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This page was generated on 2017-04-23 14:33:08 -0400 (Sun, 23 Apr 2017).
| Package 683/1377 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| IRanges 2.9.21 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | ERROR | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | ||||||
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK | ||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: IRanges |
| Version: 2.9.21 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IRanges_2.9.21.tar.gz |
| StartedAt: 2017-04-23 05:38:31 -0400 (Sun, 23 Apr 2017) |
| EndedAt: 2017-04-23 05:42:28 -0400 (Sun, 23 Apr 2017) |
| EllapsedTime: 236.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: IRanges.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IRanges_2.9.21.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/IRanges.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRanges/DESCRIPTION’ ... OK
* this is package ‘IRanges’ version ‘2.9.21’
* 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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘S4Vectors’
A package should be listed in only one of these fields.
* 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 ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘%poutside%’ ‘%pover%’ ‘%pwithin%’ ‘diff.IntegerList’
‘diff.NumericList’ ‘diff.RleList’ ‘slidingIRanges’ ‘slidingViews’
Undocumented S4 methods:
generic 'anyDuplicated' and siglist 'RangesNSBS'
generic 'c' and siglist 'SimpleList'
generic 'cbind' and siglist 'Rle'
generic 'cbind' and siglist 'RleList'
generic 'coerce' and siglist 'AtomicList,RleViews'
generic 'coerce' and siglist 'PartitioningByEnd,PartitioningMap'
generic 'coerce' and siglist 'factor,ManyToOneGrouping'
generic 'colnames' and siglist 'SDFLWrapperForTransform'
generic 'colnames' and siglist 'SplitDataFrameList'
generic 'ifelse' and siglist 'ANY,ANY,List'
generic 'ifelse' and siglist 'ANY,List,ANY'
generic 'ifelse' and siglist 'ANY,List,List'
generic 'ifelse' and siglist 'CompressedLogicalList,ANY,ANY'
generic 'ifelse' and siglist 'CompressedLogicalList,ANY,List'
generic 'ifelse' and siglist 'CompressedLogicalList,List,ANY'
generic 'ifelse' and siglist 'CompressedLogicalList,List,List'
generic 'ifelse' and siglist 'SimpleLogicalList,ANY,ANY'
generic 'ifelse' and siglist 'SimpleLogicalList,ANY,List'
generic 'ifelse' and siglist 'SimpleLogicalList,List,ANY'
generic 'ifelse' and siglist 'SimpleLogicalList,List,List'
generic 'length' and siglist 'RangesNSBS'
generic 'pcompareRecursively' and siglist 'Ranges'
generic 'relist' and siglist 'grouping,missing'
generic 'showAsCell' and siglist 'Views'
generic 'splitAsList' and siglist 'ANY'
generic 'stack' and siglist 'matrix'
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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.R’
ERROR
Running the tests in ‘tests/run_unitTests.R’ failed.
Last 13 lines of output:
ERROR in test_SplitDataFrameList_replace: Error in as.vector(x, mode) :
coercing an AtomicList object to an atomic vector is supported only for
objects with top-level elements of length <= 1
Test files with failing tests
test_DataFrameList.R
test_SplitDataFrameList_as_data.frame
test_SplitDataFrameList_replace
Error in BiocGenerics:::testPackage("IRanges") :
unit tests failed for package IRanges
Calls: <Anonymous> -> <Anonymous>
Execution halted
* 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: 1 ERROR, 2 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/IRanges.Rcheck/00check.log’
for details.
run_unitTests.Rout.fail:
R Under development (unstable) (2017-02-15 r72187) -- "Unsuffered Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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, cbind, colMeans, colSums, colnames, 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()
Timing stopped at: 0.228 0.003 0.233
Error in checkIdentical(as.data.frame(DFL), df) : FALSE
Timing stopped at: 3.176 0.008 3.19
Error in as.vector(x, mode) :
coercing an AtomicList object to an atomic vector is supported only for
objects with top-level elements of length <= 1
RUNIT TEST PROTOCOL -- Sun Apr 23 05:42:18 2017
***********************************************
Number of test functions: 91
Number of errors: 1
Number of failures: 1
1 Test Suite :
IRanges RUnit Tests - 91 test functions, 1 error, 1 failure
FAILURE in test_SplitDataFrameList_as_data.frame: Error in checkIdentical(as.data.frame(DFL), df) : FALSE
ERROR in test_SplitDataFrameList_replace: Error in as.vector(x, mode) :
coercing an AtomicList object to an atomic vector is supported only for
objects with top-level elements of length <= 1
Test files with failing tests
test_DataFrameList.R
test_SplitDataFrameList_as_data.frame
test_SplitDataFrameList_replace
Error in BiocGenerics:::testPackage("IRanges") :
unit tests failed for package IRanges
Calls: <Anonymous> -> <Anonymous>
Execution halted
IRanges.Rcheck/00install.out:
* installing *source* package ‘IRanges’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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:1163:13: 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/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Ranges_comparison.c -o Ranges_comparison.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/S4Vectors/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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 IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/IRanges.Rcheck/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘ifelse’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ 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 ‘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)
IRanges.Rcheck/IRanges-Ex.timings:
| name | user | system | elapsed | |
| AtomicList-class | 0.730 | 0.012 | 0.750 | |
| AtomicList-utils | 0.059 | 0.001 | 0.060 | |
| CompressedList-class | 0.014 | 0.001 | 0.015 | |
| DataFrame-utils | 0.342 | 0.001 | 0.345 | |
| Grouping-class | 0.141 | 0.003 | 0.146 | |
| Hits-class-leftovers | 0.199 | 0.001 | 0.200 | |
| IRanges-class | 1.594 | 0.045 | 1.656 | |
| IRanges-constructor | 0.128 | 0.004 | 0.132 | |
| IRanges-utils | 1.204 | 0.036 | 1.329 | |
| IRangesList-class | 0.14 | 0.01 | 0.15 | |
| List-class-leftovers | 0.030 | 0.000 | 0.031 | |
| MaskCollection-class | 0.129 | 0.002 | 0.132 | |
| NCList-class | 0.077 | 0.000 | 0.078 | |
| RangedData-class | 1.677 | 0.008 | 1.691 | |
| RangedSelection-class | 0.050 | 0.001 | 0.050 | |
| Ranges-class | 0.086 | 0.003 | 0.088 | |
| Ranges-comparison | 0.147 | 0.002 | 0.163 | |
| RangesList-class | 0.051 | 0.002 | 0.058 | |
| Rle-class-leftovers | 0.004 | 0.000 | 0.004 | |
| RleViews-class | 0.112 | 0.001 | 0.114 | |
| RleViewsList-class | 0.098 | 0.000 | 0.099 | |
| Views-class | 0.110 | 0.001 | 0.112 | |
| ViewsList-class | 0.002 | 0.000 | 0.002 | |
| bind-arrays | 0.020 | 0.001 | 0.021 | |
| coverage-methods | 0.295 | 0.005 | 0.302 | |
| extractList | 0.075 | 0.001 | 0.076 | |
| findOverlaps-methods | 0.396 | 0.004 | 0.405 | |
| inter-range-methods | 1.084 | 0.009 | 1.100 | |
| intra-range-methods | 0.411 | 0.007 | 0.419 | |
| multisplit | 0.018 | 0.000 | 0.019 | |
| nearest-methods | 0.152 | 0.001 | 0.154 | |
| read.Mask | 0.124 | 0.002 | 0.127 | |
| reverse-methods | 0.100 | 0.002 | 0.107 | |
| setops-methods | 0.305 | 0.003 | 0.309 | |
| slice-methods | 0.015 | 0.000 | 0.015 | |
| view-summarization-methods | 0.040 | 0.000 | 0.045 | |