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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: E:\biocbld\bbs-2.4-bioc\R\bin\R.exe CMD check --no-vignettes IRanges_1.2.3.tar.gz
StartedAt: 2009-10-20 17:22:11 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 17:24:28 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 136.8 seconds
RetCode: 0
Status: OK
CheckDir: IRanges.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/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 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' ...19,20d18
< Error in checkEquals(as.vector(aggregate.ts(x, FUN = mean, nfrequency = 1/5)),  : 
<   Mean relative difference: 0.04
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

IRanges.Rcheck/00install.out:

* Installing *source* package 'IRanges' ...
** libs
  making DLL ...
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c AEbufs.c -o AEbufs.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c IRangesList_class.c -o IRangesList_class.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c IRanges_class.c -o IRanges_class.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c IRanges_constructor.c -o IRanges_constructor.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c IntervalTree.c -o IntervalTree.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c R_init_IRanges.c -o R_init_IRanges.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -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_viewMins':
RleViews_utils.c:15: warning: 'ans' 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_viewSums':
RleViews_utils.c:197: warning: 'ans' 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
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c SEXP_utils.c -o SEXP_utils.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c SequencePtr_class.c -o SequencePtr_class.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c Sequence_class.c -o Sequence_class.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c XIntegerViews_class.c -o XIntegerViews_class.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c XIntegerViews_utils.c -o XIntegerViews_utils.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c XNumericViews_class.c -o XNumericViews_class.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c XRleIntegerViews_class.c -o XRleIntegerViews_class.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c XRleIntegerViews_utils.c -o XRleIntegerViews_utils.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c XSequence_class.c -o XSequence_class.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c chain_io.c -o chain_io.o
chain_io.c: In function 'read_chain_file':
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
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
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c common.c -o common.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c coverage.c -o coverage.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c dlist.c -o dlist.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c errabort.c -o errabort.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c hash.c -o hash.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c localmem.c -o localmem.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c memalloc.c -o memalloc.o
memalloc.c: In function 'carefulAlloc':
memalloc.c:289: warning: unused variable 'allocRequest'
memalloc.c:288: warning: unused variable 'maxAlloc'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c rbTree.c -o rbTree.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c sort_utils.c -o sort_utils.o
gcc -shared -s -o IRanges.dll tmp.def 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 -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
  ... done
** 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 chm 
  Alignment-class                   text    html    latex           chm
  AnnotatedList-class               text    html    latex   example chm
  AtomicList-class                  text    html    latex   example chm
  FilterRules-class                 text    html    latex   example chm
  IRanges-class                     text    html    latex   example chm
  IRanges-constructor               text    html    latex   example chm
  IRanges-internals                 text    html    latex           chm
  IRanges-setops                    text    html    latex   example chm
  IRanges-utils                     text    html    latex   example chm
  IRangesList-class                 text    html    latex   example chm
  IntervalTree-class                text    html    latex   example chm
  ListLike-class                    text    html    latex   example chm
  MaskCollection-class              text    html    latex   example chm
  RDApplyParams-class               text    html    latex   example chm
  RangedData-class                  text    html    latex   example chm
  RangedData-utils                  text    html    latex   example chm
  RangedDataList-class              text    html    latex   example chm
  Ranges-class                      text    html    latex   example chm
  Ranges-comparison                 text    html    latex   example chm
  RangesList-class                  text    html    latex   example chm
  RangesList-utils                  text    html    latex   example chm
  RangesMatching-class              text    html    latex   example chm
Note: removing empty section \examples in file 'RangesMatchingList-class.Rd'
Note: removing empty section \examples in file 'RangesMatchingList-class.Rd'
  RangesMatchingList-class          text    html    latex           chm
  Rle-class                         text    html    latex   example chm
  RleViews-class                    text    html    latex   example chm
  Sequence-class                    text    html    latex   example chm
  TypedList-class                   text    html    latex   example chm
  Views-class                       text    html    latex   example chm
  Views-utils                       text    html    latex   example chm
  XDataFrame-class                  text    html    latex   example chm
  XDataFrame-utils                  text    html    latex   example chm
  XDataFrameList-class              text    html    latex           chm
  XIntegerViews-class               text    html    latex   example chm
  XRanges-class                     text    html    latex           chm
  XRleIntegerViews-class            text    html    latex   example chm
  coverage                          text    html    latex   example chm
  disjoin                           text    html    latex   example chm
  nearest                           text    html    latex   example chm
  read.Mask                         text    html    latex   example chm
  reverse                           text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\BBS-2~1.4-B\meat\IRANGE~1.RCH\00_PKG~1\IRanges\chm\IRanges.chm


Compile time: 0 minutes, 1 second
41	Topics
994	Local links
0	Internet links
1	Graphic


Created e:\biocbld\BBS-2~1.4-B\meat\IRANGE~1.RCH\00_PKG~1\IRanges\chm\IRanges.chm, 143,458 bytes
Compression decreased file by 328,127 bytes.
** building package indices ...
** MD5 sums
* DONE (IRanges)