BioC 3.3: CHECK report for IRanges on linux2.bioconductor.org

Package: IRanges

Version: 2.5.4

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings IRanges_2.5.4.tar.gz

StartedAt: 2015-10-27 05:05:25 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:08:16 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 171.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: IRanges.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings IRanges_2.5.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/IRanges.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.5.4’
* 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 ... [14s/16s] OK
* 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
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
subsetByOverlaps,RangedData-RangedData: 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: 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: 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 ... WARNING
Missing link or links in documentation object 'mapCoords-methods.Rd':
  ‘[GenomicRanges]{mapCoords-methods}’
  ‘[GenomicAlignments]{mapCoords-methods}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 'all' and siglist 'CompressedAtomicList'
  generic 'any' and siglist 'CompressedAtomicList'
  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 'cbind' and siglist 'Rle'
  generic 'cbind' and siglist 'RleList'
  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 'coerce' and siglist 'Ranges,RangesList'
  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 'mean' and siglist 'CompressedIntegerList'
  generic 'mean' and siglist 'CompressedLogicalList'
  generic 'mean' and siglist 'CompressedNumericList'
  generic 'overlapsAny' and siglist 'integer,Ranges'
  generic 'paste' and siglist 'CompressedAtomicList'
  generic 'range' and siglist 'CompressedIntegerList'
  generic 'range' and siglist 'CompressedLogicalList'
  generic 'range' and siglist 'CompressedNumericList'
  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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘IRanges_unit_tests.R’ [76s/77s]
 [76s/77s] 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/IRanges.Rcheck/00check.log’
for details.

* installing *source* package ‘IRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c GappedRanges_class.c -o GappedRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c NCList.c -o NCList.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c RangedData_class.c -o RangedData_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c Ranges_class.c -o Ranges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c Ranges_comparison.c -o Ranges_comparison.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c coverage_methods.c -o coverage_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -c inter_range_methods.c -o inter_range_methods.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.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 coverage_methods.o inter_range_methods.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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 ‘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 ‘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 ‘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)

name	user	system	elapsed
AtomicList-class	0.187	0.004	0.191
CompressedList-class	0.009	0.004	0.014
DataFrame-utils	0.128	0.000	0.128
GappedRanges-class	0.078	0.000	0.078
Grouping-class	0.037	0.004	0.041
Hits-class-leftovers	0.037	0.000	0.036
IRanges-class	1.143	0.016	1.161
IRanges-constructor	0.028	0.000	0.028
IRanges-utils	1.187	0.004	1.201
IRangesList-class	0.045	0.000	0.045
List-class-leftovers	0.031	0.000	0.031
MaskCollection-class	0.097	0.004	0.113
NCList-class	0.023	0.000	0.023
RDApplyParams-class	0.496	0.000	0.509
RangedData-class	1.111	0.004	1.224
RangedDataList-class	0.028	0.004	0.032
RangedSelection-class	0.024	0.000	0.025
Ranges-class	0.091	0.004	0.095
Ranges-comparison	0.077	0.000	0.078
RangesList-class	0.073	0.000	0.097
Rle-class-leftovers	0.007	0.000	0.007
RleViews-class	0.064	0.000	0.064
RleViewsList-class	0.049	0.000	0.049
Views-class	0.071	0.000	0.071
ViewsList-class	0.002	0.000	0.002
coverage-methods	0.199	0.004	0.335
expand-methods	0.173	0.000	0.172
extractList	0.121	0.000	0.121
findOverlaps-methods	0.243	0.000	0.333
inter-range-methods	0.879	0.004	1.100
intra-range-methods	0.298	0.000	0.315
mapCoords-methods	0.001	0.000	0.001
multisplit	0.019	0.000	0.019
nearest-methods	0.049	0.000	0.050
read.Mask	0.042	0.000	0.051
reverse-methods	0.093	0.004	0.138
setops-methods	0.181	0.000	0.182
slice-methods	0.019	0.000	0.018
view-summarization-methods	0.021	0.000	0.021