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 13:33:15 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:InteractionSet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings InteractionSet_1.11.2.tar.gz |
| StartedAt: 2019-04-09 01:39:38 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:44:04 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 266.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: InteractionSet.Rcheck |
| Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:InteractionSet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings InteractionSet_1.11.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/InteractionSet.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * using platform: x86_64-apple-darwin15.6.0 (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’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Actual value: "GInteractions object with 10 interactions and 0 metadata columns:\n seqnames1 ranges1 seqnames2 ranges2\n <Rle> <IRanges> <Rle> <IRanges>\n [1] chrA 82-100 --- chrB 67-84\n [2] chrA 76-95 --- chrB 64-78\n [3] chrA 87-104 --- chrA 3-23\n [4] chrB 67-84 --- chrA 41-59\n [5] chrA 14-19 --- chrA 87-104\n [6] chrB 42-54 --- chrB 91-98\n [7] chrB 64-78 --- chrA 55-68\n [8] chrA 3-23 --- chrB 81-98\n [9] chrA 61-67 --- chrA 46-66\n [10] chrA 41-49 --- chrA 59-72\n -------\n regions: 30 ranges and 0 metadata columns\n seqinfo: 2 sequences from an unspecified genome; no seqlengths" ── 4. Failure: name handling is correct with GI objects (@test-GI.R#505) ────── `show(temp.x)` does not match "GInteractions object with 20 interactions and 0 metadata columns:\n seqnames1 ranges1 seqnames2 ranges2\n <Rle> <IRanges> <Rle> <IRanges>\n X1 chrA 94-105 --- chrA 41-48\n X2 chrB 42-54 --- chrA 94-105\n X3 chrA 41-48 --- chrA 59-72\n X4 chrB 64-78 --- chrA 55-68\n X5 chrA 41-59 --- chrA 3-23\n ... ... ... ... ... ...\n X16 chrA 76-95 --- chrB 91-98\n X17 chrA 46-66 --- chrB 67-84\n X18 chrA 68-78 --- chrA 20-33\n X19 chrA 61-67 --- chrA 87-104\n X20 chrA 18-35 --- chrB 63-76\n -------\n regions: 30 ranges and 0 metadata columns\n seqinfo: 2 sequences from an unspecified genome; no seqlengths". Actual value: "GInteractions object with 20 interactions and 0 metadata columns:\n seqnames1 ranges1 seqnames2 ranges2\n <Rle> <IRanges> <Rle> <IRanges>\n X1 chrA 82-100 --- chrB 67-84\n X2 chrA 76-95 --- chrB 64-78\n X3 chrA 87-104 --- chrA 3-23\n X4 chrB 67-84 --- chrA 41-59\n X5 chrA 14-19 --- chrA 87-104\n ... ... ... ... ... ...\n X16 chrA 59-72 --- chrA 68-78\n X17 chrA 84-103 --- chrB 94-113\n X18 chrB 89-97 --- chrA 20-33\n X19 chrA 41-59 --- chrA 84-103\n X20 chrA 86-105 --- chrA 76-95\n -------\n regions: 30 ranges and 0 metadata columns\n seqinfo: 2 sequences from an unspecified genome; no seqlengths" ══ testthat results ═══════════════════════════════════════════════════════════ OK: 1975 SKIPPED: 0 FAILED: 4 1. Failure: show methods work for GI objects (@test-GI.R#16) 2. Failure: other setters work properly for GI objects (@test-GI.R#200) 3. Failure: subsetting works for GI objects (@test-GI.R#230) 4. Failure: name handling is correct with GI objects (@test-GI.R#505) Error: testthat unit tests failed Execution halted * 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: 1 ERROR, 2 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/InteractionSet.Rcheck/00check.log’ for details.
InteractionSet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL InteractionSet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘InteractionSet’ ... ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c box_bounds.cpp -o box_bounds.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c detect_overlaps.cpp -o detect_overlaps.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c link_overlaps.cpp -o link_overlaps.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c overlap_utils.cpp -o overlap_utils.o clang++ -std=gnu++11 -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 InteractionSet.so box_bounds.o detect_overlaps.o init.o link_overlaps.o overlap_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 * DONE (InteractionSet)
InteractionSet.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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.
> 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")
── 1. Failure: show methods work for GI objects (@test-GI.R#16) ───────────────
`sub("[0-9]", " ", show(x))` does not match "GInteractions object with 20 interactions and 0 metadata columns:\n seqnames1 ranges1 seqnames2 ranges2\n <Rle> <IRanges> <Rle> <IRanges>\n [1] chrA 94-105 --- chrA 41-48\n [2] chrB 42-54 --- chrA 94-105\n [3] chrA 41-48 --- chrA 59-72\n [4] chrB 64-78 --- chrA 55-68\n [5] chrA 41-59 --- chrA 3-23\n ... ... ... ... ... ...\n [16] chrA 76-95 --- chrB 91-98\n [17] chrA 46-66 --- chrB 67-84\n [18] chrA 68-78 --- chrA 20-33\n [19] chrA 61-67 --- chrA 87-104\n [20] chrA 18-35 --- chrB 63-76\n -------\n regions: 30 ranges and 0 metadata columns\n seqinfo: 2 sequences from an unspecified genome; no seqlengths".
Actual value: "GInteractions object with 20 interactions and 0 metadata columns:\n seqnames1 ranges1 seqnames2 ranges2\n <Rle> <IRanges> <Rle> <IRanges>\n [1] chrA 82-100 --- chrB 67-84\n [2] chrA 76-95 --- chrB 64-78\n [3] chrA 87-104 --- chrA 3-23\n [4] chrB 67-84 --- chrA 41-59\n [5] chrA 14-19 --- chrA 87-104\n ... ... ... ... ... ...\n [16] chrA 59-72 --- chrA 68-78\n [17] chrA 84-103 --- chrB 94-113\n [18] chrB 89-97 --- chrA 20-33\n [19] chrA 41-59 --- chrA 84-103\n [20] chrA 86-105 --- chrA 76-95\n -------\n regions: 30 ranges and 0 metadata columns\n seqinfo: 2 sequences from an unspecified genome; no seqlengths"
── 2. Failure: other setters work properly for GI objects (@test-GI.R#200) ────
`show(x)` does not match "GInteractions object with 20 interactions and 1 metadata column:\n seqnames1 ranges1 seqnames2 ranges2 | stuff\n <Rle> <IRanges> <Rle> <IRanges> | <numeric>\n [1] chrA 94-105 --- chrA 41-48 | 0.906575692584738\n [2] chrB 42-54 --- chrA 94-105 | 0.582026617834345\n [3] chrA 41-48 --- chrA 59-72 | 0.863604818237945\n [4] chrB 64-78 --- chrA 55-68 | 0.0807054068427533\n [5] chrA 41-59 --- chrA 3-23 | 0.81304822396487\n ... ... ... ... ... ... . ...\n [16] chrA 76-95 --- chrB 91-98 | 0.95063978806138\n [17] chrA 46-66 --- chrB 67-84 | 0.508890328463167\n [18] chrA 68-78 --- chrA 20-33 | 0.398672606563196\n [19] chrA 61-67 --- chrA 87-104 | 0.523666693130508\n [20] chrA 18-35 --- chrB 63-76 | 0.482420985586941\n -------\n regions: 30 ranges and 0 metadata columns\n seqinfo: 2 sequences from an unspecified genome; no seqlengths".
Actual value: "GInteractions object with 20 interactions and 1 metadata column:\n seqnames1 ranges1 seqnames2 ranges2 | stuff\n <Rle> <IRanges> <Rle> <IRanges> | <numeric>\n [1] chrA 82-100 --- chrB 67-84 | 0.685012309812009\n [2] chrA 76-95 --- chrB 64-78 | 0.895816484699026\n [3] chrA 87-104 --- chrA 3-23 | 0.618890272220597\n [4] chrB 67-84 --- chrA 41-59 | 0.0507488863077015\n [5] chrA 14-19 --- chrA 87-104 | 0.621526781003922\n ... ... ... ... ... ... . ...\n [16] chrA 59-72 --- chrA 68-78 | 0.727361923549324\n [17] chrA 84-103 --- chrB 94-113 | 0.402884092880413\n [18] chrB 89-97 --- chrA 20-33 | 0.906575692584738\n [19] chrA 41-59 --- chrA 84-103 | 0.582026617834345\n [20] chrA 86-105 --- chrA 76-95 | 0.863604818237945\n -------\n regions: 30 ranges and 0 metadata columns\n seqinfo: 2 sequences from an unspecified genome; no seqlengths"
── 3. Failure: subsetting works for GI objects (@test-GI.R#230) ───────────────
`show(xsub)` does not match "GInteractions object with 10 interactions and 0 metadata columns:\n seqnames1 ranges1 seqnames2 ranges2\n <Rle> <IRanges> <Rle> <IRanges>\n [1] chrA 94-105 --- chrA 41-48\n [2] chrB 42-54 --- chrA 94-105\n [3] chrA 41-48 --- chrA 59-72\n [4] chrB 64-78 --- chrA 55-68\n [5] chrA 41-59 --- chrA 3-23\n [6] chrA 47-54 --- chrA 14-19\n [7] chrA 82-100 --- chrA 84-103\n [8] chrB 89-97 --- chrA 46-66\n [9] chrA 86-105 --- chrA 82-100\n [10] chrA 55-68 --- chrB 81-98\n -------\n regions: 30 ranges and 0 metadata columns\n seqinfo: 2 sequences from an unspecified genome; no seqlengths".
Actual value: "GInteractions object with 10 interactions and 0 metadata columns:\n seqnames1 ranges1 seqnames2 ranges2\n <Rle> <IRanges> <Rle> <IRanges>\n [1] chrA 82-100 --- chrB 67-84\n [2] chrA 76-95 --- chrB 64-78\n [3] chrA 87-104 --- chrA 3-23\n [4] chrB 67-84 --- chrA 41-59\n [5] chrA 14-19 --- chrA 87-104\n [6] chrB 42-54 --- chrB 91-98\n [7] chrB 64-78 --- chrA 55-68\n [8] chrA 3-23 --- chrB 81-98\n [9] chrA 61-67 --- chrA 46-66\n [10] chrA 41-49 --- chrA 59-72\n -------\n regions: 30 ranges and 0 metadata columns\n seqinfo: 2 sequences from an unspecified genome; no seqlengths"
── 4. Failure: name handling is correct with GI objects (@test-GI.R#505) ──────
`show(temp.x)` does not match "GInteractions object with 20 interactions and 0 metadata columns:\n seqnames1 ranges1 seqnames2 ranges2\n <Rle> <IRanges> <Rle> <IRanges>\n X1 chrA 94-105 --- chrA 41-48\n X2 chrB 42-54 --- chrA 94-105\n X3 chrA 41-48 --- chrA 59-72\n X4 chrB 64-78 --- chrA 55-68\n X5 chrA 41-59 --- chrA 3-23\n ... ... ... ... ... ...\n X16 chrA 76-95 --- chrB 91-98\n X17 chrA 46-66 --- chrB 67-84\n X18 chrA 68-78 --- chrA 20-33\n X19 chrA 61-67 --- chrA 87-104\n X20 chrA 18-35 --- chrB 63-76\n -------\n regions: 30 ranges and 0 metadata columns\n seqinfo: 2 sequences from an unspecified genome; no seqlengths".
Actual value: "GInteractions object with 20 interactions and 0 metadata columns:\n seqnames1 ranges1 seqnames2 ranges2\n <Rle> <IRanges> <Rle> <IRanges>\n X1 chrA 82-100 --- chrB 67-84\n X2 chrA 76-95 --- chrB 64-78\n X3 chrA 87-104 --- chrA 3-23\n X4 chrB 67-84 --- chrA 41-59\n X5 chrA 14-19 --- chrA 87-104\n ... ... ... ... ... ...\n X16 chrA 59-72 --- chrA 68-78\n X17 chrA 84-103 --- chrB 94-113\n X18 chrB 89-97 --- chrA 20-33\n X19 chrA 41-59 --- chrA 84-103\n X20 chrA 86-105 --- chrA 76-95\n -------\n regions: 30 ranges and 0 metadata columns\n seqinfo: 2 sequences from an unspecified genome; no seqlengths"
══ testthat results ═══════════════════════════════════════════════════════════
OK: 1975 SKIPPED: 0 FAILED: 4
1. Failure: show methods work for GI objects (@test-GI.R#16)
2. Failure: other setters work properly for GI objects (@test-GI.R#200)
3. Failure: subsetting works for GI objects (@test-GI.R#230)
4. Failure: name handling is correct with GI objects (@test-GI.R#505)
Error: testthat unit tests failed
Execution halted
InteractionSet.Rcheck/InteractionSet-Ex.timings
| name | user | system | elapsed | |
| ContactMatrix-accessors | 1.166 | 0.016 | 1.191 | |
| ContactMatrix-class | 0.069 | 0.006 | 0.074 | |
| ContactMatrix-distances | 0.112 | 0.018 | 0.131 | |
| ContactMatrix-overlaps | 0.457 | 0.061 | 0.520 | |
| ContactMatrix-sorting | 0.207 | 0.020 | 0.228 | |
| ContactMatrix-subset | 0.139 | 0.002 | 0.142 | |
| GInteractions-class | 0.311 | 0.002 | 0.316 | |
| InteractionSet-class | 0.380 | 0.002 | 0.385 | |
| boundingBox | 0.411 | 0.004 | 0.416 | |
| conversion | 0.905 | 0.018 | 0.926 | |
| distances | 0.389 | 0.004 | 0.396 | |
| granges-methods | 0.459 | 0.005 | 0.466 | |
| interaction-accessors | 0.704 | 0.010 | 0.721 | |
| interaction-bind | 0.758 | 0.005 | 0.785 | |
| interaction-compare | 0.675 | 0.006 | 0.690 | |
| interaction-subset | 0.747 | 0.008 | 0.760 | |
| linearize | 1.042 | 0.006 | 1.069 | |
| linkOverlaps | 0.672 | 0.003 | 0.681 | |
| overlaps | 1.734 | 0.013 | 1.763 | |
| pairs | 0.661 | 0.005 | 0.678 | |