Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H [I] J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 176/353HostnameOS / ArchBUILDCHECKBUILD BIN
IRanges 1.4.9
Biocore Team c/o BioC user list
Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/IRanges
Last Changed Rev: 43271 / Revision: 43539
Last Changed Date: 2009-11-26 06:09:41 -0800 (Thu, 26 Nov 2009)
wilson2 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: 1.4.9
Command: E:\biocbld\bbs-2.5-bioc\R\bin\R.exe CMD check --no-vignettes IRanges_1.4.9.tar.gz
StartedAt: 2009-12-14 05:20:49 -0800 (Mon, 14 Dec 2009)
EndedAt: 2009-12-14 05:23:45 -0800 (Mon, 14 Dec 2009)
EllapsedTime: 176.5 seconds
RetCode: 0
Status: OK
CheckDir: IRanges.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.5-bioc/meat/IRanges.Rcheck'
* using R version 2.10.0 (2009-10-26)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IRanges/DESCRIPTION' ... OK
* this is package 'IRanges' version '1.4.9'
* 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 ... 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:

* install options are ' --no-html'

* installing *source* package 'IRanges' ...
** libs
  making DLL ...
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c AEbufs.c -o AEbufs.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c Grouping_class.c -o Grouping_class.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c IRanges_class.c -o IRanges_class.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c IRanges_constructor.c -o IRanges_constructor.o
gcc -I"e:/biocbld/bbs-2.5-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-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c IntervalTree.c -o IntervalTree.o
gcc -I"e:/biocbld/bbs-2.5-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-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c R_init_IRanges.c -o R_init_IRanges.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c Ranges_comparison.c -o Ranges_comparison.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c RleViews_utils.c -o RleViews_utils.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c Rle_class.c -o Rle_class.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c Rle_utils.c -o Rle_utils.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c SEXP_utils.c -o SEXP_utils.o
gcc -I"e:/biocbld/bbs-2.5-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-2.5-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-2.5-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-2.5-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-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c SharedVector_class.c -o SharedVector_class.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c XDoubleViews_class.c -o XDoubleViews_class.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c XIntegerViews_class.c -o XIntegerViews_class.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c XIntegerViews_utils.c -o XIntegerViews_utils.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c XVectorList_class.c -o XVectorList_class.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c XVector_class.c -o XVector_class.o
gcc -I"e:/biocbld/bbs-2.5-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-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c common.c -o common.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c coverage.c -o coverage.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c dlist.c -o dlist.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c errabort.c -o errabort.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c hash.c -o hash.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c localmem.c -o localmem.o
gcc -I"e:/biocbld/bbs-2.5-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-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c rbTree.c -o rbTree.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c sort_utils.c -o sort_utils.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c strutils.c -o strutils.o
gcc -I"e:/biocbld/bbs-2.5-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 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-2.5-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"
Creating a new generic function for "gsub" in "IRanges"
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)