IRanges 1.0.16
Biocore Team c/o BioC user list
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/IRanges | | Last Changed Rev: 38942 / Revision: 38965 | | Last Changed Date: 2009-04-17 14:44:32 -0700 (Fri, 17 Apr 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 (10.5.6) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.3-bioc/meat/IRanges.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: UTF-8
* checking for file 'IRanges/DESCRIPTION' ... OK
* this is package 'IRanges' version '1.0.16'
* 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 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 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
* creating IRanges-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/loc/home/biocbuild/bbs-2.3-bioc/meat/IRanges.Rcheck/tests'
Running 'runalltests.R'
Comparing 'runalltests.Rout' to 'runalltests.Rout.save' ...11,12c11
< rbind,
< sapply
---
> rbind
50a50,61
> Executing test function test_IRanges_combine ... done successfully.
>
>
>
> Executing test function test_IRanges_names ... done successfully.
>
>
>
> Executing test function test_IRanges_setops ... done successfully.
>
>
>
67,71c78
< Executing test function test_IRanges_combine ... done successfully.
<
<
<
< Executing test function test_IRanges_names ... done successfully.
---
> Executing test function test_RDApplyParams_construct ... done successfully.
75c82
< Executing test function test_IRanges_setops ... done successfully.
---
> Executing test function test_RDApplyParams_rdapply ... done successfully.
123,139c130
< Executing test function test_RangesMatching_matched ... Error in t(matchMatrix(x)) :
< no function to return from, jumping to top level
< Calls: t -> t -> t -> t -> .Call
< Error in as.table(t(result)) :
< no function to return from, jumping to top level
< Timing stopped at: 0.012 0 0.011
< Error in as.vector(as.table(t(result))) :
< error in evaluating the argument 'x' in selecting a method for function 'as.vector'
< done successfully.
<
<
<
< Executing test function test_RDApplyParams_construct ... done successfully.
<
<
<
< Executing test function test_RDApplyParams_rdapply ... done successfully.
---
> Executing test function test_RangesMatching_matched ... done successfully.
OK
make[1]: Leaving directory `/loc/home/biocbuild/bbs-2.3-bioc/meat/IRanges.Rcheck/tests'
OK
* creating IRanges-manual.tex ... OK
* checking IRanges-manual.tex using pdflatex ... OK
* Installing *source* package 'IRanges' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c AEbufs.c -o AEbufs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c common.c -o common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c coverage.c -o coverage.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c dlist.c -o dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c errabort.c -o errabort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-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-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c IntervalTree.c -o IntervalTree.o
IntervalTree.c: In function ‘_IntegerIntervalTree_add’:
IntervalTree.c:48: warning: missing braces around initializer
IntervalTree.c:48: warning: (near initialization for ‘tmpInterval.interval’)
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-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-2.3-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:119: warning: ‘ans_inframe_start’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c localmem.c -o localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-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-2.3-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-2.3-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-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c RangesList_class.c -o RangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-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-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c rbTree.c -o rbTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-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-2.3-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-2.3-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-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c solve_user_SEW.c -o solve_user_SEW.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c sort_utils.c -o sort_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-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-2.3-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-2.3-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-2.3-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-2.3-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-2.3-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-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c XSequence_class.c -o XSequence_class.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o IRanges.so AEbufs.o common.o coverage.o dlist.o errabort.o IntegerPtr_utils.o IntervalTree.o IRanges_class.o IRanges_utils.o localmem.o memalloc.o memcpy_utils.o NumericPtr_utils.o RangesList_class.o RawPtr_utils.o rbTree.o R_init_IRanges.o SequencePtr_class.o SEXP_utils.o solve_user_SEW.o sort_utils.o XIntegerViews_class.o XIntegerViews_utils.o XNumericViews_class.o XRleInteger_class.o XRleIntegerViews_class.o XRleIntegerViews_utils.o XSequence_class.o -L/home/biocbuild/bbs-2.3-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 "duplicated" in "IRanges"
Creating a new generic function for "%in%" in "IRanges"
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 "as.table" in "IRanges"
Creating a new generic function for "t" 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 "append" in "IRanges"
Creating a new generic function for "unlist" in "IRanges"
Creating a new generic function for "summary" in "IRanges"
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"
** help
>>> Building/Updating help pages for package 'IRanges'
Formats: text html latex example
FilterRules-class text html latex example
GenomicData-class text html latex example
IRanges-class 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
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
RangesList-class text html latex example
RangesList-utils text html latex example
RangesMatching-class text html latex example
Sequence-class text html latex example
SplitXDataFrame-class text html latex
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
XIntegerViews-class text html latex example
XRanges-class text html latex
XRleIntegerViews-class text html latex example
coverage text html latex example
read.Mask text html latex example
reverse text html latex example
solveUserSEW text html latex example
** building package indices ...
* DONE (IRanges)