Package: PSICQUIC

Version: 1.22.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PSICQUIC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PSICQUIC_1.22.2.tar.gz

StartedAt: 2019-10-16 05:49:01 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:53:46 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 285.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: PSICQUIC.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PSICQUIC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PSICQUIC_1.22.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PSICQUIC.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.22.2’
* 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 ‘/Users/biocbuild/bbs-3.9-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 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
interactions   3.975  0.441  17.371
PSICQUIC-class 2.952  0.300  39.931
IDMapper-class 1.121  0.176   9.823
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/PSICQUIC.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PSICQUIC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, 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"
[1] "--- test_addGeneInfoMinimalTable"
checking for biomart access...
   does 'http://www.ensembl.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to 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_initialConditions"
[1] "--- test_.loadRegistry"
[1] "--- test_ctor"
[1] test providers: IntAct,VirHostNet,MBInfo
[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: HPIDb,BAR,I2D
[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: HPIDb,InnateDB-All,BAR
[1] "--- test_retrieveByPubmedID"
[1] "--- test_retrieveByPubmedIdOnly"
[1] test providers: BindingDB,I2D,EBI-GOA-miRNA
[1] IntAct not available, skipping test_retrieveByPubmedIdOnly
[1] "--- test_retrieveByOmimId"
[1] test providers: ChEMBL,BAR,UniProt
[1] "--- test_retrieveByInteractionType"
[1] test providers: BioGrid,MatrixDB,UniProt
[1] "expected psicquic sources not available, test_retrieveByDetectionMethod"
[1] "--- test_retrieveBySpeciesId"
[1] test providers: MPIDB,InnateDB,BindingDB
[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: ChEMBL,BAR,mentha
[1] "--- test_handleEmbeddedSingleQuote"
[1] test providers: MINT,BindingDB,UniProt
[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: HPIDb,ChEMBL,MatrixDB
[1] "expected psicquic sources not available, skipping test_.retrieveData"
[1] "expected psicquic sources not available, test_retrieveByDetectionMethod"
[1] "--- test_retrieveByInteractionType"
[1] test providers: MBInfo,BioGrid,MINT
[1] "--- test_retrieveByOmimId"
[1] test providers: UniProt,InnateDB,MatrixDB
[1] "--- test_retrieveByPubmedID"
[1] "--- test_retrieveByPubmedIdOnly"
[1] test providers: MPIDB,EBI-GOA-nonIntAct,bhf-ucl
[1] IntAct not available, skipping test_retrieveByPubmedIdOnly
[1] "--- test_retrieveBySpeciesId"
[1] test providers: MPIDB,mentha,InnateDB
[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 16 05:53:40 2019 
*********************************************** 
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 
 12.654   1.173  89.922 

name	user	system	elapsed
IDMapper-class	1.121	0.176	9.823
PSICQUIC-class	2.952	0.300	39.931
interactions	3.975	0.441	17.371
providers	0.028	0.005	0.801
rawQuery	0.044	0.007	1.018
webBrowser-functions	0	0	0