| Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:23:01 -0400 (Wed, 17 Oct 2018).
| Package 597/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicRanges 1.32.7 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: GenomicRanges |
| Version: 1.32.7 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GenomicRanges_1.32.7.tar.gz |
| StartedAt: 2018-10-16 00:45:40 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 00:48:57 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 196.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicRanges.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GenomicRanges_1.32.7.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/GenomicRanges.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.32.7’
* 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 42.344 3.640 46.049
GPos-class 24.876 3.120 28.060
makeGRangesFromDataFrame 0.580 0.008 17.768
* 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-3.7-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.
GenomicRanges.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL GenomicRanges
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘GenomicRanges’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-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)
GenomicRanges.Rcheck/tests/run_unitTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 Oct 16 00:48:53 2018
***********************************************
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
30.104 0.088 30.319
GenomicRanges.Rcheck/GenomicRanges-Ex.timings
| name | user | system | elapsed | |
| GNCList-class | 0.456 | 0.020 | 0.478 | |
| GPos-class | 24.876 | 3.120 | 28.060 | |
| GRanges-class | 0.668 | 0.004 | 0.674 | |
| GRangesList-class | 0.344 | 0.000 | 0.352 | |
| GenomicRanges-comparison | 0.196 | 0.000 | 0.196 | |
| absoluteRanges | 0.972 | 0.032 | 1.008 | |
| constraint | 0.728 | 0.000 | 0.728 | |
| coverage-methods | 0.236 | 0.000 | 0.235 | |
| findOverlaps-methods | 0.960 | 0.000 | 0.961 | |
| genomic-range-squeezers | 0 | 0 | 0 | |
| genomicvars | 42.344 | 3.640 | 46.049 | |
| inter-range-methods | 2.008 | 0.004 | 2.012 | |
| intra-range-methods | 0.424 | 0.000 | 0.426 | |
| makeGRangesFromDataFrame | 0.580 | 0.008 | 17.768 | |
| makeGRangesListFromDataFrame | 0.072 | 0.004 | 0.073 | |
| nearest-methods | 0.512 | 0.000 | 0.511 | |
| phicoef | 0.000 | 0.000 | 0.002 | |
| setops-methods | 2.368 | 0.000 | 2.372 | |
| strand-utils | 0.096 | 0.000 | 0.093 | |
| tile-methods | 0.072 | 0.000 | 0.073 | |
| tileGenome | 0.252 | 0.000 | 0.251 | |