| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:47:58 -0400 (Wed, 16 Oct 2019).
| Package 659/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicRanges 1.36.1 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 | |
| Package: GenomicRanges |
| Version: 1.36.1 |
| 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_1.36.1.tar.gz |
| StartedAt: 2019-10-16 03:08:40 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:15:01 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 381.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicRanges.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running 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_1.36.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GenomicRanges.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.36.1’
* 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 79.506 32.160 112.553
GPos-class 43.825 6.459 50.352
inter-range-methods 4.800 0.945 5.831
makeGRangesFromDataFrame 0.781 0.026 11.611
* 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-3.9-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/3.6/Resources/library’ * installing *source* package ‘GenomicRanges’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/00LOCK-GenomicRanges/00new/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 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 (GenomicRanges)
GenomicRanges.Rcheck/tests/run_unitTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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, 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
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 -- Wed Oct 16 03:14:48 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
51.442 0.901 52.449
GenomicRanges.Rcheck/GenomicRanges-Ex.timings
| name | user | system | elapsed | |
| GNCList-class | 0.905 | 0.084 | 0.989 | |
| GPos-class | 43.825 | 6.459 | 50.352 | |
| GRanges-class | 1.230 | 0.101 | 1.331 | |
| GRangesList-class | 0.572 | 0.057 | 0.631 | |
| GenomicRanges-comparison | 0.368 | 0.006 | 0.374 | |
| absoluteRanges | 1.271 | 0.143 | 1.414 | |
| constraint | 1.519 | 0.177 | 1.697 | |
| coverage-methods | 0.368 | 0.002 | 0.370 | |
| findOverlaps-methods | 1.679 | 0.013 | 1.693 | |
| genomic-range-squeezers | 0.000 | 0.000 | 0.001 | |
| genomicvars | 79.506 | 32.160 | 112.553 | |
| inter-range-methods | 4.800 | 0.945 | 5.831 | |
| intra-range-methods | 0.557 | 0.009 | 0.565 | |
| makeGRangesFromDataFrame | 0.781 | 0.026 | 11.611 | |
| makeGRangesListFromDataFrame | 0.121 | 0.003 | 0.124 | |
| nearest-methods | 0.802 | 0.007 | 0.808 | |
| phicoef | 0.003 | 0.001 | 0.004 | |
| setops-methods | 4.819 | 0.019 | 4.838 | |
| strand-utils | 0.194 | 0.004 | 0.199 | |
| tile-methods | 0.140 | 0.001 | 0.141 | |
| tileGenome | 0.457 | 0.011 | 0.469 | |