Bioconductor Package Maintainer
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/IRanges |
| Branch: master |
| Last Commit: f6eb2f0 |
| Last Changed Date: 2019-02-14 20:30:08 -0400 (Thu, 14 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:23:01 -0400 (Tue, 09 Apr 2019).
| Package 817/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IRanges 2.17.4 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: IRanges |
| Version: 2.17.4 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IRanges.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IRanges_2.17.4.tar.gz |
| StartedAt: 2019-04-09 01:26:39 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:29:56 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 197.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: IRanges.Rcheck |
| Warnings: 3 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IRanges.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IRanges_2.17.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/IRanges.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.17.4’
* 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
':::' call which should be '::': ‘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
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 8.934 0.3 9.692
* 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-3.9-bioc/meat/IRanges.Rcheck/00check.log’
for details.
IRanges.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL IRanges
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘IRanges’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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 ‘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 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)
IRanges.Rcheck/tests/run_unitTests.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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, 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 9 01:29:47 2019
***********************************************
Number of test functions: 89
Number of errors: 0
Number of failures: 0
1 Test Suite :
IRanges RUnit Tests - 89 test functions, 0 errors, 0 failures
Number of test functions: 89
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
97.804 0.101 98.640
IRanges.Rcheck/IRanges-Ex.timings
| name | user | system | elapsed | |
| AtomicList-class | 0.274 | 0.000 | 0.274 | |
| AtomicList-utils | 0.058 | 0.000 | 0.059 | |
| CompressedList-class | 0.014 | 0.000 | 0.014 | |
| DataFrame-utils | 0.156 | 0.000 | 0.156 | |
| Grouping-class | 0.070 | 0.000 | 0.069 | |
| Hits-class-leftovers | 0.058 | 0.000 | 0.059 | |
| IPos-class | 8.934 | 0.300 | 9.692 | |
| IPosRanges-class | 0.045 | 0.000 | 0.045 | |
| IPosRanges-comparison | 0.06 | 0.00 | 0.06 | |
| IRanges-class | 2.815 | 0.008 | 2.822 | |
| IRanges-constructor | 0.029 | 0.000 | 0.028 | |
| IRanges-utils | 2.958 | 0.020 | 2.985 | |
| IRangesList-class | 0.053 | 0.000 | 0.052 | |
| IntegerRangesList-class | 0.076 | 0.004 | 0.081 | |
| List-class-leftovers | 0.042 | 0.000 | 0.042 | |
| MaskCollection-class | 0.095 | 0.000 | 0.095 | |
| NCList-class | 0.029 | 0.000 | 0.029 | |
| RangedData-class | 0.001 | 0.000 | 0.001 | |
| RangedSelection-class | 0.017 | 0.000 | 0.018 | |
| Rle-class-leftovers | 0.005 | 0.000 | 0.005 | |
| RleViews-class | 0.045 | 0.000 | 0.046 | |
| RleViewsList-class | 0.06 | 0.00 | 0.06 | |
| Views-class | 0.031 | 0.004 | 0.036 | |
| ViewsList-class | 0.001 | 0.000 | 0.001 | |
| coverage-methods | 0.218 | 0.004 | 0.222 | |
| extractList | 0.078 | 0.000 | 0.078 | |
| extractListFragments | 0.764 | 0.068 | 0.832 | |
| findOverlaps-methods | 0.382 | 0.000 | 0.383 | |
| inter-range-methods | 0.700 | 0.004 | 0.704 | |
| intra-range-methods | 0.325 | 0.004 | 0.328 | |
| multisplit | 0.014 | 0.000 | 0.013 | |
| nearest-methods | 0.091 | 0.000 | 0.091 | |
| range-squeezers | 0.000 | 0.000 | 0.001 | |
| read.Mask | 0.019 | 0.004 | 0.137 | |
| reverse-methods | 0.035 | 0.000 | 0.035 | |
| setops-methods | 0.199 | 0.000 | 0.199 | |
| slice-methods | 0.007 | 0.000 | 0.008 | |
| view-summarization-methods | 0.012 | 0.000 | 0.012 | |