IRanges 1.5.16
Biocore Team c/o BioC user list
| Bioconductor Changelog | | Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges | | Last Changed Rev: 43434 / Revision: 43434 | | Last Changed Date: 2009-12-07 09:57:18 -0800 (Mon, 07 Dec 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ WARNINGS ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/IRanges.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-10-22 r50179)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IRanges/DESCRIPTION' ... OK
* this is package 'IRanges' version '1.5.16'
* 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 ... NOTE
prepare_Rd: DataTable-stats.Rd:14-15: Dropping empty section 'Regression'
prepare_Rd: RangesMatchingList-class.Rd:93-94: Dropping empty section \examples
prepare_Rd: XVectorList-class.Rd:52-53: Dropping empty section \examples
prepare_Rd: score.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
GappedRanges
Undocumented S4 methods:
generic '[' and siglist 'GappedRanges'
generic '[[' and siglist 'GappedRanges'
generic 'c' and siglist 'GappedRanges'
generic 'coerce' and siglist 'CompressedIRangesList,GappedRanges'
generic 'coerce' and siglist 'GappedRanges,CompressedIRangesList'
generic 'coerce' and siglist 'GappedRanges,IRangesList'
generic 'coerce' and siglist 'GappedRanges,RangesList'
generic 'elementLengths' and siglist 'GappedRanges'
generic 'end' and siglist 'GappedRanges'
generic 'gsub' and siglist 'ANY,ANY,Rle,ANY,missing'
generic 'length' and siglist 'GappedRanges'
generic 'names' and siglist 'GappedRanges'
generic 'names<-' and siglist 'GappedRanges'
generic 'narrow' and siglist 'GappedRanges'
generic 'seqselect' and siglist 'GappedRanges'
generic 'start' and siglist 'GappedRanges'
generic 'sub' and siglist 'ANY,ANY,Rle,ANY,missing'
generic 'window' and siglist 'GappedRanges'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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
WARNING: There was 1 warning, see
E:/biocbld/bbs-2.6-bioc/meat/IRanges.Rcheck/00check.log
for details
* install options are ' --no-html'
* installing *source* package 'IRanges' ...
** libs
making DLL ...
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c AEbufs.c -o AEbufs.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c GappedRanges_class.c -o GappedRanges_class.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c Grouping_class.c -o Grouping_class.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c IRanges_class.c -o IRanges_class.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c IRanges_constructor.c -o IRanges_constructor.o
gcc -I"e:/biocbld/bbs-2.6-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:74: warning: 'ans_inframe_start' may be used uninitialized in this function
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c IntervalTree.c -o IntervalTree.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
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
Ocopy_byteblocks.c: In function '_Ocopy_bytes_from_subscript_with_lkup':
Ocopy_byteblocks.c:20: warning: 'lkup_val' may be used uninitialized in this function
Ocopy_byteblocks.c:20: note: 'lkup_val' was declared here
Ocopy_byteblocks.c: In function '_Ocopy_bytes_from_i1i2_with_lkup':
Ocopy_byteblocks.c:20: warning: 'lkup_val' may be used uninitialized in this function
Ocopy_byteblocks.c:20: note: 'lkup_val' was declared here
Ocopy_byteblocks.c: In function '_Orevcopy_bytes_from_i1i2_with_lkup':
Ocopy_byteblocks.c:20: warning: 'lkup_val' may be used uninitialized in this function
Ocopy_byteblocks.c:20: note: 'lkup_val' was declared here
Ocopy_byteblocks.c: In function '_Ocopy_bytes_to_subscript_with_lkup':
Ocopy_byteblocks.c:20: warning: 'lkup_val' may be used uninitialized in this function
Ocopy_byteblocks.c:20: note: 'lkup_val' was declared here
Ocopy_byteblocks.c: In function '_Ocopy_bytes_to_i1i2_with_lkup':
Ocopy_byteblocks.c:20: warning: 'lkup_val' may be used uninitialized in this function
Ocopy_byteblocks.c:20: note: 'lkup_val' was declared here
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c R_init_IRanges.c -o R_init_IRanges.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c Ranges_comparison.c -o Ranges_comparison.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c RleViews_utils.c -o RleViews_utils.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c Rle_class.c -o Rle_class.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c Rle_utils.c -o Rle_utils.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c SEXP_utils.c -o SEXP_utils.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c Sequence_class.c -o Sequence_class.o
Sequence_class.c: In function 'vector_seqselect':
Sequence_class.c:95: warning: implicit declaration of function 'UNIMPLEMENTED_TYPE'
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c SharedDouble_utils.c -o SharedDouble_utils.o
SharedDouble_utils.c: In function 'SharedDouble_new':
SharedDouble_utils.c:24: warning: 'tag' may be used uninitialized in this function
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c SharedInteger_utils.c -o SharedInteger_utils.o
SharedInteger_utils.c: In function 'SharedInteger_new':
SharedInteger_utils.c:24: warning: 'tag' may be used uninitialized in this function
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -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 -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c SharedVector_class.c -o SharedVector_class.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c XDoubleViews_class.c -o XDoubleViews_class.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c XIntegerViews_class.c -o XIntegerViews_class.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c XIntegerViews_utils.c -o XIntegerViews_utils.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c XVectorList_class.c -o XVectorList_class.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c XVector_class.c -o XVector_class.o
gcc -I"e:/biocbld/bbs-2.6-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: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 -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c common.c -o common.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c coverage.c -o coverage.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c dlist.c -o dlist.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c errabort.c -o errabort.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c hash.c -o hash.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c localmem.c -o localmem.o
gcc -I"e:/biocbld/bbs-2.6-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-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c rbTree.c -o rbTree.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c sort_utils.c -o sort_utils.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c strutils.c -o strutils.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c vector_copy.c -o vector_copy.o
gcc -shared -s -o IRanges.dll tmp.def AEbufs.o CompressedIRangesList_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 Ranges_comparison.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o Sequence_class.o SharedDouble_utils.o SharedInteger_utils.o SharedRaw_utils.o SharedVector_class.o XDoubleViews_class.o XIntegerViews_class.o XIntegerViews_utils.o XVectorList_class.o XVector_class.o chain_io.o common.o coverage.o dlist.o errabort.o hash.o localmem.o memalloc.o rbTree.o sort_utils.o strutils.o vector_copy.o -Le:/biocbld/bbs-2.6-bioc/R/bin -lR
... done
** R
** inst
** preparing package for lazy loading
Warning in .completeClassSlots(ClassDef, where) :
undefined slot classes in definition of "Sequence": elementMetadata(class "DataTableORNULL")
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "elementMetadata<-" no definition for class: "DataTableORNULL"
Warning in .completeClassSlots(ClassDef, where) :
undefined slot classes in definition of "Sequence": elementMetadata(class "DataTableORNULL")
Creating a new generic function for "append" in "IRanges"
Creating a new generic function for "Filter" in "IRanges"
Creating a new generic function for "Find" in "IRanges"
Creating a new generic function for "head" in "IRanges"
Creating a generic for "Map" in package "IRanges"
(the supplied definition differs from and overrides the implicit generic
in package "base": Signatures differ: (...), (f))
Creating a new generic function for "Position" in "IRanges"
Creating a new generic function for "Reduce" in "IRanges"
Creating a new generic function for "rev" in "IRanges"
Creating a new generic function for "subset" in "IRanges"
Creating a new generic function for "tail" in "IRanges"
Creating a new generic function for "window" in "IRanges"
Creating a new generic function for "window<-" in "IRanges"
Creating a new generic function for "lapply" in "IRanges"
Creating a new generic function for "sapply" in "IRanges"
Creating a generic for "mapply" in package "IRanges"
(the supplied definition differs from and overrides the implicit generic
in package "base": Signatures differ: (...), (FUN, MoreArgs, SIMPLIFY, USE.NAMES))
Creating a new generic function for "aggregate" in "IRanges"
Creating a new generic function for "eval" in "IRanges"
Restoring the implicit generic function for "with" from package "base"
into package "IRanges"; the generic differs from the default conversion (Signatures differ: (data, expr), (data))
Creating a new generic function for "with" in "IRanges"
Creating a new generic function for "as.list" in "IRanges"
Warning in .completeClassSlots(ClassDef, where) :
undefined slot classes in definition of "DataTable": elementMetadata(class "DataTableORNULL")
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 new generic function for "NCOL" in "IRanges"
Creating a new generic function for "NROW" in "IRanges"
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))
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "showAsCell" no definition for class: "vectorORfactor"
Creating a new generic function for "xtabs" in "IRanges"
In method for function "xtabs": expanding the signature to include
omitted arguments in definition: sparse = "missing"
Creating a new generic function for "start" in "IRanges"
Creating a new generic function for "end" in "IRanges"
Creating a new generic function for "update" 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 "unlist" in "IRanges"
Creating a new generic function for "%in%" in "IRanges"
Creating a new generic function for "duplicated" in "IRanges"
Creating a new generic function for "unique" in "IRanges"
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 new generic function for "sort" in "IRanges"
Creating a new generic function for "rank" 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"
Warning in .completeClassSlots(ClassDef, where) :
undefined slot classes in definition of "Binning": bins(class "CompressedIntegerList")
Warning in .completeClassSlots(ClassDef, where) :
undefined slot classes in definition of "Binning": bins(class "CompressedIntegerList")
Creating a new generic function for "as.vector" in "IRanges"
Creating a new generic function for "as.factor" 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 "split" 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 "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 "IQR" in "IRanges"
Creating a new generic function for "smoothEnds" in "IRanges"
Creating a new generic function for "runmed" 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"
In method for function "sub": expanding the signature to include
omitted arguments in definition: extended = "missing"
Creating a new generic function for "gsub" in "IRanges"
In method for function "gsub": expanding the signature to include
omitted arguments in definition: extended = "missing"
Creating a new generic function for "levels" in "IRanges"
Creating a new generic function for "toString" in "IRanges"
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "coerce" no definition for class: "SimpleSplitDataFrameList"
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "coerce" no definition for class: "CompressedSplitDataFrameList"
Creating a new generic function for "nrow" in "IRanges"
Creating a new generic function for "ncol" in "IRanges"
Creating a new generic function for "rownames" in "IRanges"
Creating a new generic function for "colnames" in "IRanges"
Creating a new generic function for "rownames<-" in "IRanges"
Creating a new generic function for "colnames<-" 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 package indices ...
** MD5 sums
* DONE (IRanges)