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CHECK report for pcaExplorer on tokay2

This page was generated on 2018-10-17 08:42:08 -0400 (Wed, 17 Oct 2018).

Package 1069/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pcaExplorer 2.6.0
Federico Marini
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/pcaExplorer
Branch: RELEASE_3_7
Last Commit: 21cd327
Last Changed Date: 2018-04-30 10:35:41 -0400 (Mon, 30 Apr 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: pcaExplorer
Version: 2.6.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings pcaExplorer_2.6.0.tar.gz
StartedAt: 2018-10-17 03:52:51 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:02:08 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 557.3 seconds
RetCode: 0
Status:  OK  
CheckDir: pcaExplorer.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:pcaExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings pcaExplorer_2.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/pcaExplorer.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 'pcaExplorer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pcaExplorer' version '2.6.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'pcaExplorer' 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
pcaExplorer: no visible binding for '<<-' assignment to
  'pcaexplorer_env'
pcaExplorer : <anonymous>: no visible binding for global variable
  'airway'
pcaExplorer : <anonymous>: no visible binding for global variable
  'pcaexplorer_env'
Undefined global functions or variables:
  airway pcaexplorer_env
* 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
** running examples for arch 'x64' ... OK
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/pcaExplorer.Rcheck/00check.log'
for details.



Installation output

pcaExplorer.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/pcaExplorer_2.6.0.tar.gz && rm -rf pcaExplorer.buildbin-libdir && mkdir pcaExplorer.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pcaExplorer.buildbin-libdir pcaExplorer_2.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL pcaExplorer_2.6.0.zip && rm pcaExplorer_2.6.0.tar.gz pcaExplorer_2.6.0.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 2694k  100 2694k    0     0  34.3M      0 --:--:-- --:--:-- --:--:-- 37.5M

install for i386

* installing *source* package 'pcaExplorer' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pcaExplorer'
    finding HTML links ... done
    correlatePCs                            html  
    distro_expr                             html  
    finding level-2 HTML links ... done

    geneprofiler                            html  
    genespca                                html  
    get_annotation                          html  
    get_annotation_orgdb                    html  
    hi_loadings                             html  
    limmaquickpca2go                        html  
    makeExampleDESeqDataSet_multifac        html  
    pair_corr                               html  
    pca2go                                  html  
    pcaExplorer                             html  
    pcaplot                                 html  
    pcaplot3d                               html  
    pcascree                                html  
    plotPCcorrs                             html  
    topGOtable                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'pcaExplorer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pcaExplorer' as pcaExplorer_2.6.0.zip
* DONE (pcaExplorer)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'pcaExplorer' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

pcaExplorer.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(pcaExplorer)

> 
> test_check("pcaExplorer")
== testthat results  ===========================================================
OK: 18 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  86.57    3.26   89.86 

pcaExplorer.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(pcaExplorer)

> 
> test_check("pcaExplorer")
== testthat results  ===========================================================
OK: 18 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  77.59    1.56   79.17 

Example timings

pcaExplorer.Rcheck/examples_i386/pcaExplorer-Ex.timings

nameusersystemelapsed
correlatePCs3.670.093.76
distro_expr3.550.073.61
geneprofiler2.510.012.53
genespca3.810.033.84
get_annotation3.580.083.66
get_annotation_orgdb2.580.062.64
hi_loadings3.450.083.54
limmaquickpca2go2.060.102.15
makeExampleDESeqDataSet_multifac0.20.00.2
pair_corr2.620.072.70
pca2go2.840.042.87
pcaExplorer2.030.062.09
pcaplot3.160.233.39
pcaplot3d2.650.034.08
pcascree3.030.023.05
plotPCcorrs3.080.033.11
topGOtable2.190.112.30

pcaExplorer.Rcheck/examples_x64/pcaExplorer-Ex.timings

nameusersystemelapsed
correlatePCs4.650.014.67
distro_expr3.220.033.25
geneprofiler2.220.002.22
genespca4.380.024.39
get_annotation3.700.083.78
get_annotation_orgdb3.280.053.33
hi_loadings2.480.002.48
limmaquickpca2go1.720.091.82
makeExampleDESeqDataSet_multifac0.310.000.31
pair_corr2.000.082.08
pca2go1.800.031.83
pcaExplorer1.800.071.86
pcaplot3.150.013.17
pcaplot3d2.080.022.22
pcascree2.620.002.62
plotPCcorrs2.580.032.61
topGOtable2.330.032.36