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CHECK report for restfulSE on tokay2

This page was generated on 2018-10-17 08:44:38 -0400 (Wed, 17 Oct 2018).

Package 1224/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
restfulSE 1.2.3
Shweta Gopaulakrishnan
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/restfulSE
Branch: RELEASE_3_7
Last Commit: 55e4a84
Last Changed Date: 2018-09-27 15:56:20 -0400 (Thu, 27 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: restfulSE
Version: 1.2.3
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:restfulSE.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings restfulSE_1.2.3.tar.gz
StartedAt: 2018-10-17 04:21:58 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:27:48 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 349.7 seconds
RetCode: 0
Status:  OK  
CheckDir: restfulSE.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:restfulSE.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings restfulSE_1.2.3.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/restfulSE.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.2.3'
* 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'
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' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
RESTfulSummarizedExperiment 8.76   1.51   11.54
se100k                      3.12   0.29    5.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
RESTfulSummarizedExperiment 8.75   0.94   11.11
se100k                      3.17   0.08    5.93
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-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/3.7/bioc/src/contrib/restfulSE_1.2.3.tar.gz && rm -rf restfulSE.buildbin-libdir && mkdir restfulSE.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=restfulSE.buildbin-libdir restfulSE_1.2.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL restfulSE_1.2.3.zip && rm restfulSE_1.2.3.tar.gz restfulSE_1.2.3.zip
###
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  % 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  598k  100  598k    0     0  9683k      0 --:--:-- --:--:-- --:--:-- 10.6M

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'restfulSE' ...
** 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  
    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
In R CMD INSTALL

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_1.2.3.zip
* DONE (restfulSE)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'restfulSE' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

restfulSE.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, 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

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


> library(rhdf5client)
> 
> test_check("restfulSE")
== testthat results  ===========================================================
OK: 19 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  27.79    2.20   40.18 

restfulSE.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, 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

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


> library(rhdf5client)
> 
> test_check("restfulSE")
== testthat results  ===========================================================
OK: 19 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  26.67    1.46   36.23 

Example timings

restfulSE.Rcheck/examples_i386/restfulSE-Ex.timings

nameusersystemelapsed
BQ3_Array000
BQ3_Source000
BQM_Array000
BQM_Source000
RESTfulSummarizedExperiment 8.76 1.5111.54
bqConn000
cgcConn0.020.000.02
goPatt1.540.111.66
gtexTiss1.390.102.59
isbCgcDatasets000
isbCgcTables000
pancan_SE000
se100k3.120.295.61
seByTumor000
tasicCortex000

restfulSE.Rcheck/examples_x64/restfulSE-Ex.timings

nameusersystemelapsed
BQ3_Array000
BQ3_Source000
BQM_Array000
BQM_Source000
RESTfulSummarizedExperiment 8.75 0.9411.11
bqConn000
cgcConn000
goPatt1.580.091.67
gtexTiss1.170.082.25
isbCgcDatasets000
isbCgcTables000
pancan_SE000
se100k3.170.085.93
seByTumor0.020.000.02
tasicCortex000