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 |
* 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
* 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)