Antonio Colaprico
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/TCGAbiolinks |
| Branch: RELEASE_3_6 |
| Last Commit: 933a014 |
| Last Changed Date: 2018-02-02 10:51:08 -0400 (Fri, 02 Feb 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:13:57 -0400 (Thu, 12 Apr 2018).
| Package 1387/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TCGAbiolinks 2.6.12 Antonio Colaprico
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ ERROR ] | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: TCGAbiolinks |
| Version: 2.6.12 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TCGAbiolinks_2.6.12.tar.gz |
| StartedAt: 2018-04-12 03:16:44 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:34:08 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 1044.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TCGAbiolinks_2.6.12.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘2.6.12’
* 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 65.7Mb
sub-directories of 1Mb or more:
R 1.3Mb
data 3.5Mb
doc 60.7Mb
* 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 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
GDCquery_clinic: no visible binding for global variable ‘portions’
TCGA_MolecularSubtype: no visible binding for global variable
‘TabSubtypesCol_merged’
TCGAanalyze_DEA: no visible binding for global variable ‘barcode’
TCGAanalyze_DEA: no visible binding for global variable ‘clinical’
TCGAanalyze_DEA_Affy: no visible global function definition for
‘limmamakeContrasts’
TCGAanalyze_DEA_Affy: no visible global function definition for
‘limmacontrasts.fit’
TCGAanalyze_analyseGRN: no visible global function definition for
‘knnmi.cross’
TCGAanalyze_networkInference: no visible global function definition for
‘c3net’
TCGAanalyze_networkInference: no visible global function definition for
‘minet’
TCGAquery_recount2: no visible binding for global variable ‘rse_gene’
TCGAtumor_purity: no visible binding for global variable ‘Tumor.purity’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
‘dNetInduce’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
‘dNetPipeline’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
‘dCommSignif’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
‘visNet’
TCGAvisualize_oncoprint: no visible binding for global variable ‘value’
readTranscriptomeProfiling: no visible binding for global variable
‘ignore.case’
Undefined global functions or variables:
TabSubtypesCol_merged Tumor.purity barcode c3net clinical dCommSignif
dNetInduce dNetPipeline ignore.case knnmi.cross limmacontrasts.fit
limmamakeContrasts minet portions rse_gene value visNet
* 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
Error in .requirePackage(package) :
unable to find required package 'maftools'
Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
Execution halted
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
TCGAvisualize_starburst 27.632 0.168 80.007
GDCquery 20.784 0.300 31.046
TCGAanalyze_LevelTab 15.112 0.008 15.127
TCGAanalyze_DMR 14.956 0.024 14.985
GDCprepare 8.796 0.268 13.730
GDCdownload 8.312 0.596 57.615
TCGAanalyze_DEA 8.356 0.020 8.378
TCGAanalyze_Filtering 7.760 0.000 7.763
GDCprepare_clinic 6.068 0.180 9.413
TCGAquery_recount2 5.476 0.504 6.817
TCGAanalyze_survival 5.464 0.028 14.115
TCGAVisualize_volcano 5.140 0.008 5.153
matchedMetExp 2.976 0.044 6.286
getResults 2.904 0.016 5.230
TCGAanalyze_SurvivalKM 2.308 0.040 37.726
getDataCategorySummary 2.308 0.004 6.003
* 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:
LGm2 NA NA NA NA
LGm4 NA NA NA 0.9217168
LGm5 NA NA 0.9217168 NA
groups Mean Median Max Min
1 alive 0.3594683 0.3594683 0.3594683 0.3594683
2 dead 0.3589557 0.3608853 0.4099433 0.3240056
alive dead
alive NA NA
dead NA NA
══ testthat results ═══════════════════════════════════════════════════════════
OK: 80 SKIPPED: 0 FAILED: 1
1. Error: TCGAanalyze_survival creates pdf (@test-analyse.R#4)
Error: testthat unit tests failed
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘DT’
* 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, 4 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.
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/tests/testthat.Rout.fail
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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(TCGAbiolinks)
>
> test_check("TCGAbiolinks")
── 1. Error: TCGAanalyze_survival creates pdf (@test-analyse.R#4) ─────────────
lexical error: invalid char in json text.
<html><head><title>Hold up ther
(right here) ------^
1: GDCquery_clinic("TCGA-ACC", type = "clinical", save.csv = FALSE) at testthat/test-analyse.R:4
2: checkProjectInput(project)
3: getGDCprojects()
4: fromJSON(content(GET(url), as = "text", encoding = "UTF-8"), simplifyDataFrame = TRUE)
5: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame,
simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
6: parseJSON(txt, bigint_as_char)
7: parse_string(txt, bigint_as_char)
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trying URL 'http://zwdzwd.io/InfiniumAnnotation/current/hm450/hm450.hg38.manifest.rds'
Content type 'unknown' length 18600736 bytes (17.7 MB)
==================================================
downloaded 17.7 MB
trying URL 'http://zwdzwd.io/InfiniumAnnotation/current/hm450/hm450.hg19.manifest.rds'
Content type 'unknown' length 18546360 bytes (17.7 MB)
==================================================
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[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"
groups Mean Median Max Min
1 TP 0.3590198 0.3601768 0.4099433 0.3240056
groups Mean Median Max Min
1 TP 0.3590198 0.3601768 0.4099433 0.3240056
groups Mean Median Max Min
1 LGm1 0.3789137 0.3789137 0.3789137 0.3789137
2 LGm2 0.4099433 0.4099433 0.4099433 0.4099433
3 LGm4 0.3454189 0.3454189 0.3668322 0.3240056
4 LGm5 0.3481159 0.3524203 0.3608853 0.3267376
LGm1 LGm2 LGm4 LGm5
LGm1 NA NA NA NA
LGm2 NA NA NA NA
LGm4 NA NA NA 0.9217168
LGm5 NA NA 0.9217168 NA
groups Mean Median Max Min
1 LGm1 0.3789137 0.3789137 0.3789137 0.3789137
2 LGm2 0.4099433 0.4099433 0.4099433 0.4099433
3 LGm4 0.3454189 0.3454189 0.3668322 0.3240056
4 LGm5 0.3481159 0.3524203 0.3608853 0.3267376
LGm1 LGm2 LGm4 LGm5
LGm1 NA NA NA NA
LGm2 NA NA NA NA
LGm4 NA NA NA 0.9217168
LGm5 NA NA 0.9217168 NA
groups Mean Median Max Min
1 LGm1 0.3789137 0.3789137 0.3789137 0.3789137
2 LGm2 0.4099433 0.4099433 0.4099433 0.4099433
3 LGm4 0.3454189 0.3454189 0.3668322 0.3240056
4 LGm5 0.3481159 0.3524203 0.3608853 0.3267376
LGm1 LGm2 LGm4 LGm5
LGm1 NA NA NA NA
LGm2 NA NA NA NA
LGm4 NA NA NA 0.9217168
LGm5 NA NA 0.9217168 NA
groups Mean Median Max Min
1 alive 0.3594683 0.3594683 0.3594683 0.3594683
2 dead 0.3589557 0.3608853 0.4099433 0.3240056
alive dead
alive NA NA
dead NA NA
══ testthat results ═══════════════════════════════════════════════════════════
OK: 80 SKIPPED: 0 FAILED: 1
1. Error: TCGAanalyze_survival creates pdf (@test-analyse.R#4)
Error: testthat unit tests failed
Execution halted
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
| name | user | system | elapsed | |
| GDCdownload | 8.312 | 0.596 | 57.615 | |
| GDCprepare | 8.796 | 0.268 | 13.730 | |
| GDCprepare_clinic | 6.068 | 0.180 | 9.413 | |
| GDCquery | 20.784 | 0.300 | 31.046 | |
| GDCquery_Maf | 0.000 | 0.000 | 0.001 | |
| GDCquery_clinic | 1.424 | 0.040 | 3.514 | |
| PanCancerAtlas_subtypes | 0.016 | 0.000 | 0.013 | |
| TCGAVisualize_volcano | 5.140 | 0.008 | 5.153 | |
| TCGA_MolecularSubtype | 0.008 | 0.000 | 0.006 | |
| TCGAanalyze_DEA | 8.356 | 0.020 | 8.378 | |
| TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
| TCGAanalyze_DMR | 14.956 | 0.024 | 14.985 | |
| TCGAanalyze_EA | 0.000 | 0.000 | 0.001 | |
| TCGAanalyze_EAcomplete | 3.32 | 0.00 | 3.32 | |
| TCGAanalyze_Filtering | 7.760 | 0.000 | 7.763 | |
| TCGAanalyze_LevelTab | 15.112 | 0.008 | 15.127 | |
| TCGAanalyze_Normalization | 3.932 | 0.000 | 3.933 | |
| TCGAanalyze_Pathview | 0.004 | 0.000 | 0.001 | |
| TCGAanalyze_SurvivalKM | 2.308 | 0.040 | 37.726 | |
| TCGAanalyze_survival | 5.464 | 0.028 | 14.115 | |
| TCGAprepare_Affy | 0 | 0 | 0 | |
| TCGAquery_MatchedCoupledSampleTypes | 0.024 | 0.000 | 0.028 | |
| TCGAquery_SampleTypes | 0.000 | 0.000 | 0.001 | |
| TCGAquery_recount2 | 5.476 | 0.504 | 6.817 | |
| TCGAquery_subtype | 0.008 | 0.000 | 0.008 | |
| TCGAtumor_purity | 0.080 | 0.004 | 0.086 | |
| TCGAvisualize_EAbarplot | 3.660 | 0.084 | 3.750 | |
| TCGAvisualize_Heatmap | 2.300 | 0.000 | 2.299 | |
| TCGAvisualize_PCA | 4.212 | 0.000 | 4.213 | |
| TCGAvisualize_meanMethylation | 2.828 | 0.000 | 2.831 | |
| TCGAvisualize_oncoprint | 0.004 | 0.000 | 0.001 | |
| TCGAvisualize_starburst | 27.632 | 0.168 | 80.007 | |
| UseRaw_afterFilter | 0 | 0 | 0 | |
| calculate.pvalues | 0.000 | 0.000 | 0.001 | |
| colDataPrepare | 0.004 | 0.000 | 0.001 | |
| diffmean | 0.072 | 0.000 | 0.073 | |
| gaiaCNVplot | 0.124 | 0.000 | 0.126 | |
| getAdjacencyBiogrid | 0.004 | 0.000 | 0.004 | |
| getDataCategorySummary | 2.308 | 0.004 | 6.003 | |
| getGDCInfo | 0.124 | 0.000 | 0.385 | |
| getGDCprojects | 0.140 | 0.012 | 0.340 | |
| getManifest | 2.104 | 0.020 | 3.266 | |
| getResults | 2.904 | 0.016 | 5.230 | |
| getTSS | 0.000 | 0.000 | 0.001 | |
| isServeOK | 0.140 | 0.004 | 0.466 | |
| matchedMetExp | 2.976 | 0.044 | 6.286 | |