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This page was generated on 2017-10-18 14:31:33 -0400 (Wed, 18 Oct 2017).
| Package 1026/1381 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PSICQUIC 1.14.0 Paul Shannon
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: PSICQUIC |
| Version: 1.14.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PSICQUIC_1.14.0.tar.gz |
| StartedAt: 2017-10-18 07:35:45 -0400 (Wed, 18 Oct 2017) |
| EndedAt: 2017-10-18 07:39:04 -0400 (Wed, 18 Oct 2017) |
| EllapsedTime: 198.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: PSICQUIC.Rcheck |
| Warnings: NA |
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###
### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PSICQUIC_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PSICQUIC.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.14.0’
* 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 ... 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
Packages in Depends field not imported from:
‘httr’ ‘plyr’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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’
.loadRegistry : <anonymous>: no visible global function definition for
‘str’
.retrieveData: no visible global function definition for ‘read.table’
.retrieveData : <anonymous>: no visible global function definition for
‘str’
.translate.uniprotkb: no visible binding for global variable ‘id’
detectionMethods: no visible global function definition for ‘browseURL’
interactionTypes: no visible global function definition for ‘browseURL’
speciesIDs: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
DataFrame browseURL id read.table str
Consider adding
importFrom("utils", "browseURL", "read.table", "str")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
PSICQUIC-class 1.311 0.055 67.930
interactions 0.357 0.025 9.462
* 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:
test_IDMapper.R
test_.translate.locuslink
test_.translate.refseq
test_.translate.uniprotkb
test_.translateAll
test_addGeneInfo
test_addGeneInfoMinimalTable
test_PSICQUIC.R
test_.loadRegistry
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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/PSICQUIC.Rcheck/00check.log’
for details.
runTests.Rout.fail:
R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 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.
> 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, cbind, colMeans, colSums, colnames, 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?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.categorize"
[1] "--- test_.translate.ensemblGene"
checking for biomart access...
does 'http://www.ensembl.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.translate.ensemblProt"
[1] "--- test_.translate.locuslink"
Timing stopped at: 0.007 0 3.449
Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
[1] "--- test_.translate.refseq"
Timing stopped at: 0.007 0 0.302
Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
[1] "--- test_.translate.string"
[1] "--- test_.translate.uniprotkb"
Timing stopped at: 0.014 0.001 0.667
Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
[1] "--- test_translateAll"
Timing stopped at: 0.032 0.001 0.335
Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
[1] "--- test_addGeneInfo"
Timing stopped at: 0.043 0 0.334
Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
[1] "--- test_addGeneInfoMinimalTable"
checking for biomart access...
does 'http://www.ensembl.org' respond?
creating ensembl mart
Timing stopped at: 0.006 0.001 0.64
Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE, :
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
[1] "--- test_addStandardNames"
[1] "--- test_ctor"
checking for biomart access...
does 'http://www.ensembl.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_preserveKnownGeneIdentifiers"
Loading required package: bitops
[1] "--- test_.enumerateSearchPairs"
[1] "--- test_.loadRegistry"
Timing stopped at: 0.093 0.001 0.476
Error in checkEquals(grep("^http://", tbl$url), 1:nrow(tbl)) :
Numeric: lengths (24, 26) differ
[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: InnateDB-All,bhf-ucl,HPIDb
[1] "--- test_handleEmbeddedSingleQuote"
[1] test providers: Reactome,DIP,bhf-ucl
[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,Reactome
[1] "expected psicquic sources not available, skipping test_.retrieveData"
[1] "expected psicquic sources not available, test_retrieveByDetectionMethod"
[1] "--- test_retrieveByInteractionType"
[1] test providers: HPIDb,InnateDB-All,mentha
[1] "--- test_retrieveByOmimId"
[1] test providers: InnateDB-All,BioGrid,bhf-ucl
[1] "--- test_retrieveByPubmedID"
[1] test providers: bhf-ucl,MBInfo,Reactome
[1] "--- test_retrieveByPubmedIdOnly"
[1] test providers: InnateDB-All,Reactome-FIs,mentha
[1] IntAct not available, skipping test_retrieveByPubmedIdOnly
[1] "--- test_retrieveBySpeciesId"
[1] test providers: InnateDB-All,I2D,MBInfo
[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 -- Wed Oct 18 07:39:01 2017
***********************************************
Number of test functions: 31
Number of errors: 6
Number of failures: 1
1 Test Suite :
PSICQUIC RUnit Tests - 31 test functions, 6 errors, 1 failure
ERROR in test_.translate.locuslink: Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
ERROR in test_.translate.refseq: Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
ERROR in test_.translate.uniprotkb: Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
ERROR in test_.translateAll: Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
ERROR in test_addGeneInfo: Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
ERROR in test_addGeneInfoMinimalTable: Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE, :
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
FAILURE in test_.loadRegistry: Error in checkEquals(grep("^http://", tbl$url), 1:nrow(tbl)) :
Numeric: lengths (24, 26) differ
Test files with failing tests
test_IDMapper.R
test_.translate.locuslink
test_.translate.refseq
test_.translate.uniprotkb
test_.translateAll
test_addGeneInfo
test_addGeneInfoMinimalTable
test_PSICQUIC.R
test_.loadRegistry
Error in BiocGenerics:::testPackage("PSICQUIC") :
unit tests failed for package PSICQUIC
Execution halted
PSICQUIC.Rcheck/00install.out:
* installing *source* package ‘PSICQUIC’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (PSICQUIC)
PSICQUIC.Rcheck/PSICQUIC-Ex.timings:
| name | user | system | elapsed | |
| IDMapper-class | 0.446 | 0.018 | 4.635 | |
| PSICQUIC-class | 1.311 | 0.055 | 67.930 | |
| interactions | 0.357 | 0.025 | 9.462 | |
| providers | 0.012 | 0.002 | 0.762 | |
| rawQuery | 0.028 | 0.003 | 0.888 | |
| webBrowser-functions | 0.001 | 0.000 | 0.000 | |