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CHECK report for PSICQUIC on tokay1

This page was generated on 2019-04-13 11:23:24 -0400 (Sat, 13 Apr 2019).

Package 1212/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PSICQUIC 1.20.0
Paul Shannon
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 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)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
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: 1.20.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PSICQUIC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PSICQUIC_1.20.0.tar.gz
StartedAt: 2019-04-13 04:43:56 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:53:03 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 547.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: PSICQUIC.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PSICQUIC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PSICQUIC_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/PSICQUIC.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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 'C:/Users/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
interactions   3.53   0.25   55.08
PSICQUIC-class 2.70   0.39   60.40
IDMapper-class 0.70   0.07   13.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
PSICQUIC-class 2.80   0.25   54.84
interactions   2.88   0.13   36.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/PSICQUIC.Rcheck/00check.log'
for details.

Installation output

PSICQUIC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/PSICQUIC_1.20.0.tar.gz && rm -rf PSICQUIC.buildbin-libdir && mkdir PSICQUIC.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PSICQUIC.buildbin-libdir PSICQUIC_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL PSICQUIC_1.20.0.zip && rm PSICQUIC_1.20.0.tar.gz PSICQUIC_1.20.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 64316  100 64316    0     0  1942k      0 --:--:-- --:--:-- --:--:-- 2165k

install for i386

* 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
  converting help for package 'PSICQUIC'
    finding HTML links ... done
    IDMapper-class                          html  
    PSICQUIC-class                          html  
    PSICQUIC-package                        html  
    interactions                            html  
    providers                               html  
    rawQuery                                html  
    webBrowser-functions                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
In R CMD INSTALL

install for x64

* installing *source* package 'PSICQUIC' ...
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
* MD5 sums
packaged installation of 'PSICQUIC' as PSICQUIC_1.20.0.zip
* DONE (PSICQUIC)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'PSICQUIC' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

PSICQUIC.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


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_.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: EBI-GOA-nonIntAct,ZINC,UniProt
[1] "--- test_handleEmbeddedSingleQuote"
[1] test providers: BioGrid,bhf-ucl,MBInfo
[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: MBInfo,bhf-ucl,BAR
[1] "expected psicquic sources not available, skipping test_.retrieveData"
[1] "expected psicquic sources not available, test_retrieveByDetectionMethod"
[1] "--- test_retrieveByInteractionType"
[1] test providers: iRefIndex,IntAct,EBI-GOA-miRNA
[1] "--- test_retrieveByOmimId"
[1] test providers: BioGrid,BindingDB,HPIDb
[1] "--- test_retrieveByPubmedID"
[1] test providers: MBInfo,EBI-GOA-miRNA,BindingDB
[1] "--- test_retrieveByPubmedIdOnly"
[1] test providers: BioGrid,HPIDb,EBI-GOA-nonIntAct
[1] IntAct not available, skipping test_retrieveByPubmedIdOnly
[1] "--- test_retrieveBySpeciesId"
[1] test providers: ChEMBL,ZINC,BAR
[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 -- Sat Apr 13 04:51:38 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 
   6.26    0.31   83.78

PSICQUIC.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


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_.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,Reactome-FIs,BioGrid
[1] "--- test_handleEmbeddedSingleQuote"
[1] test providers: BAR,HPIDb,ZINC
[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: InnateDB-All,IMEx,BindingDB
[1] "expected psicquic sources not available, skipping test_.retrieveData"
[1] "expected psicquic sources not available, test_retrieveByDetectionMethod"
[1] "--- test_retrieveByInteractionType"
[1] test providers: InnateDB-All,BioGrid,IntAct
[1] "--- test_retrieveByOmimId"
[1] test providers: Reactome,MINT,MatrixDB
[1] "--- test_retrieveByPubmedID"
[1] test providers: EBI-GOA-miRNA,MPIDB,HPIDb
[1] "--- test_retrieveByPubmedIdOnly"
[1] test providers: VirHostNet,IntAct,MatrixDB
[1] "--- test_retrieveBySpeciesId"
[1] test providers: MatrixDB,Reactome-FIs,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 -- Sat Apr 13 04:52:59 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 
   7.67    0.21   80.15

Example timings

PSICQUIC.Rcheck/examples_i386/PSICQUIC-Ex.timings

nameusersystemelapsed
IDMapper-class 0.70 0.0713.05
PSICQUIC-class 2.70 0.3960.40
interactions 3.53 0.2555.08
providers0.080.000.76
rawQuery0.050.001.53
webBrowser-functions000

PSICQUIC.Rcheck/examples_x64/PSICQUIC-Ex.timings

nameusersystemelapsed
IDMapper-class0.410.114.86
PSICQUIC-class 2.80 0.2554.84
interactions 2.88 0.1336.16
providers0.030.000.76
rawQuery0.050.001.50
webBrowser-functions000