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CHECK report for IRanges on malbec1

This page was generated on 2019-04-16 11:47:53 -0400 (Tue, 16 Apr 2019).

Package 793/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRanges 2.16.0
Bioconductor Package Maintainer
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/IRanges
Branch: RELEASE_3_8
Last Commit: 26834c6
Last Changed Date: 2018-10-30 11:41:41 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: IRanges
Version: 2.16.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:IRanges.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings IRanges_2.16.0.tar.gz
StartedAt: 2019-04-16 00:53:02 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:56:40 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 217.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IRanges.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:IRanges.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings IRanges_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/IRanges.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.16.0’
* 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 'range' and siglist 'CompressedRleList'
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
IPos-class 8.62  0.232   9.062
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/IRanges.Rcheck/00check.log’
for details.



Installation output

IRanges.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL IRanges
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘IRanges’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c CompressedList_class.c -o CompressedList_class.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Grouping_class.c -o Grouping_class.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c IPosRanges_comparison.c -o IPosRanges_comparison.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_class.c -o IRanges_class.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_constructor.c -o IRanges_constructor.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c NCList.c -o NCList.o
NCList.c:202:22: warning: ‘next_top_down’ defined but not used [-Wunused-function]
 static const NCList *next_top_down(const NCList *nclist)
                      ^
NCList.c:1173:13: warning: ‘NCList_get_y_overlaps_rec’ defined but not used [-Wunused-function]
 static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
             ^
NCList.c: In function ‘NCList_find_overlaps_in_groups’:
NCList.c:1546:7: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_IRanges.c -o R_init_IRanges.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Ranges_class.c -o Ranges_class.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RleViews_utils.c -o RleViews_utils.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’:
coverage_methods.c:503:28: warning: ‘x_end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (*out_ranges_are_tiles && x_end != cvg_len)
                            ^
coverage_methods.c:419:21: note: ‘x_end’ was declared here
      i, j, x_start, x_end, shift_elt, tmp;
                     ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function ‘find_partition_overlaps’:
extractListFragments.c:85:4: warning: ‘split_partitions_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    IntAE_insert_at(split_partitions_buf,
    ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -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:165:5: warning: ‘revmap_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     IntAE_insert_at(revmap_elt,
     ^
inter_range_methods.c:154:11: warning: ‘delta’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     delta += gapwidth;
           ^
inter_range_methods.c:154:11: warning: ‘gapwidth’ may be used uninitialized in this function [-Wmaybe-uninitialized]
inter_range_methods.c:156:14: warning: ‘max_end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    width_inc = end_j - max_end;
              ^
inter_range_methods.c:131:6: warning: ‘append_or_drop’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (append_or_drop) {
      ^
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/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 -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 Apr 16 00:56:32 2019 
*********************************************** 
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 
121.900   0.084 122.349 

Example timings

IRanges.Rcheck/IRanges-Ex.timings

nameusersystemelapsed
AtomicList-class0.2840.0080.293
AtomicList-utils0.0680.0000.069
CompressedList-class0.0160.0000.016
DataFrame-utils0.1600.0000.161
Grouping-class0.0920.0000.089
Hits-class-leftovers0.0680.0000.068
IPos-class8.6200.2329.062
IPosRanges-class0.0320.0040.036
IPosRanges-comparison0.0360.0040.039
IRanges-class3.2520.0163.279
IRanges-constructor0.0400.0000.038
IRanges-utils2.7440.0082.769
IRangesList-class0.0320.0000.033
IntegerRangesList-class0.0560.0000.056
List-class-leftovers0.0240.0000.024
MaskCollection-class0.0640.0040.068
NCList-class0.0200.0000.021
RangedData-class1.2360.0481.286
RangedSelection-class0.0200.0040.027
Rle-class-leftovers0.0040.0000.006
RleViews-class0.0600.0000.059
RleViewsList-class0.0680.0000.069
Views-class0.0360.0000.033
ViewsList-class0.0000.0000.001
coverage-methods0.1880.0000.186
extractList0.0520.0000.051
extractListFragments0.5320.0000.532
findOverlaps-methods0.2480.0000.250
inter-range-methods0.5640.0000.562
intra-range-methods0.4120.0000.410
multisplit0.0160.0000.017
nearest-methods0.1120.0000.112
range-squeezers0.0000.0000.001
read.Mask0.0520.0000.308
reverse-methods0.0720.0000.072
setops-methods0.2920.0040.297
slice-methods0.0120.0000.015
view-summarization-methods0.0240.0000.026