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CHECK report for restfulSE on tokay2

This page was generated on 2019-10-16 12:39:29 -0400 (Wed, 16 Oct 2019).

Package 1359/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
restfulSE 1.6.1
Shweta Gopaulakrishnan
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/restfulSE
Branch: RELEASE_3_9
Last Commit: 0d26e30
Last Changed Date: 2019-08-19 15:46:28 -0400 (Mon, 19 Aug 2019)
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 

Summary

Package: restfulSE
Version: 1.6.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:restfulSE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings restfulSE_1.6.1.tar.gz
StartedAt: 2019-10-16 06:27:29 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:45:00 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 1050.5 seconds
RetCode: 1
Status:  ERROR  
CheckDir: restfulSE.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:restfulSE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings restfulSE_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/restfulSE.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 'restfulSE/DESCRIPTION' ... OK
* this is package 'restfulSE' version '1.6.1'
* package encoding: UTF-8
* 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 'restfulSE' 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 ... NOTE
BQ3_Source: no visible binding for global variable
  'SampleTypeLetterCode'
BQ3m2: no visible binding for global variable 'SampleTypeLetterCode'
Undefined global functions or variables:
  SampleTypeLetterCode
* 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' ... ERROR
Running examples in 'restfulSE-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RESTfulSummarizedExperiment
> ### Title: Construct RESTfulSummarizedExperiment
> ### Aliases: RESTfulSummarizedExperiment
> ###   RESTfulSummarizedExperiment,RangedSummarizedExperiment,H5S_dataset-method
> ###   .RESTfulSummarizedExperiment assay
> ###   assay,RESTfulSummarizedExperiment,missing-method
> 
> ### ** Examples
> 
> require("rhdf5client")
Loading required package: rhdf5client
> hsds = H5S_source(serverURL=URL_hsds())
Error in transl(target) : 
  error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
Calls: H5S_source -> hsdsInfo -> hsdsInfo -> transl
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'restfulSE-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RESTfulSummarizedExperiment
> ### Title: Construct RESTfulSummarizedExperiment
> ### Aliases: RESTfulSummarizedExperiment
> ###   RESTfulSummarizedExperiment,RangedSummarizedExperiment,H5S_dataset-method
> ###   .RESTfulSummarizedExperiment assay
> ###   assay,RESTfulSummarizedExperiment,missing-method
> 
> ### ** Examples
> 
> require("rhdf5client")
Loading required package: rhdf5client
> hsds = H5S_source(serverURL=URL_hsds())
Error in transl(target) : 
  error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
Calls: H5S_source -> hsdsInfo -> hsdsInfo -> transl
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
  1: H5S_source(URL_hsds()) at testthat/test_reSE.R:121
  2: hsdsInfo(tmp)
  3: hsdsInfo(tmp)
  4: transl(target)
  5: stop(paste("error: can't read JSON ", targ, sep = ""))
  
  == testthat results  ===========================================================
  [ OK: 3 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: H5S_source completes (@test_reSE.R#9) 
  2. Error: RESTfulSummarizedExperiment infrastructure works against server (@test_reSE.R#51) 
  3. Error: dim compatibility check is sensitive (@test_reSE.R#121) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
  1: H5S_source(URL_hsds()) at testthat/test_reSE.R:121
  2: hsdsInfo(tmp)
  3: hsdsInfo(tmp)
  4: transl(target)
  5: stop(paste("error: can't read JSON ", targ, sep = ""))
  
  == testthat results  ===========================================================
  [ OK: 3 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: H5S_source completes (@test_reSE.R#9) 
  2. Error: RESTfulSummarizedExperiment infrastructure works against server (@test_reSE.R#51) 
  3. Error: dim compatibility check is sensitive (@test_reSE.R#121) 
  
  Error: testthat unit tests failed
  Execution halted
* 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: 4 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/restfulSE.Rcheck/00check.log'
for details.


Installation output

restfulSE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/restfulSE_1.6.1.tar.gz && rm -rf restfulSE.buildbin-libdir && mkdir restfulSE.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=restfulSE.buildbin-libdir restfulSE_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL restfulSE_1.6.1.zip && rm restfulSE_1.6.1.tar.gz restfulSE_1.6.1.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  253k  100  253k    0     0  4079k      0 --:--:-- --:--:-- --:--:-- 4525k

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'restfulSE' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'restfulSE'
    finding HTML links ... done
    BQ3_Array-class                         html  
    BQ3_Array                               html  
    BQ3_ArraySeed-class                     html  
    BQ3_Matrix-class                        html  
    BQ3_Source-class                        html  
    BQ3_Source                              html  
    BQM_Array-class                         html  
    BQM_Array                               html  
    BQM_ArraySeed-class                     html  
    BQM_Matrix-class                        html  
    BQM_Source-class                        html  
    BQM_Source                              html  
    BQSummarizedExperiment                  html  
    RESTfulSummarizedExperiment-class       html  
    RESTfulSummarizedExperiment             html  
    assay-BQSummarizedExperiment-missing-method
                                            html  
    assayNames-BQSummarizedExperiment-method
                                            html  
    assays-RESTfulSummarizedExperiment-method
                                            html  
    basic_clinvars                          html  
    bqConn                                  html  
    cgcConn                                 html  
    dim-BQ3_ArraySeed-method                html  
    dim-BQM_ArraySeed-method                html  
    dim-RESTfulSummarizedExperiment-method
                                            html  
    dimnames-BQ3_ArraySeed-method           html  
    dimnames-BQM_ArraySeed-method           html  
    goPatt                                  html  
    gtexTiss                                html  
    isbCgcDatasets                          html  
    isbCgcTables                            html  
    pancan_SE                               html  
    se100k                                  html  
    seByTumor                               html  
    seByTumor_2016                          html  
    tasicCortex                             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

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'restfulSE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'restfulSE' as restfulSE_1.6.1.zip
* DONE (restfulSE)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'restfulSE' successfully unpacked and MD5 sums checked

Tests output

restfulSE.Rcheck/tests_i386/testthat.Rout.fail


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.

> library(testthat)
> library(restfulSE)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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

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: Biobase
Welcome to Bioconductor

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

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


> library(rhdf5client)
> 
> test_check("restfulSE")
-- 1. Error: H5S_source completes (@test_reSE.R#9)  ----------------------------
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:9
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))

-- 2. Error: RESTfulSummarizedExperiment infrastructure works against server (@t
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:51
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))

-- 3. Error: dim compatibility check is sensitive (@test_reSE.R#121)  ----------
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:121
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))

== testthat results  ===========================================================
[ OK: 3 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
1. Error: H5S_source completes (@test_reSE.R#9) 
2. Error: RESTfulSummarizedExperiment infrastructure works against server (@test_reSE.R#51) 
3. Error: dim compatibility check is sensitive (@test_reSE.R#121) 

Error: testthat unit tests failed
Execution halted

restfulSE.Rcheck/tests_x64/testthat.Rout.fail


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.

> library(testthat)
> library(restfulSE)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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

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: Biobase
Welcome to Bioconductor

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

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


> library(rhdf5client)
> 
> test_check("restfulSE")
-- 1. Error: H5S_source completes (@test_reSE.R#9)  ----------------------------
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:9
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))

-- 2. Error: RESTfulSummarizedExperiment infrastructure works against server (@t
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:51
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))

-- 3. Error: dim compatibility check is sensitive (@test_reSE.R#121)  ----------
error: can't read JSON http://hsdshdflab.hdfgroup.org/domains
1: H5S_source(URL_hsds()) at testthat/test_reSE.R:121
2: hsdsInfo(tmp)
3: hsdsInfo(tmp)
4: transl(target)
5: stop(paste("error: can't read JSON ", targ, sep = ""))

== testthat results  ===========================================================
[ OK: 3 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
1. Error: H5S_source completes (@test_reSE.R#9) 
2. Error: RESTfulSummarizedExperiment infrastructure works against server (@test_reSE.R#51) 
3. Error: dim compatibility check is sensitive (@test_reSE.R#121) 

Error: testthat unit tests failed
Execution halted

Example timings

restfulSE.Rcheck/examples_i386/restfulSE-Ex.timings

nameusersystemelapsed
BQ3_Array000
BQ3_Source000
BQM_Array000
BQM_Source000

restfulSE.Rcheck/examples_x64/restfulSE-Ex.timings

nameusersystemelapsed
BQ3_Array000
BQ3_Source000
BQM_Array000
BQM_Source000