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CHECK report for GenomicRanges on malbec1

This page was generated on 2019-04-16 11:48:52 -0400 (Tue, 16 Apr 2019).

Package 628/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicRanges 1.34.0
Bioconductor Package Maintainer
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/GenomicRanges
Branch: RELEASE_3_8
Last Commit: ebaad5c
Last Changed Date: 2018-10-30 11:41:46 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicRanges
Version: 1.34.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GenomicRanges_1.34.0.tar.gz
StartedAt: 2019-04-16 00:12:36 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:16:42 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 245.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenomicRanges.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GenomicRanges_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/GenomicRanges.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
genomicvars              59.592  4.568  64.550
GPos-class               29.304  3.600  33.061
makeGRangesFromDataFrame  0.772  0.004  10.569
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.



Installation output

GenomicRanges.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL GenomicRanges
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘GenomicRanges’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function ‘tlocs2rlocs’:
transcript_utils.c:143:38: warning: ‘end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:24: note: ‘end’ was declared here
  int nexons, j, start, end, width;
                        ^
transcript_utils.c:143:38: warning: ‘start’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:17: note: ‘start’ was declared here
  int nexons, j, start, end, width;
                 ^
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/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)

Tests output

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-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("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 00:16:36 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 
 41.396   0.168  42.319 

Example timings

GenomicRanges.Rcheck/GenomicRanges-Ex.timings

nameusersystemelapsed
GNCList-class0.6640.0440.708
GPos-class29.304 3.60033.061
GRanges-class1.0800.0001.082
GRangesList-class0.5480.0080.566
GenomicRanges-comparison0.2240.0000.226
absoluteRanges0.9880.0561.044
constraint0.9400.0040.945
coverage-methods0.3920.0000.392
findOverlaps-methods1.4920.0041.501
genomic-range-squeezers000
genomicvars59.592 4.56864.550
inter-range-methods2.7000.0082.718
intra-range-methods0.6680.0040.670
makeGRangesFromDataFrame 0.772 0.00410.569
makeGRangesListFromDataFrame0.0680.0000.066
nearest-methods0.4920.0080.501
phicoef0.0040.0000.003
setops-methods3.4480.0003.752
strand-utils0.1440.0000.147
tile-methods0.1280.0000.128
tileGenome0.4080.0040.412