Back to Multiple platform build/check report for BioC 3.10
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

CHECK report for TCGAutils on tokay1

This page was generated on 2020-04-15 12:30:26 -0400 (Wed, 15 Apr 2020).

Package 1710/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAutils 1.6.2
Marcel Ramos
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/TCGAutils
Branch: RELEASE_3_10
Last Commit: 7f5faef
Last Changed Date: 2020-01-18 12:45:57 -0400 (Sat, 18 Jan 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TCGAutils
Version: 1.6.2
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TCGAutils_1.6.2.tar.gz
StartedAt: 2020-04-15 07:03:27 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 07:17:05 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 818.3 seconds
RetCode: 0
Status:  OK  
CheckDir: TCGAutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TCGAutils_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/TCGAutils.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.6.2'
* 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 or elapsed time > 5s
                                    user system elapsed
simplifyTCGA                       35.15   2.15   38.22
TCGAprimaryTumors                  28.88   3.00   33.80
curatedTCGAData-helpers            20.52   1.23   22.72
imputeAssay                        18.31   0.80   19.97
oncoPrintTCGA                      15.49   1.02   17.27
trimColData                        13.08   2.99   16.80
makeSummarizedExperimentFromGISTIC  5.44   0.63   21.85
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                    user system elapsed
simplifyTCGA                       57.29   3.52   70.37
TCGAprimaryTumors                  31.94   2.03   34.89
trimColData                        26.57   0.81   36.93
imputeAssay                        26.66   0.70   29.38
oncoPrintTCGA                      24.34   0.86   32.87
curatedTCGAData-helpers            23.35   0.81   24.88
makeSummarizedExperimentFromGISTIC  9.55   0.63   30.11
* 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-3.10-bioc/meat/TCGAutils.Rcheck/00check.log'
for details.



Installation output

TCGAutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/TCGAutils_1.6.2.tar.gz && rm -rf TCGAutils.buildbin-libdir && mkdir TCGAutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAutils.buildbin-libdir TCGAutils_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TCGAutils_1.6.2.zip && rm TCGAutils_1.6.2.tar.gz TCGAutils_1.6.2.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 64208  100 64208    0     0   648k      0 --:--:-- --:--:-- --:--:--  674k

install for i386

* installing *source* package 'TCGAutils' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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_1.6.2.zip
* DONE (TCGAutils)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'TCGAutils' successfully unpacked and MD5 sums checked

Tests output

TCGAutils.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(TCGAutils)
> 
> test_check("TCGAutils")
== testthat results  ===========================================================
[ OK: 44 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  12.14    1.23   20.70 

TCGAutils.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(TCGAutils)
> 
> test_check("TCGAutils")
== testthat results  ===========================================================
[ OK: 44 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  16.23    0.70   20.34 

Example timings

TCGAutils.Rcheck/examples_i386/TCGAutils-Ex.timings

nameusersystemelapsed
ID-translation2.660.214.73
TCGAbarcode0.010.000.02
TCGAbiospec0.050.000.05
TCGAprimaryTumors28.88 3.0033.80
TCGAsampleSelect0.010.000.01
builds0.030.000.03
curatedTCGAData-helpers20.52 1.2322.72
findGRangesCols000
generateMap0.040.000.03
getFileName0.040.000.25
imputeAssay18.31 0.8019.97
makeGRangesListFromCopyNumber0.410.031.31
makeGRangesListFromExonFiles0.090.000.09
makeSummarizedExperimentFromGISTIC 5.44 0.6321.85
mergeColData0.250.010.26
oncoPrintTCGA15.49 1.0217.27
simplifyTCGA35.15 2.1538.22
trimColData13.08 2.9916.80

TCGAutils.Rcheck/examples_x64/TCGAutils-Ex.timings

nameusersystemelapsed
ID-translation2.900.034.81
TCGAbarcode000
TCGAbiospec0.040.000.05
TCGAprimaryTumors31.94 2.0334.89
TCGAsampleSelect0.010.000.02
builds0.030.000.03
curatedTCGAData-helpers23.35 0.8124.88
findGRangesCols000
generateMap0.030.000.03
getFileName0.030.020.20
imputeAssay26.66 0.7029.38
makeGRangesListFromCopyNumber0.740.093.13
makeGRangesListFromExonFiles0.220.000.22
makeSummarizedExperimentFromGISTIC 9.55 0.6330.11
mergeColData0.500.060.72
oncoPrintTCGA24.34 0.8632.87
simplifyTCGA57.29 3.5270.37
trimColData26.57 0.8136.93