Paul Shannon
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/RefNet |
| Branch: RELEASE_3_7 |
| Last Commit: f1d7a0a |
| Last Changed Date: 2018-04-30 10:35:33 -0400 (Mon, 30 Apr 2018) |
| 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 |
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### Running command:
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### /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
###
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* 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 | |