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This page was generated on 2019-04-16 11:55:12 -0400 (Tue, 16 Apr 2019).
| Package 628/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicRanges 1.34.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: GenomicRanges |
| Version: 1.34.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomicRanges_1.34.0.tar.gz |
| StartedAt: 2019-04-16 00:12:12 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:17:21 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 309.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicRanges.Rcheck |
| Warnings: 2 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomicRanges_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GenomicRanges.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* this is package ‘GenomicRanges’ version ‘1.34.0’
* 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 ‘GenomicRanges’ 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
poverlaps,GenomicRanges-GenomicRanges: no visible binding for global
variable ‘minoverlaps’
Undefined global functions or variables:
minoverlaps
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘sort.GRangesList’
Undocumented S4 methods:
generic 'sort' and siglist 'GRangesList'
generic 'unlist' and siglist 'GRangesList'
generic 'update' and siglist 'DelegatingGenomicRanges'
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 ... WARNING
Codoc mismatches from documentation object 'inter-range-methods':
\S4method{reduce}{GenomicRangesList}
Code: function(x, drop.empty.ranges = FALSE, ...)
Docs: function(x, drop.empty.ranges = FALSE, min.gapwidth = 1L,
with.inframe.attrib = FALSE, ignore.strand = FALSE)
Argument names in code not in docs:
...
Argument names in docs not in code:
min.gapwidth with.inframe.attrib ignore.strand
Mismatches in argument names:
Position: 3 Code: ... Docs: min.gapwidth
* checking Rd \usage sections ... OK
* 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
genomicvars 70.826 18.362 90.824
GPos-class 36.066 3.476 39.976
makeGRangesFromDataFrame 0.721 0.017 10.028
* 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: 2 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.
GenomicRanges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GenomicRanges ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘GenomicRanges’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/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"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c transcript_utils.c -o transcript_utils.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 GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/GenomicRanges/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (GenomicRanges)
GenomicRanges.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-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("GenomicRanges") || stop("unable to load GenomicRanges package")
Loading required package: GenomicRanges
Loading required package: stats4
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
[1] TRUE
> GenomicRanges:::.test()
RUNIT TEST PROTOCOL -- Tue Apr 16 00:17:12 2019
***********************************************
Number of test functions: 70
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicRanges RUnit Tests - 70 test functions, 0 errors, 0 failures
Number of test functions: 70
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
48.277 0.700 49.945
GenomicRanges.Rcheck/GenomicRanges-Ex.timings
| name | user | system | elapsed | |
| GNCList-class | 0.652 | 0.040 | 0.700 | |
| GPos-class | 36.066 | 3.476 | 39.976 | |
| GRanges-class | 1.140 | 0.088 | 1.247 | |
| GRangesList-class | 0.594 | 0.061 | 0.660 | |
| GenomicRanges-comparison | 0.301 | 0.005 | 0.307 | |
| absoluteRanges | 1.601 | 0.106 | 1.734 | |
| constraint | 1.288 | 0.112 | 1.406 | |
| coverage-methods | 0.428 | 0.002 | 0.432 | |
| findOverlaps-methods | 1.806 | 0.012 | 1.883 | |
| genomic-range-squeezers | 0.001 | 0.000 | 0.001 | |
| genomicvars | 70.826 | 18.362 | 90.824 | |
| inter-range-methods | 3.133 | 0.402 | 3.620 | |
| intra-range-methods | 0.655 | 0.006 | 0.672 | |
| makeGRangesFromDataFrame | 0.721 | 0.017 | 10.028 | |
| makeGRangesListFromDataFrame | 0.115 | 0.002 | 0.118 | |
| nearest-methods | 0.879 | 0.013 | 0.915 | |
| phicoef | 0.005 | 0.001 | 0.007 | |
| setops-methods | 4.411 | 0.047 | 4.585 | |
| strand-utils | 0.168 | 0.003 | 0.172 | |
| tile-methods | 0.121 | 0.001 | 0.124 | |
| tileGenome | 0.385 | 0.007 | 0.394 | |