Back to Multiple platform build/check report for BioC 3.13 experimental data
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

CHECK report for TCGAWorkflowData on riesling1

This page was generated on 2021-01-14 15:59:12 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE TCGAWorkflowData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 360/385HostnameOS / ArchINSTALLBUILDCHECK
TCGAWorkflowData 1.15.0
Tiago Chedraoui Silva
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/TCGAWorkflowData
Branch: master
Last Commit: c1b3065
Last Changed Date: 2020-10-27 10:22:55 -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 [ WARNINGS ]

Summary

Package: TCGAWorkflowData
Version: 1.15.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAWorkflowData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TCGAWorkflowData_1.15.0.tar.gz
StartedAt: 2021-01-14 11:44:56 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:52:25 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 448.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: TCGAWorkflowData.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAWorkflowData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TCGAWorkflowData_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/TCGAWorkflowData.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 'TCGAWorkflowData/DESCRIPTION' ... OK
* this is package 'TCGAWorkflowData' version '1.15.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'TCGAWorkflowData' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 77.5Mb
  sub-directories of 1Mb or more:
    data  77.3Mb
* 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 ... WARNING
Undocumented data sets:
  'commonCNV'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
TCGAWorkflowData 31.34   0.25   31.60
tmp.biogrid      11.52   0.04   11.56
GBMmut           10.72   0.07   10.78
LGGmut            9.44   0.09    9.54
mut               9.33   0.08    9.41
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
TCGAWorkflowData 26.14   0.38   26.52
GBMmut            9.97   0.08   10.04
tmp.biogrid       8.70   0.05    8.75
LGGmut            8.03   0.06    8.09
mut               7.88   0.14    8.02
* 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 WARNING, 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/TCGAWorkflowData.Rcheck/00check.log'
for details.



Installation output

TCGAWorkflowData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/TCGAWorkflowData_1.15.0.tar.gz && rm -rf TCGAWorkflowData.buildbin-libdir && mkdir TCGAWorkflowData.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAWorkflowData.buildbin-libdir TCGAWorkflowData_1.15.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TCGAWorkflowData_1.15.0.zip && rm TCGAWorkflowData_1.15.0.tar.gz TCGAWorkflowData_1.15.0.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 77.3M  100 77.3M    0     0   110M      0 --:--:-- --:--:-- --:--:--  110M

install for i386

* installing *source* package 'TCGAWorkflowData' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TCGAWorkflowData'
    finding HTML links ... done
    GBMmut                                  html  
REDIRECT:topic	 GBMmut -> GBMmut.html [ SUCCESS ]
    LGGmut                                  html  
REDIRECT:topic	 LGGmut -> LGGmut.html [ SUCCESS ]
    TCGAWorkflowData                        html  
REDIRECT:topic	 TCGAWorkflowData -> TCGAWorkflowData.html [ SUCCESS ]
REDIRECT:topic	 TCGAWorkflowData-package -> TCGAWorkflowData.html [ SUCCESS ]
    cnvMatrix                               html  
REDIRECT:topic	 cnvMatrix -> cnvMatrix.html [ SUCCESS ]
    exp                                     html  
REDIRECT:topic	 exp -> exp.html [ SUCCESS ]
    exp.elmer                               html  
REDIRECT:topic	 exp.elmer -> exp.elmer.html [ SUCCESS ]
    gbm.exp                                 html  
REDIRECT:topic	 gbm.exp -> gbm.exp.html [ SUCCESS ]
    gbm.samples                             html  
REDIRECT:topic	 gbm.samples -> gbm.samples.html [ SUCCESS ]
    genes                                   html  
REDIRECT:topic	 genes -> genes.html [ SUCCESS ]
    genes_GR                                html  
REDIRECT:topic	 genes_GR -> genes_GR.html [ SUCCESS ]
    gistic.allbygene                        html  
REDIRECT:topic	 gistic.allbygene -> gistic.allbygene.html [ SUCCESS ]
    gistic.thresholedbygene                 html  
REDIRECT:topic	 gistic.thresholedbygene -> gistic.thresholedbygene.html [ SUCCESS ]
    histone.marks                           html  
REDIRECT:topic	 histone.marks -> histone.marks.html [ SUCCESS ]
    lgg.exp                                 html  
REDIRECT:topic	 lgg.exp -> lgg.exp.html [ SUCCESS ]
    lgg.samples                             html  
REDIRECT:topic	 lgg.samples -> lgg.samples.html [ SUCCESS ]
    markersMatrix                           html  
REDIRECT:topic	 markersMatrix -> markersMatrix.html [ SUCCESS ]
    met                                     html  
REDIRECT:topic	 met -> met.html [ SUCCESS ]
    met.elmer                               html  
REDIRECT:topic	 met.elmer -> met.elmer.html [ SUCCESS ]
    mut                                     html  
REDIRECT:topic	 mut -> mut.html [ SUCCESS ]
    tmp.biogrid                             html  
REDIRECT:topic	 tmp.biogrid -> tmp.biogrid.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 'TCGAWorkflowData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCGAWorkflowData' as TCGAWorkflowData_1.15.0.zip
* DONE (TCGAWorkflowData)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'TCGAWorkflowData' successfully unpacked and MD5 sums checked

Tests output

TCGAWorkflowData.Rcheck/tests_i386/testthat.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.

> library(testthat)
> library(TCGAWorkflowData)
> 
> test_check("TCGAWorkflowData")
== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  33.56    0.50   34.04 

TCGAWorkflowData.Rcheck/tests_x64/testthat.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.

> library(testthat)
> library(TCGAWorkflowData)
> 
> test_check("TCGAWorkflowData")
== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  29.25    0.53   29.76 

Example timings

TCGAWorkflowData.Rcheck/examples_i386/TCGAWorkflowData-Ex.timings

nameusersystemelapsed
GBMmut10.72 0.0710.78
LGGmut9.440.099.54
TCGAWorkflowData31.34 0.2531.60
cnvMatrix0.020.000.01
exp0.500.020.52
exp.elmer0.510.000.51
gbm.exp0.390.000.39
gbm.samples0.490.030.52
genes0.150.000.15
genes_GR0.140.000.14
gistic.allbygene000
gistic.thresholedbygene0.000.010.01
histone.marks1.230.051.28
lgg.exp0.390.020.41
lgg.samples0.520.000.52
markersMatrix2.700.042.75
met0.520.020.53
met.elmer0.510.000.52
mut9.330.089.41
tmp.biogrid11.52 0.0411.56

TCGAWorkflowData.Rcheck/examples_x64/TCGAWorkflowData-Ex.timings

nameusersystemelapsed
GBMmut 9.97 0.0810.04
LGGmut8.030.068.09
TCGAWorkflowData26.14 0.3826.52
cnvMatrix000
exp0.410.010.42
exp.elmer0.410.000.41
gbm.exp0.280.020.30
gbm.samples0.40.00.4
genes0.110.030.14
genes_GR0.110.030.14
gistic.allbygene000
gistic.thresholedbygene000
histone.marks1.130.051.17
lgg.exp0.260.040.31
lgg.samples0.410.020.43
markersMatrix2.310.012.32
met0.410.020.43
met.elmer0.40.00.4
mut7.880.148.02
tmp.biogrid8.700.058.75