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CHECK report for IRanges on merida2

This page was generated on 2018-10-17 08:46:12 -0400 (Wed, 17 Oct 2018).

Package 750/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRanges 2.14.12
Bioconductor Package Maintainer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/IRanges
Branch: RELEASE_3_7
Last Commit: 00af027
Last Changed Date: 2018-09-19 23:34:20 -0400 (Wed, 19 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: IRanges
Version: 2.14.12
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_2.14.12.tar.gz
StartedAt: 2018-10-16 22:08:40 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 22:12:26 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 226.5 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_2.14.12.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/IRanges.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRanges/DESCRIPTION’ ... OK
* this is package ‘IRanges’ version ‘2.14.12’
* 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 '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’
  ‘CompressedDataFrameList’ ‘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 '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 'colnames' and siglist 'SDFLWrapperForTransform'
  generic 'colnames' and siglist 'SplitDataFrameList'
  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 '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 'pcompareRecursively' and siglist 'IPosRanges'
  generic 'relist' and siglist 'grouping,missing'
  generic 'replaceROWS' and siglist 'IRanges'
  generic 'replaceROWS' and siglist 'NormalIRanges'
  generic 'showAsCell' and siglist 'Views'
  generic 'slidingWindows' and siglist 'IntegerRanges'
  generic 'splitAsList' and siglist 'ANY'
  generic 'stack' and siglist 'matrix'
  generic 'tile' and siglist 'IntegerRanges'
  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 '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 or elapsed time > 5s
            user system elapsed
IPos-class 7.931  0.411   8.421
* 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-3.7-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
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘IRanges’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c CompressedList_class.c -o CompressedList_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Grouping_class.c -o Grouping_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c IPosRanges_comparison.c -o IPosRanges_comparison.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_class.c -o IRanges_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_constructor.c -o IRanges_constructor.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_IRanges.c -o R_init_IRanges.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Ranges_class.c -o Ranges_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RleViews_utils.c -o RleViews_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c coverage_methods.c -o coverage_methods.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c extractListFragments.c -o extractListFragments.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c inter_range_methods.c -o inter_range_methods.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 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/3.5/Resources/library/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 ‘smoothEnds’ from package ‘stats’ 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)

Tests output

IRanges.Rcheck/tests/run_unitTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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 -- Tue Oct 16 22:12:14 2018 
*********************************************** 
Number of test functions: 88 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
IRanges RUnit Tests - 88 test functions, 0 errors, 0 failures
Number of test functions: 88 
Number of errors: 0 
Number of failures: 0 
There were 22 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
113.819   0.448 114.858 

Example timings

IRanges.Rcheck/IRanges-Ex.timings

nameusersystemelapsed
AtomicList-class0.2650.0130.281
AtomicList-utils0.0670.0020.070
CompressedList-class0.0110.0000.011
DataFrame-utils0.1670.0020.168
Grouping-class0.0850.0050.090
Hits-class-leftovers0.0560.0010.057
IPos-class7.9310.4118.421
IPosRanges-class0.0440.0020.047
IPosRanges-comparison0.0450.0020.047
IRanges-class2.1430.0482.200
IRanges-constructor0.0450.0030.047
IRanges-utils2.4580.0362.506
IRangesList-class0.0510.0010.052
IntegerRangesList-class0.1110.0020.114
List-class-leftovers0.0340.0040.039
MaskCollection-class0.0880.0130.101
NCList-class0.0270.0040.031
RangedData-class1.2760.1071.390
RangedSelection-class0.0230.0010.024
Rle-class-leftovers0.0050.0000.004
RleViews-class0.0340.0010.035
RleViewsList-class0.0420.0010.043
Views-class0.0480.0010.050
ViewsList-class0.0020.0000.003
coverage-methods0.2310.0050.236
extractList0.0890.0020.093
extractListFragments0.7690.0110.782
findOverlaps-methods0.3400.0040.346
inter-range-methods0.7190.0080.727
intra-range-methods0.4660.0080.476
multisplit0.0210.0000.022
nearest-methods0.1650.0010.167
range-squeezers0.0010.0000.001
read.Mask0.0390.0020.042
reverse-methods0.0650.0010.066
setops-methods0.2630.0040.269
slice-methods0.0160.0000.018
view-summarization-methods0.0230.0010.027