Marcin Kosinski
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/RTCGA |
| Branch: RELEASE_3_7 |
| Last Commit: c4df3db |
| Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:28:01 -0400 (Wed, 17 Oct 2018).
| Package 1289/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RTCGA 1.10.0 Marcin Kosinski
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: RTCGA |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:RTCGA.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings RTCGA_1.10.0.tar.gz |
| StartedAt: 2018-10-16 03:27:37 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 03:34:53 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 436.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RTCGA.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:RTCGA.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings RTCGA_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/RTCGA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTCGA/DESCRIPTION’ ... OK
* this is package ‘RTCGA’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RTCGA’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
availableDates: no visible binding for global variable ‘.’
downloadTCGA: no visible binding for global variable ‘.’
ggbiplot: no visible binding for global variable ‘xvar’
ggbiplot: no visible binding for global variable ‘yvar’
ggbiplot: no visible global function definition for ‘muted’
ggbiplot: no visible binding for global variable ‘varname’
ggbiplot: no visible binding for global variable ‘angle’
ggbiplot: no visible binding for global variable ‘hjust’
read.mutations: no visible binding for global variable ‘.’
read.rnaseq: no visible binding for global variable ‘.’
survivalTCGA: no visible binding for global variable ‘times’
whichDateToUse: no visible binding for global variable ‘.’
Undefined global functions or variables:
. angle hjust muted times varname xvar yvar
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
expressionsTCGA 124.176 0.648 126.103
heatmapTCGA 104.452 0.132 104.814
boxplotTCGA 69.100 0.988 71.074
survivalTCGA 13.768 0.004 13.787
kmTCGA 13.096 0.012 13.367
mutationsTCGA 7.184 0.000 7.187
downloadTCGA 0.112 0.164 5.022
* 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-3.7-bioc/meat/RTCGA.Rcheck/00check.log’
for details.
RTCGA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL RTCGA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘RTCGA’ ... ** R ** 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 (RTCGA)
RTCGA.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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(RTCGA)
Welcome to the RTCGA (version: 1.10.0).
> library(RTCGA.rnaseq)
> library(Biobase)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> library(GenomicRanges)
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
> #library(RTCGA.CNV)
> #library(RTCGA.PANCAN12)
>
> test_check("RTCGA")
trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601/gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
Content type 'application/x-gzip' length 151456 bytes (147 KB)
==================================================
downloaded 147 KB
trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601/gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
Content type 'application/x-gzip' length 151456 bytes (147 KB)
==================================================
downloaded 147 KB
══ testthat results ═══════════════════════════════════════════════════════════
OK: 11 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
10.264 0.932 34.083
RTCGA.Rcheck/RTCGA-Ex.timings
| name | user | system | elapsed | |
| RTCGA-package | 0 | 0 | 0 | |
| boxplotTCGA | 69.100 | 0.988 | 71.074 | |
| checkTCGA | 0.356 | 0.004 | 1.414 | |
| convertTCGA | 1.252 | 0.228 | 1.485 | |
| datasetsTCGA | 0.000 | 0.000 | 0.001 | |
| downloadTCGA | 0.112 | 0.164 | 5.022 | |
| expressionsTCGA | 124.176 | 0.648 | 126.103 | |
| heatmapTCGA | 104.452 | 0.132 | 104.814 | |
| infoTCGA | 1.184 | 0.000 | 1.507 | |
| installTCGA | 0.004 | 0.000 | 0.000 | |
| kmTCGA | 13.096 | 0.012 | 13.367 | |
| mutationsTCGA | 7.184 | 0.000 | 7.187 | |
| pcaTCGA | 0.000 | 0.000 | 0.001 | |
| readTCGA | 0.008 | 0.000 | 0.008 | |
| survivalTCGA | 13.768 | 0.004 | 13.787 | |
| theme_RTCGA | 4.960 | 0.000 | 4.962 | |