Paul Shannon
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/RefNet |
| Branch: RELEASE_3_11 |
| Last Commit: 716e288 |
| Last Changed Date: 2020-04-27 14:40:10 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:33 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE RefNet PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1457/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Paul Shannon
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: RefNet |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RefNet.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RefNet_1.24.0.tar.gz |
| StartedAt: 2020-10-17 04:38:07 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:44:33 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 386.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RefNet.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RefNet.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RefNet_1.24.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/RefNet.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.24.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: Package 'RefNet' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.11-bioc/meat/RefNet.Rcheck/00install.out’ for details.
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RefNet-class 30.868 0.469 34.958
providerClasses 30.186 0.420 32.384
providers 29.428 0.428 31.779
interactions 26.308 0.304 28.718
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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: 1 WARNING
See
‘/home/biocbuild/bbs-3.11-bioc/meat/RefNet.Rcheck/00check.log’
for details.
RefNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL RefNet ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘RefNet’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning message: 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 from temporary location Warning: replacing previous import ‘IRanges::desc’ by ‘plyr::desc’ when loading ‘PSICQUIC’ Warning: Package 'RefNet' is deprecated and will be removed from Bioconductor version 3.12 ** testing if installed package can be loaded from final location Warning: replacing previous import ‘IRanges::desc’ by ‘plyr::desc’ when loading ‘PSICQUIC’ Warning: Package 'RefNet' is deprecated and will be removed from Bioconductor version 3.12 ** testing if installed package keeps a record of temporary installation path * DONE (RefNet)
RefNet.Rcheck/tests/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(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, 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, 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: BiocFileCache
Loading required package: dbplyr
Loading required package: RCurl
Loading required package: shiny
[1] TRUE
Warning messages:
1: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
2: Package 'RefNet' is deprecated and will be removed from Bioconductor
version 3.12
> 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(): 2020-04-27
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
[1] RefNet ready.
checking for biomart access...
does 'http://www.ensembl.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.combinations"
[1] "--- test_.filterOnColumnValue"
[1] "--- test_.findHits"
[1] "--- test_.smartRbind"
[1] "--- test_ctor"
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
snapshotDate(): 2020-04-27
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
[1] RefNet ready.
[1] "--- test_detectDuplicateInteractions"
[1] "--- test_interactions"
[1] "--- test_pickBestFromDupGroup"
[1] "--- test_providerMix_PSICQUIC_and_native"
[1] "--- test_pubmedAbstract"
[1] "--- test_recon2Interactions"
RUNIT TEST PROTOCOL -- Sat Oct 17 04:44:30 2020
***********************************************
Number of test functions: 11
Number of errors: 0
Number of failures: 0
1 Test Suite :
RefNet RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
70.868 1.033 90.317
RefNet.Rcheck/RefNet-Ex.timings
| name | user | system | elapsed | |
| RefNet-class | 30.868 | 0.469 | 34.958 | |
| detectDuplicateInteractions | 0.018 | 0.000 | 0.023 | |
| interactions | 26.308 | 0.304 | 28.718 | |
| pickBestFromDupGroup | 0.020 | 0.000 | 0.032 | |
| providerClasses | 30.186 | 0.420 | 32.384 | |
| providers | 29.428 | 0.428 | 31.779 | |
| pubmedAbstract | 0.072 | 0.000 | 0.327 | |