClassSlots(ClassDef, where) :
  undefined slot classes in definition of "AnnotatedList": elementMetadata(class "XDataFrameORNULL")
Warning in .completeClassSlots(ClassDef, where) :
  undefined slot classes in definition of "XDataFrame": elementMetadata(class "XDataFrameORNULL")
Creating a new generic function for "split" in "IRanges"
Creating a generic for "cbind" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (...), (deparse.level))
Creating a generic for "rbind" in package  "IRanges"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (...), (deparse.level))
Creating a new generic function for "eval" in "IRanges"
Creating a new generic function for "as.table" in "IRanges"
Creating a new generic function for "t" in "IRanges"
** help
*** installing help indices
 >>> Building/Updating help pages for package 'IRanges'
     Formats: text html latex example 
  Alignment-class                   text    html    latex
  AnnotatedList-class               text    html    latex   example
  AtomicList-class                  text    html    latex   example
  FilterRules-class                 text    html    latex   example
  IRanges-class                     text    html    latex   example
  IRanges-constructor               text    html    latex   example
  IRanges-internals                 text    html    latex
  IRanges-setops                    text    html    latex   example
  IRanges-utils                     text    html    latex   example
  IRangesList-class                 text    html    latex   example
  IntervalTree-class                text    html    latex   example
  ListLike-class                    text    html    latex   example
  MaskCollection-class              text    html    latex   example
  RDApplyParams-class               text    html    latex   example
  RangedData-class                  text    html    latex   example
  RangedData-utils                  text    html    latex   example
  RangedDataList-class              text    html    latex   example
  Ranges-class                      text    html    latex   example
  Ranges-comparison                 text    html    latex   example
  RangesList-class                  text    html    latex   example
  RangesList-utils                  text    html    latex   example
  RangesMatching-class              text    html    latex   example
Note: removing empty section \examples in file 'RangesMatchingList-class.Rd'
  RangesMatchingList-class          text    html    latex
  Rle-class                         text    html    latex   example
  RleViews-class                    text    html    latex   example
  Sequence-class                    text    html    latex   example
  TypedList-class                   text    html    latex   example
  Views-class                       text    html    latex   example
  Views-utils                       text    html    latex   example
  XDataFrame-class                  text    html    latex   example
  XDataFrame-utils                  text    html    latex   example
  XDataFrameList-class              text    html    latex
  XIntegerViews-class               text    html    latex   example
  XRanges-class                     text    html    latex
  XRleIntegerViews-class            text    html    latex   example
  coverage                          text    html    latex   example
  disjoin                           text    html    latex   example
  nearest                           text    html    latex   example
  read.Mask                         text    html    latex   example
  reverse                           text    html    latex   example
** building package indices ...
* DONE (IRanges)