IRanges 1.6.17
Biocore Team c/o BioC user list
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/IRanges | | Last Changed Rev: 49355 / Revision: 49923 | | Last Changed Date: 2010-09-11 16:34:58 -0700 (Sat, 11 Sep 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | [ OK ] |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* installing *source* package 'IRanges' ...
** libs
making DLL ...
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c AEbufs.c -o AEbufs.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c DataFrame_class.c -o DataFrame_class.o
DataFrame_class.c: In function 'set_DataFrame_rownames':
DataFrame_class.c:11: warning: no return statement in function returning non-void
DataFrame_class.c: In function 'set_DataFrame_nrows':
DataFrame_class.c:16: warning: no return statement in function returning non-void
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c GappedRanges_class.c -o GappedRanges_class.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c Grouping_class.c -o Grouping_class.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c IRanges_class.c -o IRanges_class.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c IRanges_constructor.c -o IRanges_constructor.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c IRanges_utils.c -o IRanges_utils.o
IRanges_utils.c: In function '_reduce_ranges':
IRanges_utils.c:78: warning: 'append_or_drop' may be used uninitialized in this function
IRanges_utils.c:78: warning: 'max_end' may be used uninitialized in this function
IRanges_utils.c:78: warning: 'gapwidth' may be used uninitialized in this function
IRanges_utils.c:78: warning: 'delta' may be used uninitialized in this function
IRanges_utils.c: In function 'IRanges_reduce':
IRanges_utils.c:139: warning: 'ans_inframe_start' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c IntervalTree.c -o IntervalTree.o
IntervalTree.c: In function '_IntegerIntervalTree_overlap':
IntervalTree.c:125: warning: 'result_inds' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
Ocopy_byteblocks.c: In function 'translate_byte':
Ocopy_byteblocks.c:20: warning: 'lkup_val' may be used uninitialized in this function
Ocopy_byteblocks.c: In function '_Ocopy_bytes_from_i1i2_to_complex':
Ocopy_byteblocks.c:466: warning: 'lkup_val.i' may be used uninitialized in this function
Ocopy_byteblocks.c:466: warning: 'lkup_val.r' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c R_init_IRanges.c -o R_init_IRanges.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c RangedData_class.c -o RangedData_class.o
RangedData_class.c: In function 'set_RangedData_ranges':
RangedData_class.c:12: warning: no return statement in function returning non-void
RangedData_class.c: In function 'set_RangedData_values':
RangedData_class.c:17: warning: no return statement in function returning non-void
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c RleViews_utils.c -o RleViews_utils.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c Rle_class.c -o Rle_class.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c Rle_utils.c -o Rle_utils.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c SEXP_utils.c -o SEXP_utils.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -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'
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c SharedVector_class.c -o SharedVector_class.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c SimpleList_class.c -o SimpleList_class.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c XDoubleViews_class.c -o XDoubleViews_class.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c XIntegerViews_class.c -o XIntegerViews_class.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c XIntegerViews_utils.c -o XIntegerViews_utils.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function '_new_XRawList_from_CharAEAE':
XVectorList_class.c:288: warning: 'lkup_length' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c XVector_class.c -o XVector_class.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c anyMissing.c -o anyMissing.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c chain_io.c -o chain_io.o
chain_io.c: In function 'read_chain_file':
chain_io.c:33: warning: 'tstart' may be used uninitialized in this function
chain_io.c:33: warning: 'qstart' may be used uninitialized in this function
chain_io.c:34: warning: 'trc' may be used uninitialized in this function
chain_io.c:34: warning: 'qrc' may be used uninitialized in this function
chain_io.c:35: warning: 'block' may be used uninitialized in this function
chain_io.c:38: warning: 'header_line' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c common.c -o common.o
common.c: In function 'mustWrite':
common.c:1605: warning: unknown conversion type character 'l' in format
common.c:1605: warning: format '%s' expects type 'char *', but argument 2 has type 'long long int'
common.c:1605: warning: too many arguments for format
common.c: In function 'mustRead':
common.c:1614: warning: unknown conversion type character 'l' in format
common.c:1614: warning: format '%s' expects type 'char *', but argument 2 has type 'long long int'
common.c:1614: warning: too many arguments for format
common.c: In function 'safecpy':
common.c:2007: warning: unknown conversion type character 'l' in format
common.c:2007: warning: unknown conversion type character 'l' in format
common.c:2007: warning: too many arguments for format
common.c: In function 'safencpy':
common.c:2016: warning: unknown conversion type character 'l' in format
common.c:2016: warning: unknown conversion type character 'l' in format
common.c:2016: warning: too many arguments for format
common.c: In function 'safecat':
common.c:2030: warning: unknown conversion type character 'l' in format
common.c:2030: warning: unknown conversion type character 'l' in format
common.c:2030: warning: too many arguments for format
common.c: In function 'safencat':
common.c:2039: warning: unknown conversion type character 'l' in format
common.c:2039: warning: unknown conversion type character 'l' in format
common.c:2039: warning: too many arguments for format
common.c: In function 'refListFromSlList':
common.c:311: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
common.c:299: note: initialized from here
common.c: In function 'slNameListFromStringArray':
common.c:311: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
common.c:299: note: initialized from here
common.c: In function 'slNameCloneList':
common.c:311: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
common.c:299: note: initialized from here
common.c: In function 'slNameListFromString':
common.c:311: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
common.c:299: note: initialized from here
common.c: In function 'slPairFromString':
common.c:311: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
common.c:299: note: initialized from here
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c compact_bitvector.c -o compact_bitvector.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c coverage.c -o coverage.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c dlist.c -o dlist.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c errabort.c -o errabort.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c hash.c -o hash.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c localmem.c -o localmem.o
localmem.c: In function 'newBlock':
localmem.c:39: warning: unknown conversion type character 'l' in format
localmem.c:39: warning: too many arguments for format
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c memalloc.c -o memalloc.o
memalloc.c: In function 'needLargeMem':
memalloc.c:91: warning: unknown conversion type character 'l' in format
memalloc.c:91: warning: unknown conversion type character 'l' in format
memalloc.c:91: warning: too many arguments for format
memalloc.c:94: warning: unknown conversion type character 'l' in format
memalloc.c:94: warning: format '%d' expects type 'int', but argument 2 has type 'size_t'
memalloc.c:94: warning: too many arguments for format
memalloc.c: In function 'needLargeMemResize':
memalloc.c:114: warning: unknown conversion type character 'l' in format
memalloc.c:114: warning: unknown conversion type character 'l' in format
memalloc.c:114: warning: too many arguments for format
memalloc.c:117: warning: unknown conversion type character 'l' in format
memalloc.c:117: warning: format '%d' expects type 'int', but argument 2 has type 'size_t'
memalloc.c:117: warning: too many arguments for format
memalloc.c: In function 'needHugeMem':
memalloc.c:139: warning: unknown conversion type character 'l' in format
memalloc.c:139: warning: format '%d' expects type 'int', but argument 2 has type 'size_t'
memalloc.c:139: warning: too many arguments for format
memalloc.c: In function 'needHugeMemResize':
memalloc.c:161: warning: unknown conversion type character 'l' in format
memalloc.c:161: warning: format '%d' expects type 'int', but argument 2 has type 'size_t'
memalloc.c:161: warning: too many arguments for format
memalloc.c: In function 'needMem':
memalloc.c:187: warning: unknown conversion type character 'l' in format
memalloc.c:187: warning: unknown conversion type character 'l' in format
memalloc.c:187: warning: too many arguments for format
memalloc.c:190: warning: unknown conversion type character 'l' in format
memalloc.c:190: warning: format '%d' expects type 'int', but argument 2 has type 'size_t'
memalloc.c:190: warning: too many arguments for format
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'
memalloc.c: In function 'carefulFree':
memalloc.c:318: warning: unknown conversion type character 'l' in format
memalloc.c:318: warning: too many arguments for format
memalloc.c:322: warning: unknown conversion type character 'l' in format
memalloc.c:322: warning: too many arguments for format
memalloc.c: In function 'carefulCheckHeap':
memalloc.c:360: warning: unknown conversion type character 'l' in format
memalloc.c:360: warning: too many arguments for format
memalloc.c:364: warning: unknown conversion type character 'l' in format
memalloc.c:364: warning: too many arguments for format
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c rbTree.c -o rbTree.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c sort_utils.c -o sort_utils.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c strutils.c -o strutils.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c vector_copy.c -o vector_copy.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o IRanges.dll tmp.def AEbufs.o CompressedIRangesList_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 Sequence_class.o SharedDouble_utils.o SharedInteger_utils.o SharedRaw_utils.o SharedVector_class.o SimpleList_class.o SimpleRangesList_class.o XDoubleViews_class.o XIntegerViews_class.o XIntegerViews_utils.o XVectorList_class.o XVector_class.o anyMissing.o chain_io.o common.o compact_bitvector.o coverage.o dlist.o errabort.o hash.o localmem.o memalloc.o rbTree.o sort_utils.o strutils.o vector_copy.o -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/x64
... done
** 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': Signatures 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 "stack" 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 "tapply" in "IRanges"
Creating a new generic function for "aggregate" in "IRanges"
Creating a new generic function for "as.list" 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 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 "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 "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 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.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 "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 "toString" 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 "within" 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 ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IRanges' as IRanges_1.6.17.zip
* DONE (IRanges)