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:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings IRanges_2.2.9.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/IRanges.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘IRanges’ can be installed ... [14s/21s] WARNING
Found the following significant warnings:
Warning: unable to find a consistent ordering of superclasses for class "StandardGenericFilterClosure": order chosen is inconsistent with the superclasses of "standardGeneric"
See ‘/home/biocbuild/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
* 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 ... WARNING
File ‘IRanges/libs/IRanges.so’:
Found ‘abort’, possibly from ‘abort’ (C)
Object: ‘errabort.o’
Found ‘exit’, possibly from ‘exit’ (C)
Object: ‘errabort.o’
Found ‘stderr’, possibly from ‘stderr’ (C)
Object: ‘errabort.o’
Found ‘stdout’, possibly from ‘stdout’ (C)
Objects: ‘IntervalTree.o’, ‘common.o’, ‘errabort.o’
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.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘IRanges_unit_tests.R’ [69s/102s]
[70s/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: 3 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.1-bioc/meat/IRanges.Rcheck/00check.log’
for details.
* installing *source* package ‘IRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c GappedRanges_class.c -o GappedRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -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]
int i, j, index, nhits;
^
IntervalTree.c: In function ‘_IntegerIntervalTree_overlap_last’:
IntervalTree.c:576:20: warning: variable ‘nhits’ set but not used [-Wunused-but-set-variable]
int i, j, index, nhits;
^
IntervalTree.c: In function ‘_IntegerIntervalTree_overlap’:
IntervalTree.c:367:3: warning: ‘result_inds’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return result_inds;
^
IntervalTree.c: In function ‘_IntegerIntervalForest_overlap’:
IntervalTree.c:395:17: warning: ‘result_inds’ may be used uninitialized in this function [-Wmaybe-uninitialized]
memset(INTEGER(result_inds), 0, LENGTH(result_inds) * sizeof(int));
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c NCList.c -o NCList.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c RangedData_class.c -o RangedData_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c Ranges_class.c -o Ranges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c Ranges_comparison.c -o Ranges_comparison.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c common.c -o common.o
common.c: In function ‘firstWordInFile’:
common.c:1787:6: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(wordBuf, wordBufSize, f);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’:
coverage_methods.c:503:28: warning: ‘x_end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (*out_ranges_are_tiles && x_end != cvg_len)
^
coverage_methods.c:419:21: note: ‘x_end’ was declared here
i, j, x_start, x_end, shift_elt, tmp;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c dlist.c -o dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c errabort.c -o errabort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -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 [-Wmaybe-uninitialized]
delta += gapwidth;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c localmem.c -o localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c memalloc.c -o memalloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c rbTree.c -o rbTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c ucsc_handlers.c -o ucsc_handlers.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o IRanges.so 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 -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/IRanges.Rcheck/IRanges/libs
** 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’
* DONE (IRanges)