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CHECK report for ExpressionAtlas on tokay2

This page was generated on 2019-04-09 12:25:44 -0400 (Tue, 09 Apr 2019).

Package 522/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ExpressionAtlas 1.11.0
Suhaib Mohammed
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/ExpressionAtlas
Branch: master
Last Commit: e6ed08d
Last Changed Date: 2018-10-30 11:54:35 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: ExpressionAtlas
Version: 1.11.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ExpressionAtlas.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ExpressionAtlas_1.11.0.tar.gz
StartedAt: 2019-04-09 02:39:38 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:43:26 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 228.4 seconds
RetCode: 1
Status:  ERROR  
CheckDir: ExpressionAtlas.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ExpressionAtlas.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ExpressionAtlas_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ExpressionAtlas.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ExpressionAtlas/DESCRIPTION' ... OK
* this is package 'ExpressionAtlas' version '1.11.0'
* 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 'ExpressionAtlas' 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
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'ExpressionAtlas-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name:  searchAtlasExperiments 
> ### Title: Search for Expression Atlas experiments
> ### Aliases: ' searchAtlasExperiments '
> 
> ### ** Examples
> 
>     
>     # Search for experiments on salt in rice.
>     atlasRes <- searchAtlasExperiments( "salt", "Oryza sativa" )
Searching for Expression Atlas experiments matching your query ...
Query successful.
No results found. Cannot continue.
> 
>     # Download data for all experiments found.
>     atlasData <- getAtlasData( atlasRes$Accession )
Error in getAtlasData(atlasRes$Accession) : 
  Please provide experiment accessions as a vector.
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'ExpressionAtlas-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name:  searchAtlasExperiments 
> ### Title: Search for Expression Atlas experiments
> ### Aliases: ' searchAtlasExperiments '
> 
> ### ** Examples
> 
>     
>     # Search for experiments on salt in rice.
>     atlasRes <- searchAtlasExperiments( "salt", "Oryza sativa" )
Searching for Expression Atlas experiments matching your query ...
Query successful.
No results found. Cannot continue.
> 
>     # Download data for all experiments found.
>     atlasData <- getAtlasData( atlasRes$Accession )
Error in getAtlasData(atlasRes$Accession) : 
  Please provide experiment accessions as a vector.
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: 2 ERRORs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/ExpressionAtlas.Rcheck/00check.log'
for details.

Installation output

ExpressionAtlas.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ExpressionAtlas_1.11.0.tar.gz && rm -rf ExpressionAtlas.buildbin-libdir && mkdir ExpressionAtlas.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ExpressionAtlas.buildbin-libdir ExpressionAtlas_1.11.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ExpressionAtlas_1.11.0.zip && rm ExpressionAtlas_1.11.0.tar.gz ExpressionAtlas_1.11.0.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  115k  100  115k    0     0  1762k      0 --:--:-- --:--:-- --:--:-- 1958k

install for i386

* installing *source* package 'ExpressionAtlas' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ExpressionAtlas'
    finding HTML links ... done
    allExps                                 html  
    atlasRes                                html  
    getAtlasData                            html  
    getAtlasExperiment                      html  
    rnaseqExps                              html  
    searchAtlasExperiments                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ExpressionAtlas' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ExpressionAtlas' as ExpressionAtlas_1.11.0.zip
* DONE (ExpressionAtlas)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ExpressionAtlas' successfully unpacked and MD5 sums checked

Tests output

ExpressionAtlas.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.

> library(testthat)
> library(ExpressionAtlas)
Loading required package: Biobase
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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: xml2
> 
> test_check("ExpressionAtlas")
== testthat results  ===========================================================
OK: 5 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   6.64    0.71    7.32

ExpressionAtlas.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.

> library(testthat)
> library(ExpressionAtlas)
Loading required package: Biobase
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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: xml2
> 
> test_check("ExpressionAtlas")
== testthat results  ===========================================================
OK: 5 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.79    0.39    8.17

Example timings

ExpressionAtlas.Rcheck/examples_i386/ExpressionAtlas-Ex.timings

nameusersystemelapsed
getAtlasData0.680.036.50
getAtlasExperiment0.270.003.28

ExpressionAtlas.Rcheck/examples_x64/ExpressionAtlas-Ex.timings

nameusersystemelapsed
getAtlasData0.580.105.55
getAtlasExperiment0.230.061.86