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CHECK report for RefNet on tokay2

This page was generated on 2019-10-15 13:04:00 -0400 (Tue, 15 Oct 2019).

Package 1349/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RefNet 1.20.0
Paul Shannon
Snapshot Date: 2019-10-14 17:00:44 -0400 (Mon, 14 Oct 2019)
URL: https://git.bioconductor.org/packages/RefNet
Branch: RELEASE_3_9
Last Commit: 1e5ca4a
Last Changed Date: 2019-05-02 11:53:47 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RefNet
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RefNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RefNet_1.20.0.tar.gz
StartedAt: 2019-10-15 06:28:04 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 06:42:04 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 839.2 seconds
RetCode: 0
Status:  OK  
CheckDir: RefNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RefNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RefNet_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RefNet.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RefNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RefNet' 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 whether package 'RefNet' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* 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
RefNet-class    31.63   1.56   69.22
interactions    30.48   1.19   58.37
providerClasses 26.61   0.90   30.74
providers       23.61   1.30   27.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
RefNet-class    26.24   1.11   44.86
interactions    25.27   1.37   28.84
providerClasses 23.11   0.74   26.53
providers       20.36   0.67   23.21
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/RefNet.Rcheck/00check.log'
for details.

Installation output

RefNet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/RefNet_1.20.0.tar.gz && rm -rf RefNet.buildbin-libdir && mkdir RefNet.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RefNet.buildbin-libdir RefNet_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RefNet_1.20.0.zip && rm RefNet_1.20.0.tar.gz RefNet_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 92266  100 92266    0     0  1346k      0 --:--:-- --:--:-- --:--:-- 1477k

install for i386

* installing *source* package 'RefNet' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC' 
** help
*** installing help indices
  converting help for package 'RefNet'
    finding HTML links ... done
    RefNet-class                            html  
    detectDuplicateInteractions             html  
    interactions                            html  
    pickBestFromDupGroup                    html  
    providerClasses                         html  
    providers                               html  
    pubmedAbstract                          html  
** 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

install for x64

* installing *source* package 'RefNet' ...
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
* MD5 sums
packaged installation of 'RefNet' as RefNet_1.20.0.zip
* DONE (RefNet)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RefNet' successfully unpacked and MD5 sums checked

Tests output

RefNet.Rcheck/tests_i386/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.

> require(RefNet) || stop("unable to load RefNet package")
Loading required package: RefNet
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

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

Loading required package: S4Vectors
Loading required package: stats4

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

Loading required package: PSICQUIC
Loading required package: biomaRt
Loading required package: httr
Loading required package: plyr

Attaching package: 'plyr'

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

    desc

The following object is masked from 'package:S4Vectors':

    rename

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: RCurl
Loading required package: bitops
Loading required package: shiny
[1] TRUE
Warning message:
replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC' 
> BiocGenerics:::testPackage('RefNet')
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:AnnotationHub':

    cache

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

    content


[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
snapshotDate(): 2019-05-02
downloading 0 resources
loading from cache 
    'AH10364 : 10364'
downloading 0 resources
loading from cache 
    'AH10365 : 10365'
downloading 0 resources
loading from cache 
    'AH12810 : 12810'
downloading 0 resources
loading from cache 
    'AH12814 : 12814'
downloading 0 resources
loading from cache 
    'AH22338 : 27766'
downloading 0 resources
loading from cache 
    'AH22339 : 27767'
downloading 0 resources
loading from cache 
    'AH22340 : 27768'
downloading 0 resources
loading from cache 
    'AH22341 : 27769'
[1] RefNet ready.
checking for biomart access...
   does 'http://www.ensembl.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.combinations"
[1] "--- test_.filterOnColumnValue"
[1] "--- test_.findHits"
[1] "--- test_.smartRbind"
[1] "--- test_ctor"
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
snapshotDate(): 2019-05-02
downloading 0 resources
loading from cache 
    'AH10364 : 10364'
downloading 0 resources
loading from cache 
    'AH10365 : 10365'
downloading 0 resources
loading from cache 
    'AH12810 : 12810'
downloading 0 resources
loading from cache 
    'AH12814 : 12814'
downloading 0 resources
loading from cache 
    'AH22338 : 27766'
downloading 0 resources
loading from cache 
    'AH22339 : 27767'
downloading 0 resources
loading from cache 
    'AH22340 : 27768'
downloading 0 resources
loading from cache 
    'AH22341 : 27769'
[1] RefNet ready.
[1] "--- test_detectDuplicateInteractions"
[1] "--- test_interactions"
[1] "--- test_pickBestFromDupGroup"
[1] "--- test_providerMix_PSICQUIC_and_native"
[1] "--- test_pubmedAbstract"
[1] "--- test_recon2Interactions"


RUNIT TEST PROTOCOL -- Tue Oct 15 06:38:22 2019 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RefNet RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In is.na(psicquic) :
  is.na() applied to non-(list or vector) of type 'S4'
2: In is.na(refnet@psicquic) :
  is.na() applied to non-(list or vector) of type 'S4'
3: In is.na(refnet@psicquic) :
  is.na() applied to non-(list or vector) of type 'S4'
> 
> proc.time()
   user  system elapsed 
  54.10    3.04  154.92

RefNet.Rcheck/tests_x64/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.

> require(RefNet) || stop("unable to load RefNet package")
Loading required package: RefNet
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

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

Loading required package: S4Vectors
Loading required package: stats4

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

Loading required package: PSICQUIC
Loading required package: biomaRt
Loading required package: httr
Loading required package: plyr

Attaching package: 'plyr'

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

    desc

The following object is masked from 'package:S4Vectors':

    rename

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: RCurl
Loading required package: bitops
Loading required package: shiny
[1] TRUE
Warning message:
replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC' 
> BiocGenerics:::testPackage('RefNet')
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:AnnotationHub':

    cache

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

    content


[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
snapshotDate(): 2019-05-02
downloading 0 resources
loading from cache 
    'AH10364 : 10364'
downloading 0 resources
loading from cache 
    'AH10365 : 10365'
downloading 0 resources
loading from cache 
    'AH12810 : 12810'
downloading 0 resources
loading from cache 
    'AH12814 : 12814'
downloading 0 resources
loading from cache 
    'AH22338 : 27766'
downloading 0 resources
loading from cache 
    'AH22339 : 27767'
downloading 0 resources
loading from cache 
    'AH22340 : 27768'
downloading 0 resources
loading from cache 
    'AH22341 : 27769'
[1] RefNet ready.
checking for biomart access...
   does 'http://www.ensembl.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.combinations"
[1] "--- test_.filterOnColumnValue"
[1] "--- test_.findHits"
[1] "--- test_.smartRbind"
[1] "--- test_ctor"
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
snapshotDate(): 2019-05-02
downloading 0 resources
loading from cache 
    'AH10364 : 10364'
downloading 0 resources
loading from cache 
    'AH10365 : 10365'
downloading 0 resources
loading from cache 
    'AH12810 : 12810'
downloading 0 resources
loading from cache 
    'AH12814 : 12814'
downloading 0 resources
loading from cache 
    'AH22338 : 27766'
downloading 0 resources
loading from cache 
    'AH22339 : 27767'
downloading 0 resources
loading from cache 
    'AH22340 : 27768'
downloading 0 resources
loading from cache 
    'AH22341 : 27769'
[1] RefNet ready.
[1] "--- test_detectDuplicateInteractions"
[1] "--- test_interactions"
[1] "--- test_pickBestFromDupGroup"
[1] "--- test_providerMix_PSICQUIC_and_native"
[1] "--- test_pubmedAbstract"
[1] "--- test_recon2Interactions"


RUNIT TEST PROTOCOL -- Tue Oct 15 06:40:48 2019 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RefNet RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In is.na(psicquic) :
  is.na() applied to non-(list or vector) of type 'S4'
2: In is.na(refnet@psicquic) :
  is.na() applied to non-(list or vector) of type 'S4'
3: In is.na(refnet@psicquic) :
  is.na() applied to non-(list or vector) of type 'S4'
> 
> proc.time()
   user  system elapsed 
  54.78    2.35  145.34

Example timings

RefNet.Rcheck/examples_i386/RefNet-Ex.timings

nameusersystemelapsed
RefNet-class31.63 1.5669.22
detectDuplicateInteractions0.030.000.08
interactions30.48 1.1958.37
pickBestFromDupGroup0.020.000.06
providerClasses26.61 0.9030.74
providers23.61 1.3027.08
pubmedAbstract0.670.231.29

RefNet.Rcheck/examples_x64/RefNet-Ex.timings

nameusersystemelapsed
RefNet-class26.24 1.1144.86
detectDuplicateInteractions0.010.000.01
interactions25.27 1.3728.84
pickBestFromDupGroup0.010.000.02
providerClasses23.11 0.7426.53
providers20.36 0.6723.21
pubmedAbstract0.560.081.04