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CHECK report for TCGAutils on malbec1

This page was generated on 2019-04-16 11:53:30 -0400 (Tue, 16 Apr 2019).

Package 1548/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAutils 1.2.2
Marcel Ramos
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/TCGAutils
Branch: RELEASE_3_8
Last Commit: b8b085b
Last Changed Date: 2019-02-13 14:40:03 -0400 (Wed, 13 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: 1.2.2
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TCGAutils_1.2.2.tar.gz
StartedAt: 2019-04-16 03:22:36 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:28:05 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 328.5 seconds
RetCode: 0
Status:  OK 
CheckDir: TCGAutils.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TCGAutils_1.2.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/TCGAutils.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAutils/DESCRIPTION’ ... OK
* this is package ‘TCGAutils’ version ‘1.2.2’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
simplifyTCGA                       30.852  0.520  32.800
qreduceTCGA                        27.544  0.652  29.111
makeSummarizedExperimentFromGISTIC 19.016  2.644  29.178
imputeAssay                         9.316  0.312  11.045
symbolsToRanges                     9.208  0.028   9.244
mirToRanges                         6.488  0.216   7.662
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/TCGAutils.Rcheck/00check.log’
for details.



Installation output

TCGAutils.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL TCGAutils
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘TCGAutils’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TCGAutils)

Tests output

TCGAutils.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
> 
> proc.time()
   user  system elapsed 
  0.264   0.040   0.297 

Example timings

TCGAutils.Rcheck/TCGAutils-Ex.timings

nameusersystemelapsed
ID-translation1.2040.0403.235
TCGAbarcode0.0000.0000.001
TCGAbiospec0.0280.0040.046
TCGAsampleSelect0.0080.0040.012
builds0.0520.0040.057
curatedTCGAData-helpers0.0160.0000.013
findGRangesCols0.0040.0000.004
generateMap0.0920.0000.094
getFileNames0.0840.0000.281
imputeAssay 9.316 0.31211.045
makeGRangesListFromCopyNumber0.6280.0281.522
makeGRangesListFromExonFiles0.1600.0000.172
makeSummarizedExperimentFromGISTIC19.016 2.64429.178
mergeColData0.4080.0080.417
mirToRanges6.4880.2167.662
qreduceTCGA27.544 0.65229.111
simplifyTCGA30.852 0.52032.800
symbolsToRanges9.2080.0289.244