Package: GenomicRanges

Version: 1.38.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GenomicRanges_1.38.0.tar.gz

StartedAt: 2020-04-15 00:46:58 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:51:39 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 280.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GenomicRanges.Rcheck

Warnings: 3

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GenomicRanges_1.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/GenomicRanges.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.38.0’
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'GenomicRangesList-class.Rd':
  ‘[IRanges]{RangesList}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘sort.GRangesList’
Undocumented S4 methods:
  generic 'sort' and siglist 'CompressedGRangesList'
  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 ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'intra-range-methods':
  ‘...’

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
genomicvars              58.124  3.532  64.379
GPos-class               40.500  4.200  44.948
makeGRangesFromDataFrame  0.724  0.016  10.206
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL GenomicRanges
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘GenomicRanges’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-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-3.10-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-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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 Apr 15 00:51:33 2020 
*********************************************** 
Number of test functions: 71 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicRanges RUnit Tests - 71 test functions, 0 errors, 0 failures
Number of test functions: 71 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 51.892   0.140  52.703 

name	user	system	elapsed
GNCList-class	0.524	0.036	0.563
GPos-class	40.500	4.200	44.948
GRanges-class	1.116	0.012	1.137
GRangesFactor-class	0.440	0.000	0.438
GRangesList-class	0.596	0.004	0.653
GenomicRanges-comparison	0.356	0.000	0.356
absoluteRanges	1.468	0.020	1.489
constraint	1.240	0.000	1.258
coverage-methods	0.424	0.000	0.426
findOverlaps-methods	1.428	0.004	1.439
genomic-range-squeezers	0	0	0
genomicvars	58.124	3.532	64.379
inter-range-methods	3.068	0.004	3.099
intra-range-methods	0.556	0.004	0.565
makeGRangesFromDataFrame	0.724	0.016	10.206
makeGRangesListFromDataFrame	0.132	0.000	0.132
nearest-methods	0.848	0.000	0.846
phicoef	0.000	0.000	0.002
setops-methods	4.112	0.008	4.123
strand-utils	0.148	0.008	0.157
tile-methods	0.168	0.000	0.167
tileGenome	0.444	0.004	0.445