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This page was generated on 2021-10-15 15:06:25 -0400 (Fri, 15 Oct 2021).

CHECK results for TCGAutils on tokay2

To the developers/maintainers of the TCGAutils package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TCGAutils.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1901/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAutils 1.12.0  (landing page)
Marcel Ramos
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/TCGAutils
git_branch: RELEASE_3_13
git_last_commit: d0b9159
git_last_commit_date: 2021-05-19 12:35:30 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TCGAutils
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TCGAutils_1.12.0.tar.gz
StartedAt: 2021-10-15 06:29:31 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 06:43:56 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 864.5 seconds
RetCode: 0
Status:   OK  
CheckDir: TCGAutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TCGAutils_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/TCGAutils.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TCGAutils/DESCRIPTION' ... OK
* this is package 'TCGAutils' version '1.12.0'
* package encoding: UTF-8
* 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 'TCGAutils' 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 ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'GenomicRanges:::.normarg_field'
  See the note in ?`:::` about the use of this operator.
* 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 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
simplifyTCGA                       45.64   2.93   50.19
TCGAprimaryTumors                  33.20   3.05   46.36
trimColData                        26.39   3.75   31.80
imputeAssay                        25.91   0.84   28.46
curatedTCGAData-helpers            25.19   1.09   27.99
oncoPrintTCGA                      20.89   1.39   25.83
makeSummarizedExperimentFromGISTIC  6.82   0.52   28.89
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
simplifyTCGA                       50.67   2.78   55.04
TCGAprimaryTumors                  31.36   2.13   55.72
imputeAssay                        30.91   1.11   34.00
curatedTCGAData-helpers            27.64   0.81   30.25
trimColData                        27.11   1.26   37.30
oncoPrintTCGA                      21.59   1.08   26.25
makeSummarizedExperimentFromGISTIC  6.33   0.41   23.91
* 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-3.13-bioc/meat/TCGAutils.Rcheck/00check.log'
for details.

Installation output

TCGAutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/TCGAutils_1.12.0.tar.gz && rm -rf TCGAutils.buildbin-libdir && mkdir TCGAutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAutils.buildbin-libdir TCGAutils_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TCGAutils_1.12.0.zip && rm TCGAutils_1.12.0.tar.gz TCGAutils_1.12.0.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 67408  100 67408    0     0   425k      0 --:--:-- --:--:-- --:--:--  430k

install for i386

* installing *source* package 'TCGAutils' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TCGAutils'
    finding HTML links ... done
    ID-translation                          html  
    TCGAbarcode                             html  
    TCGAbiospec                             html  
    TCGAprimaryTumors                       html  
    finding level-2 HTML links ... done

    TCGAsampleSelect                        html  
    TCGAutils-package                       html  
    builds                                  html  
    clinicalNames                           html  
    curatedTCGAData-helpers                 html  
    diseaseCodes                            html  
    findGRangesCols                         html  
    generateMap                             html  
    getFileName                             html  
    hidden-helpers                          html  
    imputeAssay                             html  
    makeGRangesListFromCopyNumber           html  
    makeGRangesListFromExonFiles            html  
    makeSummarizedExperimentFromGISTIC      html  
    mergeColData                            html  
    oncoPrintTCGA                           html  
    sampleTypes                             html  
    simplifyTCGA                            html  
    trimColData                             html  
** 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 'TCGAutils' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCGAutils' as TCGAutils_1.12.0.zip
* DONE (TCGAutils)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'TCGAutils' successfully unpacked and MD5 sums checked

Tests output

TCGAutils.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(TCGAutils)
> 
> test_check("TCGAutils")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 46 ]
> 
> proc.time()
   user  system elapsed 
  13.76    1.32   17.53

TCGAutils.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(TCGAutils)
> 
> test_check("TCGAutils")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 46 ]
> 
> proc.time()
   user  system elapsed 
  13.90    0.53   17.15

Example timings

TCGAutils.Rcheck/examples_i386/TCGAutils-Ex.timings

nameusersystemelapsed
ID-translation1.900.084.60
TCGAbarcode000
TCGAbiospec0.070.000.06
TCGAprimaryTumors33.20 3.0546.36
TCGAsampleSelect0.000.020.02
builds0.090.000.09
curatedTCGAData-helpers25.19 1.0927.99
findGRangesCols000
generateMap0.020.000.02
getFileName0.080.000.64
imputeAssay25.91 0.8428.46
makeGRangesListFromCopyNumber1.390.053.54
makeGRangesListFromExonFiles0.340.001.19
makeSummarizedExperimentFromGISTIC 6.82 0.5228.89
mergeColData0.250.030.28
oncoPrintTCGA20.89 1.3925.83
simplifyTCGA45.64 2.9350.19
trimColData26.39 3.7531.80

TCGAutils.Rcheck/examples_x64/TCGAutils-Ex.timings

nameusersystemelapsed
ID-translation1.610.154.36
TCGAbarcode000
TCGAbiospec0.030.010.05
TCGAprimaryTumors31.36 2.1355.72
TCGAsampleSelect0.010.000.01
builds0.130.010.14
curatedTCGAData-helpers27.64 0.8130.25
findGRangesCols000
generateMap0.030.000.03
getFileName0.010.000.24
imputeAssay30.91 1.1134.00
makeGRangesListFromCopyNumber1.370.032.39
makeGRangesListFromExonFiles0.300.020.29
makeSummarizedExperimentFromGISTIC 6.33 0.4123.91
mergeColData0.300.030.33
oncoPrintTCGA21.59 1.0826.25
simplifyTCGA50.67 2.7855.04
trimColData27.11 1.2637.30