Paul Shannon
| Snapshot Date: 2019-04-14 17:00:58 -0400 (Sun, 14 Apr 2019) |
| URL: https://git.bioconductor.org/packages/PSICQUIC |
| Branch: RELEASE_3_8 |
| Last Commit: 0019202 |
| Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-15 11:33:20 -0400 (Mon, 15 Apr 2019).
| Package 1212/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PSICQUIC 1.20.0 Paul Shannon
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ ERROR ] | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: PSICQUIC |
| Version: 1.20.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:PSICQUIC.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings PSICQUIC_1.20.0.tar.gz |
| StartedAt: 2019-04-15 02:21:22 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 02:29:10 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 467.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: PSICQUIC.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:PSICQUIC.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings PSICQUIC_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/PSICQUIC.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PSICQUIC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PSICQUIC’ version ‘1.20.0’
* 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 ‘PSICQUIC’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘IRanges::desc’ by ‘plyr::desc’ when loading ‘PSICQUIC’
See ‘/home/biocbuild/bbs-3.8-bioc/meat/PSICQUIC.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 ... NOTE
.loadRegistry: no visible global function definition for ‘DataFrame’
Undefined global functions or variables:
DataFrame
* 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 or elapsed time > 5s
user system elapsed
PSICQUIC-class 3.128 0.160 160.106
interactions 2.836 0.160 47.666
IDMapper-class 0.736 0.068 6.956
* 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:
FAILURE in test_retrieveByPubmedID: Error in checkEquals(dim(tbl), c(4, 16)) : Mean relative difference: 3
Test files with failing tests
test_IDMapper.R
/home/biocbuild/bbs-3.8-bioc/R/library/PSICQUIC/unitTests/test_IDMapper.R
test_PSICQUIC.R
test_retrieveByPubmedID
Error in BiocGenerics:::testPackage("PSICQUIC") :
unit tests failed for package PSICQUIC
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 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.8-bioc/meat/PSICQUIC.Rcheck/00check.log’
for details.
PSICQUIC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL PSICQUIC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘PSICQUIC’ ... ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘IRanges::desc’ by ‘plyr::desc’ when loading ‘PSICQUIC’ Creating a new generic function for ‘count’ in package ‘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 (PSICQUIC)
PSICQUIC.Rcheck/tests/runTests.Rout.fail
R version 3.5.3 (2019-03-11) -- "Great Truth"
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
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("PSICQUIC")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'plyr'
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
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:httr':
content
checking for biomart access...
does 'http://www.ensembl.org' respond?
Error in IDMapper("9606") : url.exists(url) is not TRUE
In addition: Warning message:
replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
Loading required package: bitops
[1] "--- test_.enumerateSearchPairs"
[1] "--- test_.loadRegistry"
[1] "--- test_.restrictBySpecies"
[1] "--- test_.retrieveData"
List of 2
$ message: chr "Could not resolve host: intentionally.bogus"
$ call : language function (type, msg, asError = TRUE) { ...
- attr(*, "class")= chr [1:4] "COULDNT_RESOLVE_HOST" "GenericCurlError" "error" "condition"
character(0)
[1] "failed url: http://intentionally.bogus"
[1] "--- test_ctor"
[1] test providers: bhf-ucl,Reactome,InnateDB
[1] "--- test_handleEmbeddedSingleQuote"
[1] test providers: Reactome,EBI-GOA-nonIntAct,BAR
[1] "--- test_initialConditions"
[1] "--- test_interactions"
[1] "--- test_interactionsFourGenes"
[1] "expected psicquic sources not available, test_interactionFourGenes"
[1] "--- test_interactionsTwoGenes"
[1] "--- test_rawQuery"
[1] test providers: EBI-GOA-nonIntAct,MINT,IMEx
[1] "expected psicquic sources not available, skipping test_.retrieveData"
[1] "expected psicquic sources not available, test_retrieveByDetectionMethod"
[1] "--- test_retrieveByInteractionType"
[1] test providers: EBI-GOA-miRNA,HPIDb,Reactome
[1] "--- test_retrieveByOmimId"
[1] test providers: Reactome-FIs,UniProt,BindingDB
[1] "--- test_retrieveByPubmedID"
[1] test providers: BioGrid,iRefIndex,MPIDB
Timing stopped at: 0.036 0.004 1.369
Error in checkEquals(dim(tbl), c(4, 16)) : Mean relative difference: 3
[1] "--- test_retrieveByPubmedIdOnly"
[1] test providers: BioGrid,mentha,EBI-GOA-nonIntAct
[1] IntAct not available, skipping test_retrieveByPubmedIdOnly
[1] "--- test_retrieveBySpeciesId"
[1] test providers: BAR,Reactome,UniProt
[1] "--- test_smallMoleculeWithoutSpeciesDesignation"
[1] retrieving from ChEMBL
[1] PSICQUIC:::.runQuery: http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/identifier:imatinib
[1] final query.url: http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/identifier:imatinib
[1] --- http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/identifier:imatinib result: 141 15
RUNIT TEST PROTOCOL -- Mon Apr 15 02:29:07 2019
***********************************************
Number of test functions: 19
Number of errors: 1
Number of failures: 1
1 Test Suite :
PSICQUIC RUnit Tests - 19 test functions, 1 error, 1 failure
ERROR in /home/biocbuild/bbs-3.8-bioc/R/library/PSICQUIC/unitTests/test_IDMapper.R: Error while sourcing /home/biocbuild/bbs-3.8-bioc/R/library/PSICQUIC/unitTests/test_IDMapper.R : Error in IDMapper("9606") : url.exists(url) is not TRUE
FAILURE in test_retrieveByPubmedID: Error in checkEquals(dim(tbl), c(4, 16)) : Mean relative difference: 3
Test files with failing tests
test_IDMapper.R
/home/biocbuild/bbs-3.8-bioc/R/library/PSICQUIC/unitTests/test_IDMapper.R
test_PSICQUIC.R
test_retrieveByPubmedID
Error in BiocGenerics:::testPackage("PSICQUIC") :
unit tests failed for package PSICQUIC
Execution halted
PSICQUIC.Rcheck/PSICQUIC-Ex.timings
| name | user | system | elapsed | |
| IDMapper-class | 0.736 | 0.068 | 6.956 | |
| PSICQUIC-class | 3.128 | 0.160 | 160.106 | |
| interactions | 2.836 | 0.160 | 47.666 | |
| providers | 0.028 | 0.000 | 1.567 | |
| rawQuery | 0.064 | 0.008 | 2.356 | |
| webBrowser-functions | 0 | 0 | 0 | |