IRanges 2.2.9
Bioconductor Package Maintainer
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/IRanges | | Last Changed Rev: 109056 / Revision: 109384 | | Last Changed Date: 2015-09-30 23:00:40 -0700 (Wed, 30 Sep 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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###
### Running command:
###
### rm -rf IRanges.buildbin-libdir IRanges.Rcheck && mkdir IRanges.buildbin-libdir IRanges.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IRanges.buildbin-libdir IRanges_2.2.9.tar.gz >IRanges.Rcheck\00install.out 2>&1 && cp IRanges.Rcheck\00install.out IRanges-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=IRanges.buildbin-libdir --install="check:IRanges-install.out" --force-multiarch --no-vignettes --timings IRanges_2.2.9.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/IRanges.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IRanges/DESCRIPTION' ... OK
* this is package 'IRanges' version '2.2.9'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'IRanges' can be installed ... WARNING
Found the following significant warnings:
common.c:1605:5: warning: too many arguments for format [-Wformat-extra-args]
common.c:1614:5: warning: too many arguments for format [-Wformat-extra-args]
common.c:2007:5: warning: too many arguments for format [-Wformat-extra-args]
common.c:2016:5: warning: too many arguments for format [-Wformat-extra-args]
common.c:2030:5: warning: too many arguments for format [-Wformat-extra-args]
common.c:2039:5: warning: too many arguments for format [-Wformat-extra-args]
localmem.c:39:5: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:316:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:320:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:358:18: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:362:18: warning: too many arguments for format [-Wformat-extra-args]
Warning: unable to find a consistent ordering of superclasses for class "StandardGenericFilterClosure": order chosen is inconsistent with the superclasses of "standardGeneric"
See 'E:/biocbld/bbs-3.1-bioc/meat/IRanges.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
* loading checks for arch 'i386'
** 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'XVector' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'stats:::window.default'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
evalSeparately,FilterRules : .local : <anonymous>: no visible global
function definition for '.'
subsetByOverlaps,RangedData-RangedData : .local: possible error in
is.na(findOverlaps(ranges(query), ranges(subject), maxgap = maxgap,
minoverlap = minoverlap, type = match.arg(type), select =
"arbitrary"), algorithm = match.arg(algorithm)): unused argument
(algorithm = match.arg(algorithm))
subsetByOverlaps,RangedData-RangesList : .local: possible error in
is.na(findOverlaps(ranges(query), subject, maxgap = maxgap,
minoverlap = minoverlap, type = match.arg(type), select =
"arbitrary"), algorithm = match.arg(algorithm)): unused argument
(algorithm = match.arg(algorithm))
subsetByOverlaps,RangesList-RangedData : .local: possible error in
is.na(findOverlaps(query, ranges(subject), maxgap = maxgap,
minoverlap = minoverlap, type = match.arg(type), select =
"arbitrary"), algorithm = match.arg(algorithm)): unused argument
(algorithm = match.arg(algorithm))
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '!' and siglist 'List'
generic '<=' and siglist 'List,List'
generic '<=' and siglist 'List,list'
generic '<=' and siglist 'list,List'
generic '==' and siglist 'List,List'
generic '==' and siglist 'List,list'
generic '==' and siglist 'list,List'
generic 'anyDuplicated' and siglist 'RangesNSBS'
generic 'anyDuplicated' and siglist 'RleNSBS'
generic 'as.integer' and siglist 'RangesNSBS'
generic 'as.integer' and siglist 'RleNSBS'
generic 'c' and siglist 'SimpleList'
generic 'coerce' and siglist 'Hits,CompressedIntegerList'
generic 'coerce' and siglist 'Hits,IRanges'
generic 'coerce' and siglist 'Hits,IntegerList'
generic 'coerce' and siglist 'Hits,Partitioning'
generic 'coerce' and siglist 'Hits,PartitioningByEnd'
generic 'coerce' and siglist 'Hits,Ranges'
generic 'coerce' and siglist 'PartitioningByEnd,PartitioningMap'
generic 'colnames' and siglist 'SDFLWrapperForTransform'
generic 'compare' and siglist 'List,List'
generic 'compare' and siglist 'List,list'
generic 'compare' and siglist 'list,List'
generic 'duplicated' and siglist 'List'
generic 'is.na' and siglist 'CompressedList'
generic 'is.na' and siglist 'List'
generic 'length' and siglist 'RangesNSBS'
generic 'length' and siglist 'RleNSBS'
generic 'match' and siglist 'CompressedList,list'
generic 'match' and siglist 'CompressedList,vector'
generic 'match' and siglist 'List,List'
generic 'match' and siglist 'List,Vector'
generic 'match' and siglist 'List,list'
generic 'match' and siglist 'List,vector'
generic 'match' and siglist 'list,List'
generic 'relistToClass' and siglist 'Hits'
generic 'splitAsList' and siglist 'ANY,List'
generic 'splitAsList' and siglist 'ANY,Rle'
generic 'splitAsList' and siglist 'ANY,vectorORfactor'
generic 'unique' and siglist 'List'
generic 'unique' and siglist 'SimpleList'
generic 'unlist' and siglist 'SimpleFactorList'
generic 'unlist' and siglist 'SimpleRleList'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.1-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/i386/IRanges.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'E:/biocbld/bbs-3.1-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/x64/IRanges.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [9s] OK
** running examples for arch 'x64' ... [11s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'IRanges_unit_tests.R' [78s]
[78s] OK
** running tests for arch 'x64' ...
Running 'IRanges_unit_tests.R' [102s]
[102s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
'E:/biocbld/bbs-3.1-bioc/meat/IRanges.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'IRanges' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c CompressedList_class.c -o CompressedList_class.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c GappedRanges_class.c -o GappedRanges_class.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Grouping_class.c -o Grouping_class.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_class.c -o IRanges_class.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_constructor.c -o IRanges_constructor.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IntervalTree.c -o IntervalTree.o
IntervalTree.c: In function '_IntegerIntervalTree_overlap_first':
IntervalTree.c:502:20: warning: variable 'nhits' set but not used [-Wunused-but-set-variable]
IntervalTree.c: In function '_IntegerIntervalTree_overlap_last':
IntervalTree.c:576:20: warning: variable 'nhits' set but not used [-Wunused-but-set-variable]
IntervalTree.c: In function '_IntegerIntervalTree_overlap':
IntervalTree.c:367:3: warning: 'result_inds' may be used uninitialized in this function [-Wuninitialized]
IntervalTree.c: In function '_IntegerIntervalForest_overlap':
IntervalTree.c:395:17: warning: 'result_inds' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c NCList.c -o NCList.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_IRanges.c -o R_init_IRanges.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c RangedData_class.c -o RangedData_class.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Ranges_class.c -o Ranges_class.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Ranges_comparison.c -o Ranges_comparison.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c RleViews_utils.c -o RleViews_utils.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c common.c -o common.o
common.c: In function 'mustWrite':
common.c:1605:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:1605:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
common.c:1605:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'mustRead':
common.c:1614:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:1614:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
common.c:1614:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safecpy':
common.c:2007:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2007:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2007:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safencpy':
common.c:2016:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2016:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2016:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safecat':
common.c:2030:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2030:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2030:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safencat':
common.c:2039:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2039:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2039:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function 'compute_coverage_from_IRanges_holder':
coverage_methods.c:503:37: warning: 'x_end' may be used uninitialized in this function [-Wuninitialized]
coverage_methods.c:419:21: note: 'x_end' was declared here
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dlist.c -o dlist.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c errabort.c -o errabort.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'reduce_ranges':
inter_range_methods.c:168:11: warning: 'gapwidth' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c localmem.c -o localmem.o
localmem.c: In function 'newBlock':
localmem.c:39:5: warning: unknown conversion type character 'l' in format [-Wformat]
localmem.c:39:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c memalloc.c -o memalloc.o
memalloc.c: In function 'needLargeMem':
memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:94:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:94:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needLargeMemResize':
memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:117:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:117:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needHugeMem':
memalloc.c:139:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:139:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needHugeMemResize':
memalloc.c:161:2: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:161:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needMem':
memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:190:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:190:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'carefulAlloc':
memalloc.c:291:2: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:291:2: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
memalloc.c: In function 'carefulFree':
memalloc.c:316:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:316:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:320:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:320:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'carefulCheckHeap':
memalloc.c:358:18: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:358:18: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:362:18: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:362:18: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rbTree.c -o rbTree.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc_handlers.c -o ucsc_handlers.o
gcc -m32 -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedIRangesList_class.o CompressedList_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o IntervalTree.o NCList.o R_init_IRanges.o RangedData_class.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o common.o coverage_methods.o dlist.o errabort.o inter_range_methods.o localmem.o memalloc.o rbTree.o ucsc_handlers.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Creating a generic function for 'window<-' from package 'stats' in package 'IRanges'
Creating a generic function for 'rev' from package 'base' in package 'IRanges'
in method for 'coerce' with signature '"Hits","PartitioningByEnd"': no definition for class "PartitioningByEnd"
in method for 'coerce' with signature '"Hits","Partitioning"': no definition for class "Partitioning"
in method for 'coerce' with signature '"Hits","Ranges"': no definition for class "Ranges"
in method for 'coerce' with signature '"Hits","IRanges"': no definition for class "IRanges"
in method for 'coerce' with signature '"Hits","CompressedIntegerList"': no definition for class "CompressedIntegerList"
in method for 'coerce' with signature '"Hits","IntegerList"': no definition for class "IntegerList"
Creating a generic function for 'stack' from package 'utils' in package 'IRanges'
in method for '!' with signature '"CompressedList"': no definition for class "CompressedList"
in method for 'match' with signature '"CompressedList","list"': no definition for class "CompressedList"
in method for 'match' with signature '"CompressedList","vector"': no definition for class "CompressedList"
in method for 'duplicated' with signature '"CompressedList"': no definition for class "CompressedList"
in method for 'unique' with signature '"CompressedList"': no definition for class "CompressedList"
in method for 'is.na' with signature '"CompressedList"': no definition for class "CompressedList"
Creating a generic function for 'mean' from package 'base' in package 'IRanges'
Creating a generic function for 'which.max' from package 'base' in package 'IRanges'
Creating a generic function for 'which.min' from package 'base' in package 'IRanges'
Creating a generic function for 'split' from package 'base' in package 'IRanges'
Creating a generic function for 'split<-' from package 'base' in package 'IRanges'
Creating a generic function for 'drop' from package 'base' in package 'IRanges'
Creating a generic function for 'which' from package 'base' in package 'IRanges'
Creating a generic function for 'diff' from package 'base' in package 'IRanges'
Creating a generic function for 'var' from package 'stats' in package 'IRanges'
Creating a generic function for 'cov' from package 'stats' in package 'IRanges'
Creating a generic function for 'cor' from package 'stats' in package 'IRanges'
Creating a generic function for 'sd' from package 'stats' in package 'IRanges'
Creating a generic function for 'median' from package 'stats' in package 'IRanges'
Creating a generic function for 'quantile' from package 'stats' in package 'IRanges'
Creating a generic function for 'mad' from package 'stats' in package 'IRanges'
Creating a generic function for 'IQR' from package 'stats' in package 'IRanges'
Creating a generic function for 'smoothEnds' from package 'stats' in package 'IRanges'
Creating a generic function for 'runmed' from package 'stats' in package 'IRanges'
Creating a generic function for 'nchar' from package 'base' in package 'IRanges'
Creating a generic function for 'chartr' from package 'base' in package 'IRanges'
Creating a generic function for 'tolower' from package 'base' in package 'IRanges'
Creating a generic function for 'toupper' from package 'base' in package 'IRanges'
Creating a generic function for 'sub' from package 'base' in package 'IRanges'
Creating a generic function for 'gsub' from package 'base' in package 'IRanges'
Warning: unable to find a consistent ordering of superclasses for class "StandardGenericFilterClosure": order chosen is inconsistent with the superclasses of "standardGeneric"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
install for x64
* installing *source* package 'IRanges' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c CompressedList_class.c -o CompressedList_class.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c GappedRanges_class.c -o GappedRanges_class.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Grouping_class.c -o Grouping_class.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_class.c -o IRanges_class.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_constructor.c -o IRanges_constructor.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IntervalTree.c -o IntervalTree.o
IntervalTree.c: In function '_IntegerIntervalTree_overlap_first':
IntervalTree.c:502:20: warning: variable 'nhits' set but not used [-Wunused-but-set-variable]
IntervalTree.c: In function '_IntegerIntervalTree_overlap_last':
IntervalTree.c:576:20: warning: variable 'nhits' set but not used [-Wunused-but-set-variable]
IntervalTree.c: In function '_IntegerIntervalTree_overlap':
IntervalTree.c:367:3: warning: 'result_inds' may be used uninitialized in this function [-Wuninitialized]
IntervalTree.c: In function '_IntegerIntervalForest_overlap':
IntervalTree.c:395:17: warning: 'result_inds' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c NCList.c -o NCList.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_IRanges.c -o R_init_IRanges.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RangedData_class.c -o RangedData_class.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Ranges_class.c -o Ranges_class.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Ranges_comparison.c -o Ranges_comparison.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RleViews_utils.c -o RleViews_utils.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c common.c -o common.o
common.c: In function 'mustWrite':
common.c:1605:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:1605:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
common.c:1605:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'mustRead':
common.c:1614:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:1614:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
common.c:1614:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safecpy':
common.c:2007:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2007:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2007:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safencpy':
common.c:2016:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2016:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2016:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safecat':
common.c:2030:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2030:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2030:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safencat':
common.c:2039:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2039:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2039:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function 'compute_coverage_from_IRanges_holder':
coverage_methods.c:503:37: warning: 'x_end' may be used uninitialized in this function [-Wuninitialized]
coverage_methods.c:419:21: note: 'x_end' was declared here
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c dlist.c -o dlist.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c errabort.c -o errabort.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'reduce_ranges':
inter_range_methods.c:179:20: warning: 'revmap_elt' may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:185:35: warning: 'delta' may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:168:11: warning: 'gapwidth' may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:170:14: warning: 'max_end' may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:145:6: warning: 'append_or_drop' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c localmem.c -o localmem.o
localmem.c: In function 'newBlock':
localmem.c:39:5: warning: unknown conversion type character 'l' in format [-Wformat]
localmem.c:39:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c memalloc.c -o memalloc.o
memalloc.c: In function 'needLargeMem':
memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:94:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:94:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needLargeMemResize':
memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:117:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:117:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needHugeMem':
memalloc.c:139:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:139:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needHugeMemResize':
memalloc.c:161:2: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:161:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needMem':
memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:190:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:190:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'carefulAlloc':
memalloc.c:291:2: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:291:2: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
memalloc.c: In function 'carefulFree':
memalloc.c:316:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:316:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:320:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:320:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'carefulCheckHeap':
memalloc.c:358:18: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:358:18: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:362:18: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:362:18: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rbTree.c -o rbTree.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc_handlers.c -o ucsc_handlers.o
gcc -m64 -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedIRangesList_class.o CompressedList_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o IntervalTree.o NCList.o R_init_IRanges.o RangedData_class.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o common.o coverage_methods.o dlist.o errabort.o inter_range_methods.o localmem.o memalloc.o rbTree.o ucsc_handlers.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'IRanges' as IRanges_2.2.9.zip
* DONE (IRanges)