Antonio Colaprico
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/TCGAbiolinks |
| Branch: master |
| Last Commit: 1ec4801 |
| Last Changed Date: 2019-04-08 12:00:05 -0400 (Mon, 08 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:14:39 -0400 (Tue, 09 Apr 2019).
| Package 1596/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TCGAbiolinks 2.11.5 Antonio Colaprico
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: TCGAbiolinks |
| Version: 2.11.5 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TCGAbiolinks_2.11.5.tar.gz |
| StartedAt: 2019-04-09 05:55:20 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 06:20:05 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 1485.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TCGAbiolinks_2.11.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TCGAbiolinks.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.11.5’
* 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 5.3Mb
sub-directories of 1Mb or more:
R 1.6Mb
data 3.5Mb
* 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 ... WARNING
'::' or ':::' import not declared from: ‘purrr’
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘move’
* 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_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’
readExonQuantification: no visible binding for global variable ‘exon’
readExonQuantification: no visible binding for global variable
‘coordinates’
Undefined global functions or variables:
Tumor.purity barcode c3net clinical coordinates dCommSignif
dNetInduce dNetPipeline exon 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
TCGAanalyze_DMR 29.003 0.323 29.510
TCGAanalyze_LevelTab 26.299 2.649 37.805
GDCprepare_clinic 16.572 0.228 86.531
TCGAanalyze_Filtering 15.314 0.537 20.528
TCGAanalyze_DEA 12.377 0.745 13.200
TCGAvisualize_PCA 7.650 0.254 8.010
GDCdownload 7.572 0.118 55.327
TCGAvisualize_EAbarplot 6.161 0.292 10.162
TCGAanalyze_Normalization 6.145 0.205 6.349
TCGAanalyze_EAcomplete 5.936 0.203 6.138
GDCprepare 4.985 0.481 7.582
getSampleFilesSummary 3.886 0.213 9.207
getManifest 3.982 0.016 10.479
getResults 3.653 0.016 8.745
GDCquery 3.546 0.014 9.903
matchedMetExp 3.489 0.023 9.742
TCGAvisualize_Heatmap 3.225 0.045 5.701
getDataCategorySummary 2.327 0.049 5.314
* 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 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘TCGAbiolinks’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (TCGAbiolinks)
TCGAbiolinks.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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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[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: 67 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
288.155 9.321 664.700
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
| name | user | system | elapsed | |
| GDCdownload | 7.572 | 0.118 | 55.327 | |
| GDCprepare | 4.985 | 0.481 | 7.582 | |
| GDCprepare_clinic | 16.572 | 0.228 | 86.531 | |
| GDCquery | 3.546 | 0.014 | 9.903 | |
| GDCquery_ATAC_seq | 0.001 | 0.000 | 0.001 | |
| GDCquery_Maf | 0.000 | 0.001 | 0.000 | |
| GDCquery_clinic | 1.485 | 0.671 | 2.580 | |
| PanCancerAtlas_subtypes | 0.024 | 0.004 | 0.027 | |
| TCGAVisualize_volcano | 0.533 | 0.020 | 0.554 | |
| TCGA_MolecularSubtype | 0.687 | 0.006 | 0.693 | |
| TCGAanalyze_DEA | 12.377 | 0.745 | 13.200 | |
| TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
| TCGAanalyze_DMR | 29.003 | 0.323 | 29.510 | |
| TCGAanalyze_EA | 0.001 | 0.001 | 0.001 | |
| TCGAanalyze_EAcomplete | 5.936 | 0.203 | 6.138 | |
| TCGAanalyze_Filtering | 15.314 | 0.537 | 20.528 | |
| TCGAanalyze_LevelTab | 26.299 | 2.649 | 37.805 | |
| TCGAanalyze_Normalization | 6.145 | 0.205 | 6.349 | |
| TCGAanalyze_Pathview | 0.000 | 0.001 | 0.000 | |
| TCGAanalyze_SurvivalKM | 0.116 | 0.001 | 0.117 | |
| TCGAanalyze_survival | 4.357 | 0.157 | 4.515 | |
| TCGAprepare_Affy | 0.000 | 0.000 | 0.001 | |
| TCGAquery_MatchedCoupledSampleTypes | 0.005 | 0.000 | 0.006 | |
| TCGAquery_SampleTypes | 0.002 | 0.000 | 0.003 | |
| TCGAquery_recount2 | 0.000 | 0.000 | 0.001 | |
| TCGAquery_subtype | 0.013 | 0.001 | 0.014 | |
| TCGAtumor_purity | 0.161 | 0.002 | 0.162 | |
| TCGAvisualize_EAbarplot | 6.161 | 0.292 | 10.162 | |
| TCGAvisualize_Heatmap | 3.225 | 0.045 | 5.701 | |
| TCGAvisualize_PCA | 7.650 | 0.254 | 8.010 | |
| TCGAvisualize_meanMethylation | 4.811 | 0.068 | 4.882 | |
| TCGAvisualize_oncoprint | 0.001 | 0.000 | 0.001 | |
| TCGAvisualize_starburst | 0.001 | 0.001 | 0.002 | |
| UseRaw_afterFilter | 0.000 | 0.000 | 0.001 | |
| calculate.pvalues | 0.000 | 0.000 | 0.001 | |
| colDataPrepare | 0.000 | 0.000 | 0.001 | |
| diffmean | 0.133 | 0.001 | 0.133 | |
| gaiaCNVplot | 0.033 | 0.001 | 0.034 | |
| getAdjacencyBiogrid | 0.006 | 0.001 | 0.007 | |
| getDataCategorySummary | 2.327 | 0.049 | 5.314 | |
| getGDCInfo | 0.010 | 0.002 | 0.182 | |
| getGDCprojects | 0.028 | 0.002 | 0.215 | |
| getManifest | 3.982 | 0.016 | 10.479 | |
| getResults | 3.653 | 0.016 | 8.745 | |
| getSampleFilesSummary | 3.886 | 0.213 | 9.207 | |
| getTSS | 0 | 0 | 0 | |
| isServeOK | 0.011 | 0.002 | 0.184 | |
| matchedMetExp | 3.489 | 0.023 | 9.742 | |