Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2022-04-13 12:07:28 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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? 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 1939/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAutils 1.14.1  (landing page)
Marcel Ramos
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/TCGAutils
git_branch: RELEASE_3_14
git_last_commit: 94577cb
git_last_commit_date: 2022-04-04 13:46:19 -0400 (Mon, 04 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.14.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings TCGAutils_1.14.1.tar.gz
StartedAt: 2022-04-13 03:56:02 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 04:10:20 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 858.3 seconds
RetCode: 0
Status:   OK  
CheckDir: TCGAutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings TCGAutils_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/TCGAutils.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.14.1'
* 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'
  'S4Vectors:::selectSome'
  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                       49.45   2.80   53.82
TCGAprimaryTumors                  37.38   3.81   52.53
trimColData                        29.71   2.79   34.26
imputeAssay                        29.67   0.89   32.03
curatedTCGAData-helpers            28.72   1.00   31.36
oncoPrintTCGA                      22.66   1.30   27.25
makeSummarizedExperimentFromGISTIC  6.67   0.51   23.70
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
simplifyTCGA                       46.31   3.04   50.74
TCGAprimaryTumors                  34.05   1.91   38.20
imputeAssay                        29.21   1.06   31.70
trimColData                        29.44   0.82   31.86
curatedTCGAData-helpers            28.97   0.83   31.44
oncoPrintTCGA                      22.61   0.96   26.76
makeSummarizedExperimentFromGISTIC  7.65   0.43   24.32
* 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-3.14-bioc/meat/TCGAutils.Rcheck/00check.log'
for details.

Installation output

TCGAutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/TCGAutils_1.14.1.tar.gz && rm -rf TCGAutils.buildbin-libdir && mkdir TCGAutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAutils.buildbin-libdir TCGAutils_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL TCGAutils_1.14.1.zip && rm TCGAutils_1.14.1.tar.gz TCGAutils_1.14.1.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
 99 67427   99 67312    0     0   313k      0 --:--:-- --:--:-- --:--:--  313k
100 67427  100 67427    0     0   238k      0 --:--:-- --:--:-- --:--:--  237k

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_1.14.1.zip
* DONE (TCGAutils)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'TCGAutils' successfully unpacked and MD5 sums checked

Tests output

TCGAutils.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 48 ]
> 
> proc.time()
   user  system elapsed 
  15.15    1.10   20.60

TCGAutils.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 48 ]
> 
> proc.time()
   user  system elapsed 
  16.06    0.54   21.04

Example timings

TCGAutils.Rcheck/examples_i386/TCGAutils-Ex.timings

nameusersystemelapsed
ID-translation2.110.164.95
TCGAbarcode000
TCGAbiospec0.010.020.03
TCGAprimaryTumors37.38 3.8152.53
TCGAsampleSelect0.010.000.02
builds0.140.000.14
curatedTCGAData-helpers28.72 1.0031.36
findGRangesCols000
generateMap0.030.000.03
getFileName0.080.010.47
imputeAssay29.67 0.8932.03
makeGRangesListFromCopyNumber1.360.102.47
makeGRangesListFromExonFiles0.330.000.34
makeSummarizedExperimentFromGISTIC 6.67 0.5123.70
mergeColData0.270.000.27
oncoPrintTCGA22.66 1.3027.25
simplifyTCGA49.45 2.8053.82
trimColData29.71 2.7934.26

TCGAutils.Rcheck/examples_x64/TCGAutils-Ex.timings

nameusersystemelapsed
ID-translation1.610.094.54
TCGAbarcode000
TCGAbiospec0.050.000.05
TCGAprimaryTumors34.05 1.9138.20
TCGAsampleSelect0.010.000.01
builds0.140.000.14
curatedTCGAData-helpers28.97 0.8331.44
findGRangesCols000
generateMap0.030.000.03
getFileName0.010.000.22
imputeAssay29.21 1.0631.70
makeGRangesListFromCopyNumber1.360.002.44
makeGRangesListFromExonFiles0.310.030.32
makeSummarizedExperimentFromGISTIC 7.65 0.4324.32
mergeColData0.270.000.26
oncoPrintTCGA22.61 0.9626.76
simplifyTCGA46.31 3.0450.74
trimColData29.44 0.8231.86