| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L M N O P Q R S [T] U V W X Y Z |
This page was generated on 2015-11-10 14:50:05 -0800 (Tue, 10 Nov 2015).
| Package 1046/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| TCGAbiolinks 1.0.1 Antonio Colaprico
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK |  | |||||
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ ERROR ] | OK | ||||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
| Package: TCGAbiolinks |
| Version: 1.0.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCGAbiolinks_1.0.1.tar.gz |
| StartedAt: 2015-11-10 10:05:36 -0800 (Tue, 10 Nov 2015) |
| EndedAt: 2015-11-10 10:20:41 -0800 (Tue, 10 Nov 2015) |
| EllapsedTime: 904.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCGAbiolinks_1.0.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘1.0.1’
* 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 ‘TCGAbiolinks’ can be installed ... [51s/52s] OK
* checking installed package size ... NOTE
installed size is 16.1Mb
sub-directories of 1Mb or more:
data 6.2Mb
doc 8.0Mb
R 1.7Mb
* 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 loading without being on the library search path ... 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 ... 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 ... NOTE
Note: found 1 marked UTF-8 string
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [109s/135s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
TCGAanalyze_LevelTab 27.404 2.650 30.149
TCGAanalyze_DEA 12.353 0.394 12.731
TCGAanalyze_Filtering 10.111 0.320 10.426
TCGAvisualize_PCA 5.607 0.184 5.788
TCGAanalyze_Normalization 5.316 0.182 5.494
TCGAanalyze_EAcomplete 4.988 0.236 5.221
TCGAquery 3.834 0.094 8.008
TCGAquery_Version 2.632 0.053 8.176
TCGAdownload 1.244 0.052 14.186
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [24s/350s]
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
|
| | 0%
Downloading:unc.edu_LUSC.IlluminaHiSeq_RNASeqV2.mage-tab.1.11.0.tar.gz
|
|======================================================================| 100%
testthat results ================================================================
OK: 22 SKIPPED: 0 FAILED: 1
1. Error: It can download a file
Error: testthat unit tests failed
Execution halted
* 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 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.
TCGAbiolinks.Rcheck/tests/testthat.Rout.fail:
R version 3.2.2 Patched (2015-10-08 r69496) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (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(TCGAbiolinks)
>
> test_check("TCGAbiolinks")
|
| | 0%1. Error: It can download a file -----------------------------------------------
Couldn't connect to server
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls, message = function(c) invokeRestart("muffleMessage"))
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: TCGAdownload(query, path = "dataTest", type = "rsem.genes.results", samples = sample) at test-prepare-download.R:7
5: suppressWarnings(download(paste0(root, url, "/", files[i]), file.path(path, folder,
files[i]), quiet = TRUE))
6: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
7: download(paste0(root, url, "/", files[i]), file.path(path, folder, files[i]), quiet = TRUE)
8: download.file(url, method = method, ...)
|
| | 0%
Downloading:unc.edu_LUSC.IlluminaHiSeq_RNASeqV2.mage-tab.1.11.0.tar.gz
|
|======================================================================| 100%
testthat results ================================================================
OK: 22 SKIPPED: 0 FAILED: 1
1. Error: It can download a file
Error: testthat unit tests failed
Execution halted
TCGAbiolinks.Rcheck/00install.out:
* installing *source* package ‘TCGAbiolinks’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (TCGAbiolinks)
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings:
| name | user | system | elapsed | |
| TCGAVisualize_volcano | 0.375 | 0.018 | 0.393 | |
| TCGAanalyze_DEA | 12.353 | 0.394 | 12.731 | |
| TCGAanalyze_DEA_Affy | 0.000 | 0.000 | 0.001 | |
| TCGAanalyze_DMR | 4.696 | 0.081 | 4.855 | |
| TCGAanalyze_EA | 0.000 | 0.001 | 0.001 | |
| TCGAanalyze_EAcomplete | 4.988 | 0.236 | 5.221 | |
| TCGAanalyze_Filtering | 10.111 | 0.320 | 10.426 | |
| TCGAanalyze_LevelTab | 27.404 | 2.650 | 30.149 | |
| TCGAanalyze_Normalization | 5.316 | 0.182 | 5.494 | |
| TCGAanalyze_Preprocessing | 0.126 | 0.019 | 0.145 | |
| TCGAanalyze_SurvivalKM | 0.017 | 0.000 | 0.017 | |
| TCGAanalyze_survival | 0.376 | 0.005 | 0.419 | |
| TCGAdownload | 1.244 | 0.052 | 14.186 | |
| TCGAprepare | 0.573 | 0.050 | 2.090 | |
| TCGAprepare_Affy | 0 | 0 | 0 | |
| TCGAprepare_elmer | 0.007 | 0.002 | 0.009 | |
| TCGAquery | 3.834 | 0.094 | 8.008 | |
| TCGAquery_Investigate | 0.019 | 0.000 | 0.019 | |
| TCGAquery_MatchedCoupledSampleTypes | 0.001 | 0.000 | 0.001 | |
| TCGAquery_SampleTypes | 0.001 | 0.000 | 0.002 | |
| TCGAquery_Social | 0.251 | 0.013 | 0.928 | |
| TCGAquery_Version | 2.632 | 0.053 | 8.176 | |
| TCGAquery_clinic | 0.130 | 0.007 | 1.305 | |
| TCGAquery_clinicFilt | 0.052 | 0.005 | 0.056 | |
| TCGAquery_integrate | 0.123 | 0.000 | 0.123 | |
| TCGAquery_maf | 0.001 | 0.000 | 0.000 | |
| TCGAquery_samplesfilter | 0.062 | 0.001 | 0.063 | |
| TCGAquery_subtype | 0.002 | 0.001 | 0.002 | |
| TCGAvisualize_BarPlot | 0.020 | 0.001 | 0.021 | |
| TCGAvisualize_EAbarplot | 4.678 | 0.087 | 4.761 | |
| TCGAvisualize_Heatmap | 0.019 | 0.001 | 0.019 | |
| TCGAvisualize_PCA | 5.607 | 0.184 | 5.788 | |
| TCGAvisualize_Tables | 0.066 | 0.001 | 0.068 | |
| TCGAvisualize_meanMethylation | 0.391 | 0.007 | 0.399 | |
| TCGAvisualize_starburst | 1.931 | 0.088 | 2.127 | |
| calculate.pvalues | 0.001 | 0.000 | 0.001 | |
| diffmean | 0.001 | 0.001 | 0.001 | |