Aaron Lun
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/InteractionSet |
| Branch: master |
| Last Commit: bcbcf98 |
| Last Changed Date: 2019-03-16 21:16:43 -0400 (Sat, 16 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:45:52 -0400 (Tue, 09 Apr 2019).
| Package 805/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| InteractionSet 1.11.2 Aaron Lun
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: InteractionSet |
| Version: 1.11.2 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:InteractionSet.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings InteractionSet_1.11.2.tar.gz |
| StartedAt: 2019-04-09 01:23:59 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:27:57 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 237.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: InteractionSet.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:InteractionSet.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings InteractionSet_1.11.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/InteractionSet.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘InteractionSet/DESCRIPTION’ ... OK * this is package ‘InteractionSet’ version ‘1.11.2’ * 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 ‘InteractionSet’ 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 ... NOTE Unexported objects imported by ':::' calls: ‘GenomicRanges:::extraColumnSlotNames’ ‘S4Vectors:::disableValidity’ ‘S4Vectors:::makeClassinfoRowForCompactPrinting’ ‘S4Vectors:::makePrettyMatrixForCompactPrinting’ ‘S4Vectors:::prepare_objects_to_bind’ ‘S4Vectors:::selectSome’ See the note in ?`:::` about the use of this operator. * 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 ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/InteractionSet.Rcheck/00check.log’ for details.
InteractionSet.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL InteractionSet
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘InteractionSet’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c box_bounds.cpp -o box_bounds.o
box_bounds.cpp: In function ‘SEXPREC* get_box_bounds(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
box_bounds.cpp:10:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (npts!=Adex.size()) {
˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c detect_overlaps.cpp -o detect_overlaps.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c link_overlaps.cpp -o link_overlaps.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c overlap_utils.cpp -o overlap_utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o InteractionSet.so box_bounds.o detect_overlaps.o init.o link_overlaps.o overlap_utils.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-InteractionSet/00new/InteractionSet/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 (InteractionSet)
InteractionSet.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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
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Type 'q()' to quit R.
> library(testthat)
> library(InteractionSet)
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, 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
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
>
> test_check("InteractionSet")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 1979 SKIPPED: 0 FAILED: 0
>
>
> proc.time()
user system elapsed
75.319 0.410 75.756
InteractionSet.Rcheck/InteractionSet-Ex.timings
| name | user | system | elapsed | |
| ContactMatrix-accessors | 1.070 | 0.012 | 1.098 | |
| ContactMatrix-class | 0.049 | 0.003 | 0.052 | |
| ContactMatrix-distances | 0.048 | 0.020 | 0.068 | |
| ContactMatrix-overlaps | 0.245 | 0.040 | 0.285 | |
| ContactMatrix-sorting | 0.140 | 0.004 | 0.144 | |
| ContactMatrix-subset | 0.082 | 0.000 | 0.082 | |
| GInteractions-class | 0.204 | 0.004 | 0.208 | |
| InteractionSet-class | 0.242 | 0.000 | 0.242 | |
| boundingBox | 0.263 | 0.000 | 0.299 | |
| conversion | 0.626 | 0.020 | 0.646 | |
| distances | 0.267 | 0.000 | 0.267 | |
| granges-methods | 0.331 | 0.000 | 0.331 | |
| interaction-accessors | 0.515 | 0.000 | 0.515 | |
| interaction-bind | 0.462 | 0.000 | 0.462 | |
| interaction-compare | 0.500 | 0.004 | 0.505 | |
| interaction-subset | 0.767 | 0.000 | 0.775 | |
| linearize | 0.699 | 0.000 | 0.699 | |
| linkOverlaps | 0.619 | 0.004 | 0.623 | |
| overlaps | 1.683 | 0.000 | 1.683 | |
| pairs | 0.67 | 0.00 | 0.67 | |