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BioC 3.0: CHECK report for IRanges on oaxaca

This page was generated on 2015-04-10 10:01:10 -0700 (Fri, 10 Apr 2015).

Package 465/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRanges 2.0.1
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/IRanges
Last Changed Rev: 97568 / Revision: 102249
Last Changed Date: 2014-12-11 11:40:54 -0800 (Thu, 11 Dec 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: IRanges
Version: 2.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IRanges_2.0.1.tar.gz
StartedAt: 2015-04-10 00:41:43 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:45:07 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 204.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IRanges.Rcheck
Warnings: 5

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IRanges_2.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/IRanges.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRanges/DESCRIPTION’ ... OK
* this is package ‘IRanges’ version ‘2.0.1’
* 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 ... [22s/23s] WARNING
Found the following significant warnings:
  Warning: undefined slot classes in definition of "RangesNSBS": subscript(class "Ranges")
See ‘/Users/biocbuild/bbs-3.0-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 ... WARNING
duplicated:
  function(x, incomparables, ...)
duplicated.CompressedIntegerList:
  function(x, incomparables, fromLast)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘NCList’
Undocumented S4 classes:
  ‘NCList’
Undocumented S4 methods:
  generic '!' and siglist 'CompressedList'
  generic '!' and siglist 'List'
  generic '$<-' and siglist 'CompressedList'
  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 '[[<-' and siglist 'CompressedList'
  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,IntegerList'
  generic 'coerce' and siglist 'PartitioningByEnd,PartitioningMap'
  generic 'coerce' and siglist 'list,RangesList'
  generic 'compare' and siglist 'List,List'
  generic 'compare' and siglist 'List,list'
  generic 'compare' and siglist 'list,List'
  generic 'duplicated' and siglist 'List'
  generic 'end' and siglist 'NCList'
  generic 'intersect' and siglist 'Ranges,Ranges'
  generic 'is.na' and siglist 'CompressedList'
  generic 'is.na' and siglist 'List'
  generic 'length' and siglist 'NCList'
  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 'names' and siglist 'NCList'
  generic 'pgap' and siglist 'Ranges,Ranges'
  generic 'pintersect' and siglist 'Ranges,Ranges'
  generic 'psetdiff' and siglist 'Ranges,Ranges'
  generic 'punion' and siglist 'Ranges,Ranges'
  generic 'relistToClass' and siglist 'DataFrame'
  generic 'relistToClass' and siglist 'Hits'
  generic 'relistToClass' and siglist 'data.frame'
  generic 'setdiff' and siglist 'Ranges,Ranges'
  generic 'show' and siglist 'Hits'
  generic 'splitAsList' and siglist 'ANY,Rle'
  generic 'splitAsList' and siglist 'ANY,vectorORfactor'
  generic 'splitAsListReturnedClass' and siglist 'DataFrame'
  generic 'splitAsListReturnedClass' and siglist 'Hits'
  generic 'splitAsListReturnedClass' and siglist 'data.frame'
  generic 'start' and siglist 'NCList'
  generic 'union' and siglist 'Ranges,Ranges'
  generic 'unique' and siglist 'List'
  generic 'unique' and siglist 'SimpleList'
  generic 'width' and siglist 'NCList'
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 ... WARNING
Codoc mismatches from documentation object 'extractList':
splitAsList
  Code: function(x, f, drop = FALSE, ...)
  Docs: function(x, f, drop = FALSE)
  Argument names in code not in docs:
    ...

* 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 ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘errabort.o’
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Objects: ‘IntervalTree.o’, ‘common.o’, ‘errabort.o’
  Found ‘_abort’, possibly from ‘abort’ (C)
    Object: ‘errabort.o’
  Found ‘_exit’, possibly from ‘exit’ (C)
    Object: ‘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 ... [14s/15s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘IRanges_unit_tests.R’ [42s/43s]
 [42s/43s] 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

WARNING: There were 5 warnings.
NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/IRanges.Rcheck/00check.log’
for details.

IRanges.Rcheck/00install.out:

* installing *source* package ‘IRanges’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c CompressedList_class.c -o CompressedList_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c DataFrame_class.c -o DataFrame_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c GappedRanges_class.c -o GappedRanges_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Grouping_class.c -o Grouping_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IRanges_class.c -o IRanges_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IRanges_constructor.c -o IRanges_constructor.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IntervalTree.c -o IntervalTree.o
IntervalTree.c:357:14: warning: variable 'result_inds' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  } else if (find_type == FIND_ARBITRARY) {
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
IntervalTree.c:362:24: note: uninitialized use occurs here
  int *r_elt = INTEGER(result_inds);
                       ^˜˜˜˜˜˜˜˜˜˜
IntervalTree.c:357:10: note: remove the 'if' if its condition is always true
  } else if (find_type == FIND_ARBITRARY) {
         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
IntervalTree.c:348:19: note: initialize the variable 'result_inds' to silence this warning
  SEXP result_inds;
                  ^
                   = NULL
IntervalTree.c:392:14: warning: variable 'result_inds' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  } else if (find_type == FIND_ARBITRARY) {
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
IntervalTree.c:395:18: note: uninitialized use occurs here
  memset(INTEGER(result_inds), 0, LENGTH(result_inds) * sizeof(int));
                 ^˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:77:27: note: expanded from macro 'memset'
  __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))
                          ^
IntervalTree.c:392:10: note: remove the 'if' if its condition is always true
  } else if (find_type == FIND_ARBITRARY) {
         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
IntervalTree.c:380:19: note: initialize the variable 'result_inds' to silence this warning
  SEXP result_inds;
                  ^
                   = NULL
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c NCList.c -o NCList.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_IRanges.c -o R_init_IRanges.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RangedData_class.c -o RangedData_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Ranges_class.c -o Ranges_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Ranges_comparison.c -o Ranges_comparison.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RleViews_utils.c -o RleViews_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c SimpleRangesList_class.c -o SimpleRangesList_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c common.c -o common.o
common.c:13:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: common.c,v 1.117 2008/05/31 07:39:20 galt Exp $";
                  ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c coverage_methods.c -o coverage_methods.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c dlist.c -o dlist.o
dlist.c:8:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: dlist.c,v 1.11 2005/07/04 18:44:09 markd Exp $";
                  ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c errabort.c -o errabort.o
errabort.c:18:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: errabort.c,v 1.13 2004/11/10 00:10:50 markd Exp $";
                  ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c inter_range_methods.c -o inter_range_methods.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c localmem.c -o localmem.o
localmem.c:14:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: localmem.c,v 1.10 2005/04/11 07:20:03 markd Exp $";
                  ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c memalloc.c -o memalloc.o
memalloc.c:16:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: memalloc.c,v 1.31 2007/04/24 18:35:43 hiram Exp $";
                  ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c rbTree.c -o rbTree.o
rbTree.c:12:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: rbTree.c,v 1.11 2007/11/26 02:09:52 kent Exp $";
                  ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc_handlers.c -o ucsc_handlers.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o IRanges.so CompressedIRangesList_class.o CompressedList_class.o DataFrame_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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/IRanges.Rcheck/IRanges/libs
** R
** inst
** preparing package for lazy loading
Warning: undefined slot classes in definition of "RangesNSBS": subscript(class "Ranges")
in method for ‘NSBS’ with signature ‘"Ranges"’: no definition for class “Ranges”
in method for ‘extractROWS’ with signature ‘"vectorORfactor","Ranges"’: no definition for class “Ranges”
in method for ‘extractROWS’ with signature ‘"matrix","Ranges"’: no definition for class “Ranges”
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 ‘window’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘with’ from package ‘base’ in package ‘IRanges’
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’
** 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-class0.3980.0070.407
CompressedList-class0.0170.0000.017
DataFrame-utils0.2050.0020.206
FilterRules-class0.1310.0010.132
GappedRanges-class0.1700.0010.172
Grouping-class0.0830.0030.087
Hits-class-leftovers0.0570.0010.058
IRanges-class1.6140.0411.672
IRanges-constructor0.0490.0020.051
IRanges-utils1.4030.0421.527
IRangesList-class0.0510.0000.064
IntervalForest-class0.0330.0000.034
IntervalTree-class0.0520.0080.060
List-class-leftovers0.0380.0010.039
MaskCollection-class0.1330.0020.134
RDApplyParams-class0.7030.0020.707
RangedData-class1.5180.0101.550
RangedDataList-class0.0400.0010.046
RangedSelection-class0.0280.0000.029
Ranges-class0.1110.0030.115
Ranges-comparison0.0960.0020.101
RangesList-class0.0870.0020.091
Rle-class-leftovers0.0060.0000.006
RleViews-class0.0780.0010.078
RleViewsList-class0.0650.0010.067
Views-class0.0820.0010.083
ViewsList-class0.0020.0000.002
coverage-methods0.2200.0050.227
expand-methods0.1950.0010.196
extractList0.1430.0010.148
findOverlaps-methods0.3730.0030.384
inter-range-methods1.1540.0131.244
intra-range-methods0.3520.0070.359
mapCoords-methods0.0010.0000.001
multisplit0.0200.0010.021
nearest-methods0.0510.0010.059
read.Mask0.0540.0020.057
reverse-methods0.1190.0010.122
setops-methods0.2680.0050.274
slice-methods0.0230.0010.023
view-summarization-methods0.0200.0010.021