Multiple platform build/check report for BioC 3.11 - CHECK report for IRanges on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:IRanges.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings IRanges_2.22.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/IRanges.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.22.2’
* 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 ... NOTE
':::' calls which should be '::':
  ‘S4Vectors:::makePrettyMatrixForCompactPrinting’
  ‘S4Vectors:::transform.DataTable’
  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
.dotargsAsList: no visible global function definition for
  ‘strsplitAsListOfIntegerVectors’
setCompressedListSummaryMethod : <anonymous>: no visible binding for
  global variable ‘C_fun’
setCompressedListWhichSummaryMethod : def: no visible binding for
  global variable ‘C_fun’
[[,RangedData: no visible global function definition for ‘Defunct’
[[<-,RangedData: no visible global function definition for ‘Defunct’
colnames,RangedData: no visible global function definition for
  ‘Defunct’
ncol,RangedData: no visible global function definition for ‘Defunct’
nrow,RangedData: no visible global function definition for ‘Defunct’
rownames,RangedData: no visible global function definition for
  ‘Defunct’
space,RangedData: no visible global function definition for ‘Defunct’
universe,RangedData: no visible global function definition for
  ‘Defunct’
universe<-,RangedData: no visible global function definition for
  ‘Defunct’
Undefined global functions or variables:
  C_fun Defunct strsplitAsListOfIntegerVectors
* 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 'showAsCell' and siglist 'Ranges'
  generic 'showAsCell' and siglist 'Views'
  generic 'slidingWindows' and siglist 'IntegerRanges'
  generic 'stack' and siglist 'matrix'
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
IPos-class 8.093    0.2   8.293
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/IRanges.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL IRanges
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘IRanges’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c NCList.c -o NCList.o
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:202:22: warning: ‘next_top_down’ defined but not used [-Wunused-function]
 static const NCList *next_top_down(const NCList *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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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:66:5: warning: ‘split_partitions_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     IntAE_insert_at(split_partitions_buf,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      IntAE_get_nelt(split_partitions_buf),
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      q_prev_end);
      ~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c inter_range_methods.c -o inter_range_methods.o
gcc -shared -L/home/biocbuild/bbs-3.11-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-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/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


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, 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, 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 -- Sat Oct 17 02:31:56 2020 
*********************************************** 
Number of test functions: 95 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
IRanges RUnit Tests - 95 test functions, 0 errors, 0 failures
Number of test functions: 95 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
127.899   0.140 128.116

name	user	system	elapsed
AtomicList-class	0.226	0.012	0.238
AtomicList-utils	0.047	0.004	0.051
CompressedList-class	0.011	0.000	0.012
DataFrame-utils	0.141	0.000	0.141
Grouping-class	0.051	0.000	0.051
Hits-class-leftovers	0.054	0.000	0.054
IPos-class	8.093	0.200	8.293
IPosRanges-class	0.05	0.00	0.05
IPosRanges-comparison	0.052	0.000	0.052
IRanges-class	2.806	0.020	2.826
IRanges-constructor	0.060	0.000	0.059
IRanges-utils	2.710	0.004	2.714
IRangesList-class	0.036	0.004	0.040
IntegerRangesList-class	0.063	0.000	0.063
List-class-leftovers	0.031	0.000	0.032
MaskCollection-class	0.073	0.000	0.073
NCList-class	0.026	0.000	0.026
RangedData-class	0.001	0.000	0.001
RangedSelection-class	0.022	0.000	0.022
Rle-class-leftovers	0.004	0.000	0.004
RleViews-class	0.045	0.000	0.045
RleViewsList-class	0.051	0.000	0.051
Views-class	0.047	0.000	0.047
ViewsList-class	0.001	0.000	0.001
coverage-methods	0.183	0.020	0.202
extractList	0.071	0.008	0.079
extractListFragments	0.687	0.008	0.695
findOverlaps-methods	0.407	0.000	0.408
inter-range-methods	0.773	0.004	0.776
intra-range-methods	0.602	0.000	0.602
multisplit	0.017	0.000	0.017
nearest-methods	0.133	0.000	0.133
range-squeezers	0	0	0
read.Mask	0.031	0.000	0.049
reverse-methods	0.059	0.000	0.059
setops-methods	0.227	0.000	0.228
slice-methods	0.017	0.000	0.017
view-summarization-methods	0.022	0.000	0.021

CHECK report for IRanges on malbec2

Summary

Command output

Installation output

Tests output

Example timings