IRanges 1.11.1
Biocore Team c/o BioC user list
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges | | Last Changed Rev: 55009 / Revision: 55359 | | Last Changed Date: 2011-04-20 22:58:51 -0700 (Wed, 20 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRanges/DESCRIPTION’ ... OK
* this is package ‘IRanges’ version ‘1.11.1’
* 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 installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 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 Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
‘library’ or ‘require’ call not declared from: ‘BSgenome.Celegans.UCSC.ce2’
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘IRanges_unit_tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package ‘IRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c AEbufs.c -o AEbufs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c DataFrame_class.c -o DataFrame_class.o
DataFrame_class.c: In function ‘set_DataFrame_rownames’:
DataFrame_class.c:11:1: warning: no return statement in function returning non-void
DataFrame_class.c: In function ‘set_DataFrame_nrows’:
DataFrame_class.c:16:1: warning: no return statement in function returning non-void
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c GappedRanges_class.c -o GappedRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_utils.c -o IRanges_utils.o
IRanges_utils.c: In function ‘_reduce_ranges’:
IRanges_utils.c:77:6: warning: ‘append_or_drop’ may be used uninitialized in this function
IRanges_utils.c:77:22: warning: ‘max_end’ may be used uninitialized in this function
IRanges_utils.c:77:31: warning: ‘gapwidth’ may be used uninitialized in this function
IRanges_utils.c:77:41: warning: ‘delta’ may be used uninitialized in this function
IRanges_utils.c: In function ‘IRanges_reduce’:
IRanges_utils.c:138:41: warning: ‘ans_inframe_start’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c IntervalTree.c -o IntervalTree.o
IntervalTree.c: In function ‘_IntegerIntervalTree_overlap’:
IntervalTree.c:125:8: warning: ‘result_inds’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
Ocopy_byteblocks.c: In function ‘translate_byte’:
Ocopy_byteblocks.c:20:16: warning: ‘lkup_val’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c RangedData_class.c -o RangedData_class.o
RangedData_class.c: In function ‘set_RangedData_ranges’:
RangedData_class.c:12:1: warning: no return statement in function returning non-void
RangedData_class.c: In function ‘set_RangedData_values’:
RangedData_class.c:17:1: warning: no return statement in function returning non-void
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c Rle_class.c -o Rle_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c Rle_utils.c -o Rle_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c SharedDouble_utils.c -o SharedDouble_utils.o
SharedDouble_utils.c: In function ‘SharedDouble_new’:
SharedDouble_utils.c:24:7: warning: ‘tag’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c SharedInteger_utils.c -o SharedInteger_utils.o
SharedInteger_utils.c: In function ‘SharedInteger_new’:
SharedInteger_utils.c:24:7: warning: ‘tag’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c SharedRaw_utils.c -o SharedRaw_utils.o
SharedRaw_utils.c: In function ‘SharedRaw_new’:
SharedRaw_utils.c:24:7: warning: ‘tag’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c SharedVector_class.c -o SharedVector_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c SimpleList_class.c -o SimpleList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c Vector_class.c -o Vector_class.o
Vector_class.c: In function ‘vector_seqselect’:
Vector_class.c:95:4: warning: implicit declaration of function ‘UNIMPLEMENTED_TYPE’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c XDoubleViews_class.c -o XDoubleViews_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-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-2.9-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-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function ‘alloc_XVectorList’:
XVectorList_class.c:340:40: warning: ‘ans’ may be used uninitialized in this function
XVectorList_class.c: In function ‘_new_XRawList_from_CharAEAE’:
XVectorList_class.c:421:6: warning: ‘lkup_length’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c XVector_class.c -o XVector_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c common.c -o common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c compact_bitvector.c -o compact_bitvector.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c coverage.c -o coverage.o
coverage.c: In function ‘IRanges_coverage’:
coverage.c:34:7: warning: ‘values_buf’ may be used uninitialized in this function
coverage.c:34:20: warning: ‘lengths_buf’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c dlist.c -o dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c errabort.c -o errabort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c int_utils.c -o int_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c localmem.c -o localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c memalloc.c -o memalloc.o
memalloc.c: In function ‘carefulAlloc’:
memalloc.c:293:2: warning: format ‘%d’ expects type ‘int’, but argument 2 has type ‘size_t’
memalloc.c:293:2: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘size_t’
memalloc.c:289:10: warning: unused variable ‘allocRequest’
memalloc.c:288:10: warning: unused variable ‘maxAlloc’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c rbTree.c -o rbTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c str_utils.c -o str_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c vector_copy.c -o vector_copy.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o IRanges.so AEbufs.o CompressedIRangesList_class.o CompressedList_class.o DataFrame_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 RangedData_class.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o SharedDouble_utils.o SharedInteger_utils.o SharedRaw_utils.o SharedVector_class.o SimpleList_class.o SimpleRangesList_class.o Vector_class.o XDoubleViews_class.o XIntegerViews_class.o XIntegerViews_utils.o XVectorList_class.o XVector_class.o anyMissing.o common.o compact_bitvector.o coverage.o dlist.o errabort.o int_utils.o localmem.o memalloc.o rbTree.o sort_utils.o str_utils.o vector_copy.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a new generic function for "NROW" in "IRanges"
Creating a new generic function for "nlevels" 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 "head" in "IRanges"
Creating a new generic function for "tail" in "IRanges"
Creating a new generic function for "rev" 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 "subset" in "IRanges"
Creating a new generic function for "append" in "IRanges"
Creating a new generic function for "tapply" in "IRanges"
Creating a new generic function for "aggregate" 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 "as.list" in "IRanges"
Creating a new generic function for "stack" in "IRanges"
Creating a new generic function for "relist" in "IRanges"
Creating a new generic function for "Reduce" in "IRanges"
Creating a new generic function for "Filter" in "IRanges"
Creating a new generic function for "Find" 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 generic for ‘eval’ in package ‘IRanges’
(the supplied definition differs from and overrides the implicit generic
in package ‘base’: Classes: "nonstandardGenericFunction", "standardGeneric")
Creating a new generic function for "with" 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 "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 "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 "%in%" in "IRanges"
Creating a generic for ‘union’ in package ‘IRanges’
(the supplied definition differs from and overrides the implicit generic
in package ‘base’: Formal arguments differ: (x, y, ...), (x, y))
Creating a generic for ‘intersect’ in package ‘IRanges’
(the supplied definition differs from and overrides the implicit generic
in package ‘base’: Formal arguments differ: (x, y, ...), (x, y))
Creating a generic for ‘setdiff’ in package ‘IRanges’
(the supplied definition differs from and overrides the implicit generic
in package ‘base’: Formal arguments differ: (x, y, ...), (x, y))
Creating a new generic function for "NCOL" in "IRanges"
Creating a new generic function for "na.omit" in "IRanges"
Creating a new generic function for "na.exclude" in "IRanges"
Creating a new generic function for "complete.cases" 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 "xtabs" 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 "is.unsorted" in "IRanges"
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 "ifelse" 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 generic for ‘paste’ in package ‘IRanges’
(the supplied definition differs from and overrides the implicit generic
in package ‘base’: Signatures differ: (...), (sep, collapse))
Creating a new generic function for "levels" in "IRanges"
Creating a new generic function for "which.max" in "IRanges"
Creating a new generic function for "which.min" in "IRanges"
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 "merge" in "IRanges"
Creating a new generic function for "within" 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"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘IRangesOverview.Rnw’
‘RleTricks.Rnw’
** testing if installed package can be loaded
* DONE (IRanges)