Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:52:53 -0400 (Wed, 17 Oct 2018).
Package 1215/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
RefNet 1.16.0 Paul Shannon
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
Package: RefNet |
Version: 1.16.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RefNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RefNet_1.16.0.tar.gz |
StartedAt: 2018-10-16 23:36:10 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 23:39:57 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 226.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: RefNet.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RefNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RefNet_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/RefNet.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RefNet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RefNet’ version ‘1.16.0’ * 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 ‘RefNet’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed RefNet-class 19.121 0.880 23.208 providers 18.618 0.803 21.256 interactions 18.431 0.762 20.396 providerClasses 18.207 0.771 20.228 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: 1 Test Suite : RefNet RUnit Tests - 1 test function, 1 error, 0 failures ERROR in /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RefNet/unitTests/test_RefNet.R: Error while sourcing /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RefNet/unitTests/test_RefNet.R : Error in interactions(psicquic, id = "CCNG1", species = "9606", provider = "IntAct") : Error! these providers not recognized: IntAct Test files with failing tests test_RefNet.R /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RefNet/unitTests/test_RefNet.R Error in BiocGenerics:::testPackage("RefNet") : unit tests failed for package RefNet 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, 1 NOTE See ‘/Users/biocbuild/bbs-3.7-bioc/meat/RefNet.Rcheck/00check.log’ for details.
RefNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RefNet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘RefNet’ ... ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘IRanges::desc’ by ‘plyr::desc’ when loading ‘PSICQUIC’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import ‘IRanges::desc’ by ‘plyr::desc’ when loading ‘PSICQUIC’ * DONE (RefNet)
RefNet.Rcheck/tests/runTests.Rout.fail
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" 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. > require(RefNet) || stop("unable to load RefNet package") Loading required package: RefNet Loading required package: IRanges 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 Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: PSICQUIC Loading required package: biomaRt Loading required package: httr Loading required package: plyr Attaching package: 'plyr' The following object is masked from 'package:IRanges': desc The following object is masked from 'package:S4Vectors': rename Loading required package: AnnotationHub Loading required package: RCurl Loading required package: bitops Loading required package: shiny [1] TRUE Warning message: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC' > BiocGenerics:::testPackage('RefNet') Loading required package: AnnotationDbi 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")'. Attaching package: 'Biobase' The following object is masked from 'package:AnnotationHub': cache The following object is masked from 'package:httr': content [1] initializing PSICQUIC... [1] initializing RefNet from AnnotationHub... snapshotDate(): 2018-04-30 downloading 0 resources loading from cache '/Users/biocbuild//.AnnotationHub/10364' downloading 0 resources loading from cache '/Users/biocbuild//.AnnotationHub/10365' downloading 0 resources loading from cache '/Users/biocbuild//.AnnotationHub/12810' downloading 0 resources loading from cache '/Users/biocbuild//.AnnotationHub/12814' downloading 0 resources loading from cache '/Users/biocbuild//.AnnotationHub/27766' downloading 0 resources loading from cache '/Users/biocbuild//.AnnotationHub/27767' downloading 0 resources loading from cache '/Users/biocbuild//.AnnotationHub/27768' downloading 0 resources loading from cache '/Users/biocbuild//.AnnotationHub/27769' [1] RefNet ready. checking for biomart access... does 'http://www.ensembl.org' respond? creating ensembl mart hsapiens_gene_ensembl dataset provided? connecting to biomart... Error in interactions(psicquic, id = "CCNG1", species = "9606", provider = "IntAct") : Error! these providers not recognized: IntAct In addition: Warning message: In is.na(psicquic) : is.na() applied to non-(list or vector) of type 'S4' RUNIT TEST PROTOCOL -- Tue Oct 16 23:39:52 2018 *********************************************** Number of test functions: 1 Number of errors: 1 Number of failures: 0 1 Test Suite : RefNet RUnit Tests - 1 test function, 1 error, 0 failures ERROR in /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RefNet/unitTests/test_RefNet.R: Error while sourcing /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RefNet/unitTests/test_RefNet.R : Error in interactions(psicquic, id = "CCNG1", species = "9606", provider = "IntAct") : Error! these providers not recognized: IntAct Test files with failing tests test_RefNet.R /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RefNet/unitTests/test_RefNet.R Error in BiocGenerics:::testPackage("RefNet") : unit tests failed for package RefNet Execution halted
RefNet.Rcheck/RefNet-Ex.timings
name | user | system | elapsed | |
RefNet-class | 19.121 | 0.880 | 23.208 | |
detectDuplicateInteractions | 0.025 | 0.001 | 0.027 | |
interactions | 18.431 | 0.762 | 20.396 | |
pickBestFromDupGroup | 0.017 | 0.001 | 0.017 | |
providerClasses | 18.207 | 0.771 | 20.228 | |
providers | 18.618 | 0.803 | 21.256 | |
pubmedAbstract | 0.017 | 0.002 | 0.729 | |