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BioC 2.12: CHECK report for IRanges on george2

This page was generated on 2013-10-09 09:37:13 -0700 (Wed, 09 Oct 2013).

Package 346/671HostnameOS / ArchBUILDCHECKBUILD BIN
IRanges 1.18.4
Bioconductor Package Maintainer
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/IRanges
Last Changed Rev: 80662 / Revision: 81334
Last Changed Date: 2013-09-23 10:08:48 -0700 (Mon, 23 Sep 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: IRanges
Version: 1.18.4
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings IRanges_1.18.4.tar.gz
StartedAt: 2013-10-09 02:44:26 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:50:45 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 379.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IRanges.Rcheck
Warnings: 3

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/IRanges.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.18.4’
* 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 ... [46s/47s] OK
* checking installed package size ... OK
* checking package 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 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 ... WARNING
Found .Internal calls in the following functions:
  ‘isNotSorted’ ‘isNotStrictlySorted’
with calls to .Internal functions
  ‘is.unsorted’

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘as.list.CompressedList’ ‘as.list.CompressedNormalIRangesList’
  ‘as.list.Hits’ ‘as.list.List’ ‘as.list.Rle’ ‘as.list.SimpleList’
  ‘duplicated.AtomicList’ ‘duplicated.CompressedAtomicList’
  ‘duplicated.DataTable’ ‘duplicated.Dups’ ‘duplicated.Ranges’
  ‘duplicated.Rle’ ‘duplicated.XRawList’ ‘levels.OverlapEncodings’
  ‘levels.Rle’ ‘sort.Rle’ ‘sort.RleList’ ‘sort.Vector’ ‘splitAsList’
  ‘splitAsListReturnedClass’ ‘subsetByRanges’
  ‘unique.CompressedAtomicList’ ‘unique.CompressedRleList’
  ‘unique.DataTable’ ‘unique.Rle’ ‘unique.SimpleRleList’
  ‘unique.Vector’ ‘window.DataTable’ ‘window.GappedRanges’
  ‘window.GroupedIRanges’ ‘window.IRanges’ ‘window.NULL’ ‘window.Rle’
  ‘window.Vector’ ‘window.XVector’ ‘window.XVectorList’ ‘window.factor’
  ‘window.vector’ ‘window<-.DataTable’ ‘window<-.RangedData’
  ‘window<-.Vector’ ‘window<-.factor’ ‘window<-.vector’
Undocumented S4 methods:
  generic '<=' and siglist 'XRawList,XRawList'
  generic '==' and siglist 'XRawList,XRawList'
  generic 'Ops' and siglist 'SimpleAtomicList,atomic'
  generic 'Ops' and siglist 'atomic,SimpleAtomicList'
  generic '[[<-' and siglist 'SharedRaw_Pool'
  generic 'coerce' and siglist 'ANY,DataFrame'
  generic 'compare' and siglist 'XRawList,XRawList'
  generic 'duplicated' and siglist 'CompressedAtomicList'
  generic 'duplicated' and siglist 'Rle'
  generic 'duplicated' and siglist 'XRawList'
  generic 'elementLengths' and siglist 'XVectorList'
  generic 'is.unsorted' and siglist 'XRawList'
  generic 'match' and siglist 'XRawList,XRawList'
  generic 'mstack' and siglist 'DataFrame'
  generic 'order' and siglist 'XRawList'
  generic 'rank' and siglist 'XRawList'
  generic 'relist' and siglist 'ANY,PartitioningByEnd'
  generic 'relist' and siglist 'Vector,list'
  generic 'splitAsListReturnedClass' and siglist 'ANY'
  generic 'splitAsListReturnedClass' and siglist 'DataFrame'
  generic 'splitAsListReturnedClass' and siglist 'Hits'
  generic 'splitAsListReturnedClass' and siglist 'data.frame'
  generic 'subsetByRanges' and siglist 'ANY'
  generic 'subsetByRanges' and siglist 'IRanges'
  generic 'subsetByRanges' and siglist 'NULL'
  generic 'subsetByRanges' and siglist 'vector'
  generic 'unique' and siglist 'CompressedAtomicList'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File ‘/home/biocbuild/bbs-2.12-bioc/meat/IRanges.Rcheck/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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [28s/28s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
IRanges-class 5.564  0.124   5.949
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘IRanges_unit_tests.R’ [76s/77s]
 [76s/78s] 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

WARNING: There were 3 warnings.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/IRanges.Rcheck/00check.log’
for details.

IRanges.Rcheck/00install.out:

* installing *source* package ‘IRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c AEbufs.c -o AEbufs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c DataFrame_class.c -o DataFrame_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c GappedRanges_class.c -o GappedRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Hits_class.c -o Hits_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c IntervalTree.c -o IntervalTree.o
IntervalTree.c: In function ‘IntegerIntervalTree_overlap_first’:
IntervalTree.c:303:20: warning: variable ‘nhits’ set but not used [-Wunused-but-set-variable]
IntervalTree.c: In function ‘IntegerIntervalTree_overlap_last’:
IntervalTree.c:344:20: warning: variable ‘nhits’ set but not used [-Wunused-but-set-variable]
IntervalTree.c: In function ‘_IntegerIntervalTree_overlap’:
IntervalTree.c:142:17: warning: ‘result_inds’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c RangedData_class.c -o RangedData_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Ranges_comparison.c -o Ranges_comparison.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rle_class.c -o Rle_class.o
Rle_class.c: In function ‘compute_CHARSXP_runs’:
Rle_class.c:132:31: warning: ‘val0’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rle_utils.c -o Rle_utils.o
Rle_utils.c: In function ‘Rle_integer_runsum’:
Rle_utils.c:97:5: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
Rle_utils.c: In function ‘Rle_integer_runwtsum’:
Rle_utils.c:461:5: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
Rle_utils.c: In function ‘Rle_real_runwtsum’:
Rle_utils.c:509:10: warning: unused variable ‘m_value’ [-Wunused-variable]
Rle_utils.c:508:7: warning: unused variable ‘m_length’ [-Wunused-variable]
Rle_utils.c:507:33: warning: unused variable ‘m_offset’ [-Wunused-variable]
Rle_utils.c: In function ‘Rle_integer_runq’:
Rle_utils.c:735:6: warning: implicit declaration of function ‘roundingScale’ [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c SEXP_utils.c -o SEXP_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedDouble_class.c -o SharedDouble_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedInteger_class.c -o SharedInteger_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c: In function ‘SharedRaw_read_complexes_from_subscript’:
SharedRaw_class.c:363:13: warning: variable ‘src_tag’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedVector_class.c -o SharedVector_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c SimpleList_class.c -o SimpleList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Vector_class.c -o Vector_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c XDoubleViews_utils.c -o XDoubleViews_utils.o
XDoubleViews_utils.c: In function ‘get_cachedDoubleSeq_which_max’:
XDoubleViews_utils.c:223:36: warning: ‘cur_max’ may be used uninitialized in this function [-Wuninitialized]
XDoubleViews_utils.c: In function ‘get_cachedDoubleSeq_which_min’:
XDoubleViews_utils.c:196:36: warning: ‘cur_min’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c XIntegerViews_utils.c -o XIntegerViews_utils.o
XIntegerViews_utils.c: In function ‘get_cachedIntSeq_which_min’:
XIntegerViews_utils.c:171:36: warning: ‘cur_min’ may be used uninitialized in this function [-Wuninitialized]
XIntegerViews_utils.c: In function ‘get_cachedIntSeq_which_max’:
XIntegerViews_utils.c:194:36: warning: ‘cur_max’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c XRawList_comparison.c -o XRawList_comparison.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function ‘_new_XRawList_from_CharAEAE’:
XVectorList_class.c:451:33: warning: ‘lkup_length’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c XVector_class.c -o XVector_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/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]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c compact_bitvector.c -o compact_bitvector.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c coverage_methods.c -o coverage_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c dlist.c -o dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c errabort.c -o errabort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c hash_utils.c -o hash_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c int_utils.c -o int_utils.o
int_utils.c: In function ‘Integer_tabulate2’:
int_utils.c:486:31: warning: unused variable ‘ans_elt’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/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:177:21: warning: ‘mapping_elt’ may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:183:35: warning: ‘delta’ may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:166:11: warning: ‘gapwidth’ may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:168:14: warning: ‘max_end’ may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:143:6: warning: ‘append_or_drop’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c localmem.c -o localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c memalloc.c -o memalloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rbTree.c -o rbTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c safe_arithm.c -o safe_arithm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sort_utils.c -o sort_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c str_utils.c -o str_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ucsc_handlers.c -o ucsc_handlers.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c vector_copy.c -o vector_copy.o
gcc -std=gnu99 -shared -L/usr/local/lib -o IRanges.so AEbufs.o CompressedIRangesList_class.o CompressedList_class.o DataFrame_class.o GappedRanges_class.o Grouping_class.o Hits_class.o IRanges_class.o IRanges_constructor.o IntervalTree.o Ocopy_byteblocks.o R_init_IRanges.o RangedData_class.o Ranges_comparison.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o SimpleList_class.o SimpleRangesList_class.o Vector_class.o XDoubleViews_utils.o XIntegerViews_utils.o XRawList_comparison.o XVectorList_class.o XVector_class.o anyMissing.o common.o compact_bitvector.o coverage_methods.o dlist.o encodeOverlaps_methods.o errabort.o hash_utils.o int_utils.o inter_range_methods.o localmem.o memalloc.o rbTree.o safe_arithm.o sort_utils.o str_utils.o ucsc_handlers.o vector_copy.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/IRanges.Rcheck/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘window’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘head’ from package ‘utils’ in package ‘IRanges’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘IRanges’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘subset’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘%in%’ from package ‘base’ in package ‘IRanges’
in method for ‘coerce’ with signature ‘"Vector","double"’: no definition for class “double”
Creating a generic function for ‘append’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘relist’ from package ‘utils’ in package ‘IRanges’
in method for ‘relist’ with signature ‘"ANY","PartitioningByEnd"’: no definition for class “PartitioningByEnd”
in method for ‘relist’ with signature ‘"ANY","List"’: no definition for class “List”
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 ‘aggregate’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘as.list’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘unsplit’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘stack’ from package ‘utils’ in package ‘IRanges’
Creating a generic function for ‘with’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘within’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘start’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘end’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘na.omit’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘na.exclude’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘merge’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘by’ from package ‘base’ in package ‘IRanges’
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 ‘as.vector’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘is.unsorted’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘ifelse’ 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 ‘substr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘substring’ 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’
Creating a generic function for ‘levels’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘rownames<-’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘colnames<-’ from package ‘base’ in package ‘IRanges’
in method for ‘coerce’ with signature ‘"xtabs","DataFrame"’: no definition for class “xtabs”
Creating a generic function for ‘as.table’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘t’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toString’ from package ‘base’ in package ‘IRanges’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IRanges)

IRanges.Rcheck/IRanges-Ex.timings:

nameusersystemelapsed
AtomicList-class0.8880.0360.992
DataFrame-class0.8760.0040.880
DataTable-API0.0360.0000.035
DataTable-stats0.0320.0040.040
FilterRules-class0.1560.0000.158
GappedRanges-class0.6920.0040.696
Grouping-class0.2440.0160.261
Hits-class0.1160.0000.118
IRanges-class5.5640.1245.949
IRanges-constructor0.0800.0040.083
IRanges-utils3.2050.0163.224
IRangesList-class0.0880.0000.087
IntervalTree-class0.0760.0040.083
List-class0.0160.0000.015
MaskCollection-class0.1880.0000.187
OverlapEncodings-class0.0880.0000.092
RDApplyParams-class1.4560.0001.456
RangedData-class2.2640.0162.283
RangedDataList-class0.0880.0000.087
RangedSelection-class0.0520.0000.056
Ranges-class0.1040.0000.109
Ranges-comparison0.1080.0120.122
RangesList-class0.4000.0040.404
Rle-class0.2920.0000.292
RleViews-class0.0840.0000.085
RleViewsList-class0.0960.0000.098
SimpleList-class0.0200.0000.021
Vector-class0.0280.0000.028
Views-class0.5000.0160.517
Views-utils0.1120.0000.114
ViewsList-class0.0160.0000.016
XDoubleViews-class0.1040.0000.106
XIntegerViews-class0.0840.0000.087
XVector-class0.1080.0000.108
classNameForDisplay-methods0.0280.0000.027
compact-methods0.5320.0040.537
coverage-methods0.1440.0080.153
encodeOverlaps-methods0.0600.0000.059
endoapply0.0160.0000.017
expand-methods0.3000.0000.301
findOverlaps-methods0.4040.0000.404
funprog-methods0.1800.0000.182
inter-range-methods1.1400.0041.190
intra-range-methods0.4920.0080.501
isConstant0.0280.0000.029
multisplit0.0440.0000.045
nearest-methods0.0840.0080.091
read.Mask0.0960.0000.093
reverse-methods0.1040.0040.107
runstat0.0880.0000.087
seqapply0.1080.0000.106
setops-methods0.3520.0000.356
strutils0.0120.0000.014