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CHECK report for MetaGxOvarian on riesling1

This page was generated on 2021-01-18 15:58:48 -0500 (Mon, 18 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE MetaGxOvarian PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 217/385HostnameOS / ArchINSTALLBUILDCHECK
MetaGxOvarian 1.11.0
Michael Zon
Snapshot Date: 2021-01-18 09:00:15 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/MetaGxOvarian
Branch: master
Last Commit: 0f765b3
Last Changed Date: 2020-10-27 10:26:19 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: MetaGxOvarian
Version: 1.11.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaGxOvarian.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MetaGxOvarian_1.11.0.tar.gz
StartedAt: 2021-01-18 11:31:12 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 11:38:21 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 428.7 seconds
RetCode: 0
Status:  OK  
CheckDir: MetaGxOvarian.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaGxOvarian.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MetaGxOvarian_1.11.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/MetaGxOvarian.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MetaGxOvarian/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetaGxOvarian' version '1.11.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Biobase', 'lattice', 'impute', 'AnnotationHub', 'ExperimentHub',
  'SummarizedExperiment'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'MetaGxOvarian' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    html   6.9Mb
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
loadOvarianEsets    45.96   2.87   52.68
loadOvarianDatasets 41.65   3.04   57.31
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
loadOvarianEsets    45.92   3.08   52.78
loadOvarianDatasets 41.92   2.67   48.92
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'required.R'
 OK
** running tests for arch 'x64' ...
  Running 'required.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
  'D:/biocbuild/bbs-3.13-data-experiment/meat/MetaGxOvarian.Rcheck/00check.log'
for details.



Installation output

MetaGxOvarian.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/MetaGxOvarian_1.11.0.tar.gz && rm -rf MetaGxOvarian.buildbin-libdir && mkdir MetaGxOvarian.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MetaGxOvarian.buildbin-libdir MetaGxOvarian_1.11.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MetaGxOvarian_1.11.0.zip && rm MetaGxOvarian_1.11.0.tar.gz MetaGxOvarian_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  240k  100  240k    0     0  3820k      0 --:--:-- --:--:-- --:--:-- 3820k

install for i386

* installing *source* package 'MetaGxOvarian' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MetaGxOvarian'
    finding HTML links ... done
    E.MTAB.386                              html  
REDIRECT:topic	  E.MTAB.386  -> E.MTAB.386.html [ SUCCESS ]
REDIRECT:file	 E.MTAB.386.html -> E.MTAB.386.html [ SUCCESS ]
    GSE12418                                html  
REDIRECT:topic	  GSE12418  -> GSE12418.html [ SUCCESS ]
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REDIRECT:topic	  PMID15897565  -> PMID15897565.html [ SUCCESS ]
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REDIRECT:topic	  PMID19318476  -> PMID19318476.html [ SUCCESS ]
REDIRECT:file	 PMID19318476.html -> PMID19318476.html [ SUCCESS ]
    TCGA.RNASeqV2                           html  
REDIRECT:topic	  TCGA.RNASeqV2  -> TCGA.RNASeqV2.html [ SUCCESS ]
REDIRECT:file	 TCGA.RNASeqV2.html -> TCGA.RNASeqV2.html [ SUCCESS ]
    TCGAOVARIAN                             html  
REDIRECT:topic	  TCGAOVARIAN  -> TCGAOVARIAN.html [ SUCCESS ]
REDIRECT:file	 TCGAOVARIAN.html -> TCGAOVARIAN.html [ SUCCESS ]
    attention                               html  
REDIRECT:topic	 attention -> attention.html [ SUCCESS ]
    duplicates                              html  
REDIRECT:topic	 duplicates -> duplicates.html [ SUCCESS ]
    loadOvarianDatasets                     html  
REDIRECT:topic	 loadOvarianDatasets -> loadOvarianDatasets.html [ SUCCESS ]
    loadOvarianEsets                        html  
REDIRECT:topic	 loadOvarianEsets -> loadOvarianEsets.html [ SUCCESS ]
** 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 'MetaGxOvarian' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MetaGxOvarian' as MetaGxOvarian_1.11.0.zip
* DONE (MetaGxOvarian)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'MetaGxOvarian' successfully unpacked and MD5 sums checked

Tests output

MetaGxOvarian.Rcheck/tests_i386/required.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 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.

> #
> 
> proc.time()
   user  system elapsed 
   0.10    0.01    0.10 

MetaGxOvarian.Rcheck/tests_x64/required.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 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.

> #
> 
> proc.time()
   user  system elapsed 
   0.12    0.01    0.10 

Example timings

MetaGxOvarian.Rcheck/examples_i386/MetaGxOvarian-Ex.timings

nameusersystemelapsed
loadOvarianDatasets41.65 3.0457.31
loadOvarianEsets45.96 2.8752.68

MetaGxOvarian.Rcheck/examples_x64/MetaGxOvarian-Ex.timings

nameusersystemelapsed
loadOvarianDatasets41.92 2.6748.92
loadOvarianEsets45.92 3.0852.78