| 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 2016-09-21 03:54:44 -0700 (Wed, 21 Sep 2016).
| Package 1194/1257 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| TCGAbiolinks 2.1.7 Antonio Colaprico
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | ERROR | ||||||
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | ERROR | OK | ||||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: TCGAbiolinks |
| Version: 2.1.7 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCGAbiolinks_2.1.7.tar.gz |
| StartedAt: 2016-09-20 13:49:04 -0700 (Tue, 20 Sep 2016) |
| EndedAt: 2016-09-20 14:08:49 -0700 (Tue, 20 Sep 2016) |
| EllapsedTime: 1185.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCGAbiolinks_2.1.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.1.7’
* 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 ... OK
* checking installed package size ... NOTE
installed size is 24.9Mb
sub-directories of 1Mb or more:
data 6.2Mb
doc 17.6Mb
* 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 object imported by a ':::' call: ‘sjPlot:::sj.setGeomColors’
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 ... NOTE
GDCquery_clinic: no visible binding for global variable ‘portions’
TCGAanalyze_DMR: no visible global function definition for ‘as’
TCGAvisualize_oncoprint: no visible binding for global variable ‘value’
TCGAvisualize_starburst: no visible global function definition for ‘as’
checkTumorInput: no visible binding for global variable ‘project’
get.mutation.matrix: no visible binding for global variable ‘Tumor’
update.clinical.with.last.followup: no visible binding for global
variable ‘bcr_patient_barcode’
Undefined global functions or variables:
Tumor as bcr_patient_barcode portions project value
Consider adding
importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... ERROR
Running examples in ‘TCGAbiolinks-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GDCdownload
> ### Title: Download GDC data
> ### Aliases: GDCdownload
>
> ### ** Examples
>
> query <- GDCquery(project = "TCGA-ACC",
+ data.category = "Copy number variation",
+ legacy = TRUE,
+ file.type = "hg19.seg",
+ barcode = c("TCGA-OR-A5LR-01A-11D-A29H-01", "TCGA-OR-A5LJ-10A-01D-A29K-01"))
Accessing GDC. This might take a while...
> # data will be saved in GDCdata/TCGA-ACC/legacy/Copy_number_variation/Copy_number_segmentation
> GDCdownload(query, method = "api")
GDCdownload will download: 69.081 KB compressed in a tar.gz file
Downloading as: Tue_Sep_20_13_54_18_2016.tar.gz
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> query <- GDCquery(project = "TARGET-AML",
+ data.category = "Transcriptome Profiling",
+ data.type = "miRNA Expression Quantification",
+ workflow.type = "BCGSC miRNA Profiling",
+ barcode = c("TARGET-20-PARUDL-03A-01R","TARGET-20-PASRRB-03A-01R"))
Accessing GDC. This might take a while...
> # data will be saved in example_data_dir/TARGET-AML/harmonized/Transcriptome_Profiling/miRNA_Expression_Quantification
> GDCdownload(query, method = "client", directory = "example_data_dir")
downloaded 0 bytes
Warning in download.file(url, method = method, ...) :
URL 'https://gdc.cancer.gov/https://gdc.cancer.gov/files/public/file/gdc-client_v1.1.0_OSX_x64.zip': status was '404 Not Found'
Error in download.file(url, method = method, ...) :
cannot download all files
Calls: GDCdownload -> GDCclientInstall -> download -> download.file
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
|alive |NA |NA |
|dead |NA |NA |
trying URL 'https://gdc-api.nci.nih.gov/data//abbe72a5-cb39-48e4-8df5-5fd2349f2bb2'
Content type 'unknown' length 1589730 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
testthat results ================================================================
OK: 70 SKIPPED: 0 FAILED: 1
1. Error: GDCdownload API method for one files is working (@test-prepare-download.R#20)
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: 2 ERRORs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.
testthat.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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")
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Downloading: 14 kB 1. Error: GDCdownload API method for one files is working (@test-prepare-download.R#20)
HTTP error 500.
1: GDCquery(project = "TCGA-ACC", data.category = "Copy number variation", legacy = TRUE,
file.type = "hg19.seg", barcode = c("TCGA-OR-A5LR-01A-11D-A29H-01")) at testthat/test-prepare-download.R:20
2: paste0("size=", getNbFiles(project, data.category, legacy))
3: getNbFiles(project, data.category, legacy)
4: getProjectSummary(project, legacy)
5: fromJSON(url, simplifyDataFrame = TRUE)
6: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame,
simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
7: parseJSON(txt, bigint_as_char)
8: parse_con(txt, 1024^2, bigint_as_char)
9: open(con, "rb")
10: open.connection(con, "rb")
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|======================================================================| 100%trying URL 'https://gdc-api.nci.nih.gov/data//abbe72a5-cb39-48e4-8df5-5fd2349f2bb2'
Content type 'unknown' length 1589730 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
trying URL 'https://gdc-api.nci.nih.gov/data//abbe72a5-cb39-48e4-8df5-5fd2349f2bb2'
Content type 'unknown' length 1589730 bytes (1.5 MB)
==================================================
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|
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|======================================================================| 100%
|groups | Mean| Median| Max| Min|
|:------|---------:|---------:|---------:|---------:|
|TP | 0.2785957| 0.2733131| 0.3270671| 0.2341192|
|groups | Mean| Median| Max| Min|
|:------|---------:|---------:|---------:|---------:|
|TP | 0.2785957| 0.2733131| 0.3270671| 0.2341192|
|groups | Mean| Median| Max| Min|
|:------|---------:|---------:|---------:|---------:|
|LGm1 | 0.3270671| 0.3270671| 0.3270671| 0.3270671|
|LGm2 | 0.3232846| 0.3232846| 0.3232846| 0.3232846|
|LGm5 | 0.2577566| 0.2487907| 0.2961445| 0.2373007|
|NA | 0.2736938| 0.2736938| 0.3132684| 0.2341192|
| |LGm1 |LGm2 |LGm5 |
|:----|:----|:----|:----|
|LGm1 |NA |NA |NA |
|LGm2 |NA |NA |NA |
|LGm5 |NA |NA |NA |
|groups | Mean| Median| Max| Min|
|:------|---------:|---------:|---------:|---------:|
|LGm1 | 0.3270671| 0.3270671| 0.3270671| 0.3270671|
|LGm2 | 0.3232846| 0.3232846| 0.3232846| 0.3232846|
|LGm5 | 0.2577566| 0.2487907| 0.2961445| 0.2373007|
|NA | 0.2736938| 0.2736938| 0.3132684| 0.2341192|
| |LGm1 |LGm2 |LGm5 |
|:----|:----|:----|:----|
|LGm1 |NA |NA |NA |
|LGm2 |NA |NA |NA |
|LGm5 |NA |NA |NA |
|groups | Mean| Median| Max| Min|
|:------|---------:|---------:|---------:|---------:|
|LGm1 | 0.3270671| 0.3270671| 0.3270671| 0.3270671|
|LGm2 | 0.3232846| 0.3232846| 0.3232846| 0.3232846|
|LGm5 | 0.2577566| 0.2487907| 0.2961445| 0.2373007|
|NA | 0.2736938| 0.2736938| 0.3132684| 0.2341192|
| |LGm1 |LGm2 |LGm5 |
|:----|:----|:----|:----|
|LGm1 |NA |NA |NA |
|LGm2 |NA |NA |NA |
|LGm5 |NA |NA |NA |
|groups | Mean| Median| Max| Min|
|:------|---------:|---------:|---------:|---------:|
|alive | 0.2961445| 0.2961445| 0.2961445| 0.2961445|
|dead | 0.2760888| 0.2504818| 0.3270671| 0.2341192|
| |alive |dead |
|:-----|:-----|:----|
|alive |NA |NA |
|dead |NA |NA |
trying URL 'https://gdc-api.nci.nih.gov/data//abbe72a5-cb39-48e4-8df5-5fd2349f2bb2'
Content type 'unknown' length 1589730 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
testthat results ================================================================
OK: 70 SKIPPED: 0 FAILED: 1
1. Error: GDCdownload API method for one files is working (@test-prepare-download.R#20)
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 |