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CHECK report for PSICQUIC on malbec1

This page was generated on 2020-04-15 12:08:13 -0400 (Wed, 15 Apr 2020).

Package 1326/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PSICQUIC 1.24.0
Paul Shannon
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/PSICQUIC
Branch: RELEASE_3_10
Last Commit: 9eb3444
Last Changed Date: 2019-10-29 13:08:50 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: PSICQUIC
Version: 1.24.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PSICQUIC.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PSICQUIC_1.24.0.tar.gz
StartedAt: 2020-04-15 01:57:44 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:02:07 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 263.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: PSICQUIC.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PSICQUIC.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PSICQUIC_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/PSICQUIC.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.24.0’
* 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 ‘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-3.10-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 5.020  0.168  51.314
interactions   3.808  0.244  23.399
IDMapper-class 1.176  0.028   5.936
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/PSICQUIC.Rcheck/00check.log’
for details.

Installation output

PSICQUIC.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL PSICQUIC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘PSICQUIC’ ...
** using staged installation
** 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 from temporary location
Warning: replacing previous import ‘IRanges::desc’ by ‘plyr::desc’ when loading ‘PSICQUIC’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘IRanges::desc’ by ‘plyr::desc’ when loading ‘PSICQUIC’
** testing if installed package keeps a record of temporary installation path
* DONE (PSICQUIC)

Tests output

PSICQUIC.Rcheck/tests/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

> 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, 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


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"
[1] "--- test_.translate.ensemblProt"
[1] "--- test_.translate.locuslink"
[1] "--- test_.translate.refseq"
[1] "--- test_.translate.string"
[1] "--- test_.translate.uniprotkb"
[1] "--- test_translateAll"
[1] "--- test_addGeneInfo"
Cache found
[1] "--- test_addGeneInfoMinimalTable"
checking for biomart access...
   does 'http://www.ensembl.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to biomart...
Cache found
[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"
[1] "--- test_initialConditions"
[1] "--- test_.loadRegistry"
[1] "--- test_ctor"
[1] test providers: BAR,Reactome-FIs,IntAct
[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_rawQuery"
[1] test providers: InnateDB-All,VirHostNet,DIP
[1] "expected psicquic sources not available, skipping test_.retrieveData"
[1] "--- test_.enumerateSearchPairs"
[1] "--- test_.restrictBySpecies"
[1] "--- test_interactions"
[1] "--- test_interactionsTwoGenes"
[1] "--- test_interactionsFourGenes"
[1] "expected psicquic sources not available, test_interactionFourGenes"
[1] "--- test_handleEmbeddedSingleQuote"
[1] test providers: I2D,BindingDB,ChEMBL
[1] "--- test_retrieveByPubmedID"
[1] "--- test_retrieveByPubmedIdOnly"
[1] test providers: MINT,bhf-ucl,DIP
[1] IntAct not available, skipping test_retrieveByPubmedIdOnly
[1] "--- test_retrieveByOmimId"
[1] test providers: DIP-IMEx,DIP,BioGrid
List of 2
 $ message: chr "server certificate verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none"
 $ call   : language function (type, msg, asError = TRUE)  { ...
 - attr(*, "class")= chr [1:4] "SSL_CACERT" "GenericCurlError" "error" "condition"
character(0)
[1] "failed url: https://imex.mbi.ucla.edu/xpsq-dip-imex/service/soap/current/species:9606%20AND%20pubid:00109135"
List of 2
 $ message: chr "server certificate verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none"
 $ call   : language function (type, msg, asError = TRUE)  { ...
 - attr(*, "class")= chr [1:4] "SSL_CACERT" "GenericCurlError" "error" "condition"
character(0)
[1] "failed url: https://imex.mbi.ucla.edu/xpsq-dip-all/service/soap/currentspecies:9606%20AND%20pubid:00109135"
List of 2
 $ message: chr "server certificate verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none"
 $ call   : language function (type, msg, asError = TRUE)  { ...
 - attr(*, "class")= chr [1:4] "SSL_CACERT" "GenericCurlError" "error" "condition"
character(0)
[1] "failed url: https://imex.mbi.ucla.edu/xpsq-dip-imex/service/soap/current/species:9606%20AND%20pubid:00137800"
List of 2
 $ message: chr "server certificate verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none"
 $ call   : language function (type, msg, asError = TRUE)  { ...
 - attr(*, "class")= chr [1:4] "SSL_CACERT" "GenericCurlError" "error" "condition"
character(0)
[1] "failed url: https://imex.mbi.ucla.edu/xpsq-dip-all/service/soap/currentspecies:9606%20AND%20pubid:00137800"
[1] "--- test_retrieveByInteractionType"
[1] test providers: Reactome,MPIDB,Reactome-FIs
[1] "expected psicquic sources not available, test_retrieveByDetectionMethod"
[1] "--- test_retrieveBySpeciesId"
[1] test providers: InnateDB,ChEMBL,IMEx
[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
[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: MINT,bhf-ucl,VirHostNet
[1] "--- test_handleEmbeddedSingleQuote"
[1] test providers: VirHostNet,bhf-ucl,ChEMBL
[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: bhf-ucl,VirHostNet,BAR
[1] "expected psicquic sources not available, skipping test_.retrieveData"
[1] "expected psicquic sources not available, test_retrieveByDetectionMethod"
[1] "--- test_retrieveByInteractionType"
[1] test providers: IMEx,MBInfo,DIP
[1] "--- test_retrieveByOmimId"
[1] test providers: mentha,MBInfo,Reactome
[1] "--- test_retrieveByPubmedID"
[1] "--- test_retrieveByPubmedIdOnly"
[1] test providers: InnateDB,MINT,EBI-GOA-miRNA
[1] IntAct not available, skipping test_retrieveByPubmedIdOnly
[1] "--- test_retrieveBySpeciesId"
[1] test providers: Reactome-FIs,VirHostNet,DIP
[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 Apr 15 02:02:03 2020 
*********************************************** 
Number of test functions: 31 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
PSICQUIC RUnit Tests - 31 test functions, 0 errors, 0 failures
Number of test functions: 31 
Number of errors: 0 
Number of failures: 0 
Warning message:
replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC' 
> 
> proc.time()
   user  system elapsed 
 14.692   0.324  78.030

Example timings

PSICQUIC.Rcheck/PSICQUIC-Ex.timings

nameusersystemelapsed
IDMapper-class1.1760.0285.936
PSICQUIC-class 5.020 0.16851.314
interactions 3.808 0.24423.399
providers0.0240.0000.825
rawQuery0.0440.0001.134
webBrowser-functions0.0000.0000.001