| 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 03:40:07 -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: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TCGAbiolinks_2.1.7.tar.gz |
| StartedAt: 2016-09-20 13:15:08 -0700 (Tue, 20 Sep 2016) |
| EndedAt: 2016-09-20 13:34:07 -0700 (Tue, 20 Sep 2016) |
| EllapsedTime: 1139.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TCGAbiolinks_2.1.7.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 19.7Mb
sub-directories of 1Mb or more:
data 6.2Mb
doc 12.4Mb
* 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: GDCprepare
> ### Title: Prepare GDC data
> ### Aliases: GDCprepare
>
> ### ** Examples
>
> query <- GDCquery(project = "TCGA-KIRP",
+ data.category = "Simple Nucleotide Variation",
+ data.type = "Masked Somatic Mutation")
Accessing GDC. This might take a while...
> GDCdownload(query, method = "api", directory = "maf")
GDCdownload will download: 5.415645 MB
Downloading as: TCGA.KIRP.mutect.b1c13b93-7ad6-4d09-b613-84a7c55e61d9.somatic.maf.gz
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|======================================================================| 100%Download completed
> GDCdownload(query, method = "api", directory = "maf")
All samples have been already downloded
> maf <- GDCprepare(query, directory = "maf")
>
> 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"))
Error in open.connection(con, "rb") :
Failure when receiving data from the peer
Calls: GDCquery ... fromJSON_string -> parseJSON -> parse_con -> open -> open.connection
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 'application/octet-stream' length 1589730 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
testthat results ================================================================
OK: 70 SKIPPED: 0 FAILED: 1
1. Failure: GDCdownload API method for one files is working (@test-prepare-download.R#33)
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
‘/home/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-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(TCGAbiolinks)
>
> test_check("TCGAbiolinks")
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Downloading: 14 kB /bin/tar: MANIFEST.txt: time stamp 2016-09-20 13:24:48 is 158.168675267 s in the future
/bin/tar: 72696f81-2171-4ebc-957c-9c9a15b70a91/AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_D02_1348388.hg19.seg.txt: time stamp 2016-09-20 13:24:48 is 158.168522735 s in the future
/bin/tar: f5485bf0-138c-4630-bc42-4e9430d7b67c/AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_D10_1348300.hg19.seg.txt: time stamp 2016-09-20 13:24:49 is 159.168408873 s in the future
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|======================================================================| 100%1. Failure: GDCdownload API method for one files is working (@test-prepare-download.R#33)
all(file.exists(files)) isn't true.
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|======================================================================| 100%trying URL 'https://gdc-api.nci.nih.gov/data//abbe72a5-cb39-48e4-8df5-5fd2349f2bb2'
Content type 'application/octet-stream' 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 'application/octet-stream' length 1589730 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
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|======================================================================| 100%[1] "I need about 1 minute to finish complete Enrichment analysis GO[BP,MF,CC] and Pathways... "
[1] "GO Enrichment Analysis BP completed....done"
[1] "GO Enrichment Analysis MF completed....done"
[1] "GO Enrichment Analysis CC completed....done"
[1] "Pathway Enrichment Analysis completed....done"
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/bin/tar: 58c691a3-e8e1-4535-84cc-f85d2dc5c5cf/jhu-usc.edu_GBM.HumanMethylation27.9.lvl-3.TCGA-19-4068-01A-01D-1228-05.txt: time stamp 2016-09-20 13:35:46 is 119.584837967 s in the future
/bin/tar: a2195132-51f9-48c0-ad01-b756a6d95167/jhu-usc.edu_GBM.HumanMethylation27.2.lvl-3.TCGA-16-0848-01A-01D-0392-05.txt: time stamp 2016-09-20 13:35:47 is 120.571440832 s in the future
/bin/tar: b6055a27-bc7a-4a2f-9ffd-3844ee0c0137/jhu-usc.edu_GBM.HumanMethylation27.3.lvl-3.TCGA-06-0155-01B-01D-0521-05.txt: time stamp 2016-09-20 13:35:47 is 120.558039943 s in the future
/bin/tar: cf57c4fd-28b7-48fc-a4f1-a087176ac87c/jhu-usc.edu_GBM.HumanMethylation27.1.lvl-3.TCGA-02-0058-01A-01D-0186-05.txt: time stamp 2016-09-20 13:35:47 is 120.544350129 s in the future
/bin/tar: cf995c79-0968-4eac-a807-995ac3106836/jhu-usc.edu_GBM.HumanMethylation27.2.lvl-3.TCGA-12-0829-01A-01D-0392-05.txt: time stamp 2016-09-20 13:35:48 is 121.530981282 s in the future
/bin/tar: e572a52d-8a5b-4375-a379-e08b3c27626c/jhu-usc.edu_GBM.HumanMethylation27.8.lvl-3.TCGA-12-1597-01B-01D-0915-05.txt: time stamp 2016-09-20 13:35:48 is 121.51757016 s in the future
/bin/tar: e72a6249-c38e-4ec5-8c11-3431f68858d0/jhu-usc.edu_GBM.HumanMethylation27.5.lvl-3.TCGA-19-1788-01A-01D-0595-05.txt: time stamp 2016-09-20 13:35:49 is 122.504151006 s in the future
/bin/tar: e8d2338d-119e-4c73-bfdb-5346756dd5bb/jhu-usc.edu_GBM.HumanMethylation27.4.lvl-3.TCGA-02-0099-01A-01D-0199-05.txt: time stamp 2016-09-20 13:35:49 is 122.490739715 s in the future
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|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 'application/octet-stream' length 1589730 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
testthat results ================================================================
OK: 70 SKIPPED: 0 FAILED: 1
1. Failure: GDCdownload API method for one files is working (@test-prepare-download.R#33)
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 | |
| GDCdownload | 27.608 | 3.096 | 43.884 | |