Back to Multiple platform build/check report for BioC 3.13 experimental data
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for MetaGxBreast on riesling1

This page was generated on 2021-01-14 15:59:09 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE MetaGxBreast PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 216/385HostnameOS / ArchINSTALLBUILDCHECK
MetaGxBreast 1.11.0
Michael Zon
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/MetaGxBreast
Branch: master
Last Commit: 51a013c
Last Changed Date: 2020-10-27 10:26:22 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: MetaGxBreast
Version: 1.11.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaGxBreast.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MetaGxBreast_1.11.0.tar.gz
StartedAt: 2021-01-14 11:27:16 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:33:12 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 356.1 seconds
RetCode: 0
Status:  OK  
CheckDir: MetaGxBreast.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaGxBreast.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MetaGxBreast_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/MetaGxBreast.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 'MetaGxBreast/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetaGxBreast' 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 'MetaGxBreast' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
loadBreastDatasets 66.75   5.74   97.02
loadBreastEsets    18.97   1.20   21.33
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
loadBreastDatasets 69.27   4.54   79.78
loadBreastEsets    17.90   1.32   20.39
* 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/MetaGxBreast.Rcheck/00check.log'
for details.



Installation output

MetaGxBreast.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/MetaGxBreast_1.11.0.tar.gz && rm -rf MetaGxBreast.buildbin-libdir && mkdir MetaGxBreast.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MetaGxBreast.buildbin-libdir MetaGxBreast_1.11.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MetaGxBreast_1.11.0.zip && rm MetaGxBreast_1.11.0.tar.gz MetaGxBreast_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
  3 35263    3  1219    0     0  10418      0  0:00:03 --:--:--  0:00:03 10330
100 35263  100 35263    0     0   291k      0 --:--:-- --:--:-- --:--:--  291k

install for i386

* installing *source* package 'MetaGxBreast' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MetaGxBreast'
    finding HTML links ... done
    CAL                                     html  
REDIRECT:topic	  CAL  -> CAL.html [ SUCCESS ]
REDIRECT:file	 CAL.html -> CAL.html [ SUCCESS ]
    DFHCC                                   html  
REDIRECT:topic	  DFHCC  -> DFHCC.html [ SUCCESS ]
REDIRECT:file	 DFHCC.html -> DFHCC.html [ SUCCESS ]
    DFHCC2                                  html  
REDIRECT:topic	  DFHCC2  -> DFHCC2.html [ SUCCESS ]
REDIRECT:file	 DFHCC2.html -> DFHCC2.html [ SUCCESS ]
    DFHCC3                                  html  
REDIRECT:topic	  DFHCC3  -> DFHCC3.html [ SUCCESS ]
REDIRECT:file	 DFHCC3.html -> DFHCC3.html [ SUCCESS ]
    DUKE                                    html  
REDIRECT:topic	  DUKE  -> DUKE.html [ SUCCESS ]
REDIRECT:file	 DUKE.html -> DUKE.html [ SUCCESS ]
    DUKE2                                   html  
REDIRECT:topic	  DUKE2  -> DUKE2.html [ SUCCESS ]
REDIRECT:file	 DUKE2.html -> DUKE2.html [ SUCCESS ]
    EMC2                                    html  
REDIRECT:topic	  EMC2  -> EMC2.html [ SUCCESS ]
REDIRECT:file	 EMC2.html -> EMC2.html [ SUCCESS ]
    EORTC10994                              html  
REDIRECT:topic	  EORTC10994  -> EORTC10994.html [ SUCCESS ]
REDIRECT:file	 EORTC10994.html -> EORTC10994.html [ SUCCESS ]
    EXPO                                    html  
REDIRECT:topic	  EXPO  -> EXPO.html [ SUCCESS ]
REDIRECT:file	 EXPO.html -> EXPO.html [ SUCCESS ]
    FNCLCC                                  html  
REDIRECT:topic	  FNCLCC  -> FNCLCC.html [ SUCCESS ]
REDIRECT:file	 FNCLCC.html -> FNCLCC.html [ SUCCESS ]
    GSE25066                                html  
REDIRECT:topic	  GSE25066  -> GSE25066.html [ SUCCESS ]
REDIRECT:file	 GSE25066.html -> GSE25066.html [ SUCCESS ]
    GSE32646                                html  
REDIRECT:topic	  GSE32646  -> GSE32646.html [ SUCCESS ]
REDIRECT:file	 GSE32646.html -> GSE32646.html [ SUCCESS ]
    GSE48091                                html  
REDIRECT:topic	  GSE48091  -> GSE48091.html [ SUCCESS ]
REDIRECT:file	 GSE48091.html -> GSE48091.html [ SUCCESS ]
    GSE58644                                html  
REDIRECT:topic	  GSE58644  -> GSE58644.html [ SUCCESS ]
REDIRECT:file	 GSE58644.html -> GSE58644.html [ SUCCESS ]
    HLP                                     html  
REDIRECT:topic	  HLP  -> HLP.html [ SUCCESS ]
REDIRECT:file	 HLP.html -> HLP.html [ SUCCESS ]
    IRB                                     html  
REDIRECT:topic	  IRB  -> IRB.html [ SUCCESS ]
REDIRECT:file	 IRB.html -> IRB.html [ SUCCESS ]
    KOO                                     html  
REDIRECT:topic	  KOO  -> KOO.html [ SUCCESS ]
REDIRECT:file	 KOO.html -> KOO.html [ SUCCESS ]
    LUND                                    html  
REDIRECT:topic	  LUND  -> LUND.html [ SUCCESS ]
REDIRECT:file	 LUND.html -> LUND.html [ SUCCESS ]
    LUND2                                   html  
REDIRECT:topic	  LUND2  -> LUND2.html [ SUCCESS ]
REDIRECT:file	 LUND2.html -> LUND2.html [ SUCCESS ]
    MAINZ                                   html  
REDIRECT:topic	  MAINZ  -> MAINZ.html [ SUCCESS ]
REDIRECT:file	 MAINZ.html -> MAINZ.html [ SUCCESS ]
    MAQC2                                   html  
REDIRECT:topic	  MAQC2  -> MAQC2.html [ SUCCESS ]
REDIRECT:file	 MAQC2.html -> MAQC2.html [ SUCCESS ]
    MCCC                                    html  
REDIRECT:topic	  MCCC  -> MCCC.html [ SUCCESS ]
REDIRECT:file	 MCCC.html -> MCCC.html [ SUCCESS ]
    MDA4                                    html  
REDIRECT:topic	  MDA4  -> MDA4.html [ SUCCESS ]
REDIRECT:file	 MDA4.html -> MDA4.html [ SUCCESS ]
    METABRIC                                html  
REDIRECT:topic	  METABRIC  -> METABRIC.html [ SUCCESS ]
REDIRECT:file	 METABRIC.html -> METABRIC.html [ SUCCESS ]
    MSK                                     html  
REDIRECT:topic	  MSK  -> MSK.html [ SUCCESS ]
REDIRECT:file	 MSK.html -> MSK.html [ SUCCESS ]
    MUG                                     html  
REDIRECT:topic	  MUG  -> MUG.html [ SUCCESS ]
REDIRECT:file	 MUG.html -> MUG.html [ SUCCESS ]
    NCCS                                    html  
REDIRECT:topic	  NCCS  -> NCCS.html [ SUCCESS ]
REDIRECT:file	 NCCS.html -> NCCS.html [ SUCCESS ]
    NCI                                     html  
REDIRECT:topic	  NCI  -> NCI.html [ SUCCESS ]
REDIRECT:file	 NCI.html -> NCI.html [ SUCCESS ]
    NKI                                     html  
REDIRECT:topic	  NKI  -> NKI.html [ SUCCESS ]
REDIRECT:file	 NKI.html -> NKI.html [ SUCCESS ]
    PNC                                     html  
REDIRECT:topic	  PNC  -> PNC.html [ SUCCESS ]
REDIRECT:file	 PNC.html -> PNC.html [ SUCCESS ]
    STK                                     html  
REDIRECT:topic	  STK  -> STK.html [ SUCCESS ]
REDIRECT:file	 STK.html -> STK.html [ SUCCESS ]
    STNO2                                   html  
REDIRECT:topic	  STNO2  -> STNO2.html [ SUCCESS ]
REDIRECT:file	 STNO2.html -> STNO2.html [ SUCCESS ]
    TCGA                                    html  
REDIRECT:topic	  TCGA  -> TCGA.html [ SUCCESS ]
REDIRECT:file	 TCGA.html -> TCGA.html [ SUCCESS ]
    TRANSBIG                                html  
REDIRECT:topic	  TRANSBIG  -> TRANSBIG.html [ SUCCESS ]
REDIRECT:file	 TRANSBIG.html -> TRANSBIG.html [ SUCCESS ]
    UCSF                                    html  
REDIRECT:topic	  UCSF  -> UCSF.html [ SUCCESS ]
REDIRECT:file	 UCSF.html -> UCSF.html [ SUCCESS ]
    UNC4                                    html  
REDIRECT:topic	  UNC4  -> UNC4.html [ SUCCESS ]
REDIRECT:file	 UNC4.html -> UNC4.html [ SUCCESS ]
    UNT                                     html  
REDIRECT:topic	  UNT  -> UNT.html [ SUCCESS ]
REDIRECT:file	 UNT.html -> UNT.html [ SUCCESS ]
    UPP                                     html  
REDIRECT:topic	  UPP  -> UPP.html [ SUCCESS ]
REDIRECT:file	 UPP.html -> UPP.html [ SUCCESS ]
    VDX                                     html  
REDIRECT:topic	  VDX  -> VDX.html [ SUCCESS ]
REDIRECT:file	 VDX.html -> VDX.html [ SUCCESS ]
    duplicates                              html  
REDIRECT:topic	 dupplicates -> duplicates.html [ SUCCESS ]
REDIRECT:file	 duplicates.html -> duplicates.html [ SUCCESS ]
    loadBreastDatasets                      html  
REDIRECT:topic	 loadBreastDatasets -> loadBreastDatasets.html [ SUCCESS ]
    loadBreastEsets                         html  
REDIRECT:topic	 loadBreastEsets -> loadBreastEsets.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 'MetaGxBreast' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MetaGxBreast' as MetaGxBreast_1.11.0.zip
* DONE (MetaGxBreast)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'MetaGxBreast' successfully unpacked and MD5 sums checked

Tests output

MetaGxBreast.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 
   0.07    0.04    0.12 

MetaGxBreast.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 
   0.04    0.06    0.10 

Example timings

MetaGxBreast.Rcheck/examples_i386/MetaGxBreast-Ex.timings

nameusersystemelapsed
loadBreastDatasets66.75 5.7497.02
loadBreastEsets18.97 1.2021.33

MetaGxBreast.Rcheck/examples_x64/MetaGxBreast-Ex.timings

nameusersystemelapsed
loadBreastDatasets69.27 4.5479.78
loadBreastEsets17.90 1.3220.39