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CHECK report for IRanges on merida1

This page was generated on 2021-05-06 12:35:24 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the IRanges package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 912/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRanges 2.24.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/IRanges
Branch: RELEASE_3_12
Last Commit: 6c61fdd
Last Changed Date: 2020-12-11 20:11:23 -0400 (Fri, 11 Dec 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: IRanges
Version: 2.24.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IRanges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IRanges_2.24.1.tar.gz
StartedAt: 2021-05-06 02:56:30 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:00:58 -0400 (Thu, 06 May 2021)
EllapsedTime: 268.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: IRanges.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IRanges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IRanges_2.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/IRanges.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRanges/DESCRIPTION’ ... OK
* this is package ‘IRanges’ version ‘2.24.1’
* package encoding: UTF-8
* 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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
setCompressedListSummaryMethod : <anonymous>: no visible binding for
  global variable ‘C_fun’
setCompressedListWhichSummaryMethod : def: no visible binding for
  global variable ‘C_fun’
Undefined global functions or variables:
  C_fun
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'IntegerRangesList-class.Rd':
  ‘[IRanges]{RangesList}’

Missing link or links in documentation object 'intra-range-methods.Rd':
  ‘RangesList’

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

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘%poutside%’ ‘%pover%’ ‘%pwithin%’ ‘RangesList’ ‘cvg’ ‘heads’
  ‘slidingIRanges’ ‘slidingViews’ ‘tails’ ‘windows’
Undocumented S4 classes:
  ‘SimpleRangesList’ ‘IPosList’ ‘SimpleIPosList’ ‘Pos’
  ‘CompressedIPosList’ ‘RangesList’ ‘BaseManyToManyGrouping’ ‘Ranges’
  ‘CompressedRangesList’ ‘CompressedIntegerRangesList’ ‘SimplePosList’
  ‘PosList’ ‘CompressedPosList’
Undocumented S4 methods:
  generic 'anyDuplicated' and siglist 'RangesNSBS'
  generic 'as.factor' and siglist 'ManyToOneGrouping'
  generic 'as.integer' and siglist 'NormalIRanges'
  generic 'as.integer' and siglist 'Pos'
  generic 'as.integer' and siglist 'RangesNSBS'
  generic 'cbind' and siglist 'Rle'
  generic 'cbind' and siglist 'RleList'
  generic 'chartr' and siglist 'ANY,ANY,CharacterList'
  generic 'chartr' and siglist 'ANY,ANY,RleList'
  generic 'coerce' and siglist 'ANY,IPosRanges'
  generic 'coerce' and siglist 'AtomicList,RleViews'
  generic 'coerce' and siglist 'IPosRanges,CompressedIntegerList'
  generic 'coerce' and siglist 'IPosRanges,IntegerList'
  generic 'coerce' and siglist 'IRanges,IPosList'
  generic 'coerce' and siglist 'IntegerRanges,CompressedIPosList'
  generic 'coerce' and siglist 'IntegerRanges,IPosList'
  generic 'coerce' and siglist 'PartitioningByEnd,PartitioningMap'
  generic 'coerce' and siglist 'factor,ManyToOneGrouping'
  generic 'cvg' and siglist 'IntegerRanges'
  generic 'cvg' and siglist 'IntegerRangesList'
  generic 'extractROWS' and siglist 'CompressedList,ANY'
  generic 'extractROWS' and siglist 'IPos,ANY'
  generic 'extractROWS' and siglist 'MaskCollection,ANY'
  generic 'extractROWS' and siglist 'NormalIRanges,ANY'
  generic 'extractROWS' and siglist 'Partitioning,ANY'
  generic 'extractROWS' and siglist 'Rle,RangesNSBS'
  generic 'extractROWS' and siglist 'vector_OR_factor,RangesNSBS'
  generic 'getListElement' and siglist 'CompressedList'
  generic 'getListElement' and siglist 'CompressedNormalIRangesList'
  generic 'getListElement' and siglist 'H2LGrouping'
  generic 'getListElement' and siglist 'MaskCollection'
  generic 'getListElement' and siglist 'NCLists'
  generic 'getListElement' and siglist 'Partitioning'
  generic 'getListElement' and siglist 'Views'
  generic 'gsub' and siglist 'ANY,ANY,CharacterList'
  generic 'gsub' and siglist 'ANY,ANY,RleList'
  generic 'ifelse2' and siglist 'ANY,List,List'
  generic 'is.unsorted' and siglist 'CompressedIntegerList'
  generic 'is.unsorted' and siglist 'CompressedLogicalList'
  generic 'is.unsorted' and siglist 'CompressedNumericList'
  generic 'isNormal' and siglist 'IntegerRanges'
  generic 'length' and siglist 'RangesNSBS'
  generic 'nchar' and siglist 'CharacterList'
  generic 'nchar' and siglist 'RleList'
  generic 'pcompareRecursively' and siglist 'IPosRanges'
  generic 'range' and siglist 'CompressedRleList'
  generic 'relist' and siglist 'grouping,missing'
  generic 'replaceROWS' and siglist 'IRanges'
  generic 'replaceROWS' and siglist 'NormalIRanges'
  generic 'slidingWindows' and siglist 'IntegerRanges'
  generic 'sub' and siglist 'ANY,ANY,CharacterList'
  generic 'sub' and siglist 'ANY,ANY,RleList'
  generic 'tile' and siglist 'IntegerRanges'
  generic 'tolower' and siglist 'CharacterList'
  generic 'tolower' and siglist 'RleList'
  generic 'toupper' and siglist 'CharacterList'
  generic 'toupper' and siglist 'RleList'
  generic 'updateObject' and siglist 'CompressedList'
  generic 'updateObject' and siglist 'IPosRanges'
  generic 'whichFirstNotNormal' and siglist 'IntegerRanges'
  generic 'windows' and siglist 'list_OR_List'
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 ... WARNING
Documented arguments not in \usage in documentation object 'extractList':
  ‘f’

Documented arguments not in \usage in documentation object 'nearest-methods':
  ‘hits’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
IPos-class 10.142  0.469  10.629
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/IRanges.Rcheck/00check.log’
for details.



Installation output

IRanges.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL IRanges
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘IRanges’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c CompressedList_class.c -o CompressedList_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Grouping_class.c -o Grouping_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c IPosRanges_comparison.c -o IPosRanges_comparison.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_class.c -o IRanges_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_constructor.c -o IRanges_constructor.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c NCList.c -o NCList.o
NCList.c:202:22: warning: unused function 'next_top_down' [-Wunused-function]
static const NCList *next_top_down(const NCList *nclist)
                     ^
NCList.c:1173:13: warning: function 'NCList_get_y_overlaps_rec' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
            ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_IRanges.c -o R_init_IRanges.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Ranges_class.c -o Ranges_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RleViews_utils.c -o RleViews_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c coverage_methods.c -o coverage_methods.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c extractListFragments.c -o extractListFragments.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c inter_range_methods.c -o inter_range_methods.o
clang -mmacosx-version-min=10.13 -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 CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-IRanges/00new/IRanges/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ 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 ‘startsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (IRanges)

Tests output

IRanges.Rcheck/tests/run_unitTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("IRanges") || stop("unable to load IRanges package")
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

[1] TRUE
> IRanges:::.test()


RUNIT TEST PROTOCOL -- Thu May  6 03:00:43 2021 
*********************************************** 
Number of test functions: 96 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
IRanges RUnit Tests - 96 test functions, 0 errors, 0 failures
Number of test functions: 96 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In recycleListElements(e1, en) :
  Some element lengths are not multiples of their corresponding element length in e1
2: In x + y :
  longer object length is not a multiple of shorter object length
3: In recycleListElements(e1, en) :
  Some element lengths are not multiples of their corresponding element length in e1
4: In x + y :
  longer object length is not a multiple of shorter object length
> 
> proc.time()
   user  system elapsed 
143.815   0.636 144.634 

Example timings

IRanges.Rcheck/IRanges-Ex.timings

nameusersystemelapsed
AtomicList-class0.3290.0220.350
AtomicList-utils0.0610.0020.064
CompressedList-class0.0200.0010.022
Grouping-class0.0830.0080.091
Hits-class-leftovers0.0770.0030.081
IPos-class10.142 0.46910.629
IPosRanges-class0.0440.0050.049
IPosRanges-comparison0.0610.0060.067
IRanges-class2.7050.0412.750
IRanges-constructor0.0650.0030.068
IRanges-utils2.7800.0262.810
IRangesList-class0.0710.0020.073
IntegerRangesList-class0.0910.0040.095
MaskCollection-class0.0920.0040.096
NCList-class0.0260.0000.026
RangedSelection-class0.0190.0010.020
Rle-class-leftovers0.0040.0010.004
RleViews-class0.0520.0020.054
RleViewsList-class0.0560.0060.063
Views-class0.0590.0080.067
ViewsList-class0.0020.0010.002
coverage-methods0.2840.0660.446
extractList0.1040.0120.117
extractListFragments0.9770.0421.023
findOverlaps-methods0.4350.0090.444
inter-range-methods0.9860.0151.004
intra-range-methods0.7970.0170.817
multisplit0.0210.0000.022
nearest-methods0.1750.0020.177
range-squeezers0.0010.0010.000
read.Mask0.0420.0040.047
reverse-methods0.0820.0030.085
setops-methods0.2780.0050.283
slice-methods0.0170.0010.017
view-summarization-methods0.0280.0010.029