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 'E:/biocbld/bbs-2.3-bioc/meat/IRanges.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* 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 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 `/cygdrive/e/biocbld/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: 0.02 0 0.01
< 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 `/cygdrive/e/biocbld/bbs-2.3-bioc/meat/IRanges.Rcheck/tests'
OK
* creating IRanges-manual.tex ... OK
* checking IRanges-manual.tex using pdflatex ... OK
installing R.css in E:/biocbld/bbs-2.3-bioc/meat/IRanges.Rcheck
---------- Making package IRanges ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making AEbufs.d from AEbufs.c
making IRanges_class.d from IRanges_class.c
making IRanges_utils.d from IRanges_utils.c
making IntegerPtr_utils.d from IntegerPtr_utils.c
making IntervalTree.d from IntervalTree.c
making NumericPtr_utils.d from NumericPtr_utils.c
making R_init_IRanges.d from R_init_IRanges.c
making RangesList_class.d from RangesList_class.c
making RawPtr_utils.d from RawPtr_utils.c
making SEXP_utils.d from SEXP_utils.c
making SequencePtr_class.d from SequencePtr_class.c
making XIntegerViews_class.d from XIntegerViews_class.c
making XIntegerViews_utils.d from XIntegerViews_utils.c
making XNumericViews_class.d from XNumericViews_class.c
making XRleIntegerViews_class.d from XRleIntegerViews_class.c
making XRleIntegerViews_utils.d from XRleIntegerViews_utils.c
making XRleInteger_class.d from XRleInteger_class.c
making XSequence_class.d from XSequence_class.c
making common.d from common.c
making coverage.d from coverage.c
making dlist.d from dlist.c
making errabort.d from errabort.c
making localmem.d from localmem.c
making memalloc.d from memalloc.c
making memcpy_utils.d from memcpy_utils.c
making rbTree.d from rbTree.c
making solve_user_SEW.d from solve_user_SEW.c
making sort_utils.d from sort_utils.c
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c AEbufs.c -o AEbufs.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c RangesList_class.c -o RangesList_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c SEXP_utils.c -o SEXP_utils.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c SequencePtr_class.c -o SequencePtr_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c XIntegerViews_class.c -o XIntegerViews_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c XIntegerViews_utils.c -o XIntegerViews_utils.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c XNumericViews_class.c -o XNumericViews_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c XRleIntegerViews_class.c -o XRleIntegerViews_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c XRleIntegerViews_utils.c -o XRleIntegerViews_utils.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c XSequence_class.c -o XSequence_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c common.c -o common.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c coverage.c -o coverage.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c dlist.c -o dlist.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c errabort.c -o errabort.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c localmem.c -o localmem.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -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 -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c rbTree.c -o rbTree.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c solve_user_SEW.c -o solve_user_SEW.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c sort_utils.c -o sort_utils.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-bioc/R/include -i IRanges_res.rc -o IRanges_res.o
gcc -std=gnu99 -shared -s -o IRanges.dll IRanges.def AEbufs.o IRanges_class.o IRanges_utils.o IntegerPtr_utils.o IntervalTree.o NumericPtr_utils.o R_init_IRanges.o RangesList_class.o RawPtr_utils.o SEXP_utils.o SequencePtr_class.o XIntegerViews_class.o XIntegerViews_utils.o XNumericViews_class.o XRleIntegerViews_class.o XRleIntegerViews_utils.o XRleInteger_class.o XSequence_class.o common.o coverage.o dlist.o errabort.o localmem.o memalloc.o memcpy_utils.o rbTree.o solve_user_SEW.o sort_utils.o IRanges_res.o -Le:/biocbld/bbs-2.3-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
preparing package IRanges 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"
installing man source files
installing indices
installing help
>>> Building/Updating help pages for package 'IRanges'
Formats: text html latex example chm
FilterRules-class text html latex example chm
GenomicData-class text html latex example chm
IRanges-class 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
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
RangesList-class text html latex example chm
RangesList-utils text html latex example chm
RangesMatching-class text html latex example chm
Sequence-class text html latex example chm
SplitXDataFrame-class text html latex 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
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
read.Mask text html latex example chm
reverse text html latex example chm
solveUserSEW text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-bioc\meat\IRanges.Rcheck\00_pkg_src\IRanges\chm\IRanges.chm
Compile time: 0 minutes, 0 seconds
32 Topics
644 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.3-bioc\meat\IRanges.Rcheck\00_pkg_src\IRanges\chm\IRanges.chm, 105,124 bytes
Compression decreased file by 219,892 bytes.
adding MD5 sums
* DONE (IRanges)