Tiago Chedraoui Silva
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/TCGAbiolinks |
| Branch: RELEASE_3_11 |
| Last Commit: e3b011da |
| Last Changed Date: 2020-09-08 11:07:02 -0400 (Tue, 08 Sep 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:59:46 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE TCGAbiolinks PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1784/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TCGAbiolinks 2.16.4 Tiago Chedraoui Silva
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: TCGAbiolinks |
| Version: 2.16.4 |
| 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_2.16.4.tar.gz |
| StartedAt: 2020-10-17 05:49:51 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:01:23 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 691.8 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_2.16.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.16.4’
* 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 7.0Mb
sub-directories of 1Mb or more:
R 2.5Mb
data 4.3Mb
* 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: ‘sesameData’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GDCquery: no visible global function definition for ‘contains’
GDCquery : <anonymous>: no visible binding for global variable
‘submitter_id’
GDCquery : <anonymous>: no visible binding for global variable
‘is_ffpe’
TCGAanalyze_DEA: no visible binding for global variable ‘barcode’
TCGAanalyze_DEA: no visible binding for global variable ‘clinical’
TCGAquery_recount2: no visible binding for global variable ‘rse_gene’
TCGAtumor_purity: no visible binding for global variable ‘Tumor.purity’
TCGAvisualize_oncoprint: no visible binding for global variable ‘value’
TCGAvisualize_starburst: no visible global function definition for
‘values’
readExonQuantification: no visible binding for global variable ‘exon’
readExonQuantification: no visible binding for global variable
‘coordinates’
readGeneExpressionQuantification : <anonymous>: no visible binding for
'<<-' assignment to ‘assay.list’
readGeneExpressionQuantification: no visible binding for global
variable ‘assay.list’
Undefined global functions or variables:
Tumor.purity assay.list barcode clinical contains coordinates exon
is_ffpe rse_gene submitter_id value values
* 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 (user + system) or elapsed time > 5s
user system elapsed
GDCquery_clinic 25.197 0.405 39.537
TCGAanalyze_LevelTab 19.077 2.628 21.721
TCGAanalyze_DEA 17.153 0.369 17.537
TCGAanalyze_Filtering 11.113 0.174 11.291
TCGAvisualize_PCA 6.208 0.083 6.297
TCGAanalyze_Stemness 5.467 0.069 5.544
GDCdownload 5.335 0.151 34.754
TCGAanalyze_Normalization 5.273 0.071 5.351
GDCprepare_clinic 3.418 0.119 49.900
getDataCategorySummary 2.500 0.020 5.374
matchedMetExp 1.589 0.024 5.644
getResults 0.792 0.011 5.308
getManifest 0.632 0.009 7.179
* 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-3.11-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/4.0/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 version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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%
|========================== | 50% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|========================== | 50% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
[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"
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 45 | SKIPPED: 21 | WARNINGS: 4 | FAILED: 0 ]
>
> proc.time()
user system elapsed
67.628 2.209 77.858
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
| name | user | system | elapsed | |
| GDCdownload | 5.335 | 0.151 | 34.754 | |
| GDCprepare | 0.000 | 0.001 | 0.001 | |
| GDCprepare_clinic | 3.418 | 0.119 | 49.900 | |
| GDCquery | 0.818 | 0.011 | 4.928 | |
| GDCquery_ATAC_seq | 0.378 | 0.025 | 0.995 | |
| GDCquery_Maf | 0 | 0 | 0 | |
| GDCquery_clinic | 25.197 | 0.405 | 39.537 | |
| PanCancerAtlas_subtypes | 0.025 | 0.003 | 0.027 | |
| TCGAVisualize_volcano | 0.395 | 0.010 | 0.406 | |
| TCGA_MolecularSubtype | 0.723 | 0.002 | 0.726 | |
| TCGAanalyze_DEA | 17.153 | 0.369 | 17.537 | |
| TCGAanalyze_DEA_Affy | 0.000 | 0.001 | 0.000 | |
| TCGAanalyze_DMC | 1.537 | 0.062 | 1.602 | |
| TCGAanalyze_EA | 0.000 | 0.000 | 0.001 | |
| TCGAanalyze_EAcomplete | 4.122 | 0.067 | 4.195 | |
| TCGAanalyze_Filtering | 11.113 | 0.174 | 11.291 | |
| TCGAanalyze_LevelTab | 19.077 | 2.628 | 21.721 | |
| TCGAanalyze_Normalization | 5.273 | 0.071 | 5.351 | |
| TCGAanalyze_Pathview | 0.000 | 0.001 | 0.001 | |
| TCGAanalyze_Stemness | 5.467 | 0.069 | 5.544 | |
| TCGAanalyze_SurvivalKM | 0.159 | 0.003 | 0.162 | |
| TCGAanalyze_survival | 4.036 | 0.069 | 4.110 | |
| TCGAprepare_Affy | 0 | 0 | 0 | |
| TCGAquery_MatchedCoupledSampleTypes | 0.004 | 0.000 | 0.004 | |
| TCGAquery_SampleTypes | 0.002 | 0.000 | 0.003 | |
| TCGAquery_recount2 | 0.000 | 0.000 | 0.001 | |
| TCGAquery_subtype | 0.012 | 0.001 | 0.012 | |
| TCGAtumor_purity | 0.168 | 0.000 | 0.170 | |
| TCGAvisualize_EAbarplot | 4.159 | 0.069 | 4.230 | |
| TCGAvisualize_Heatmap | 2.692 | 0.050 | 2.745 | |
| TCGAvisualize_PCA | 6.208 | 0.083 | 6.297 | |
| TCGAvisualize_meanMethylation | 3.863 | 0.041 | 3.911 | |
| TCGAvisualize_oncoprint | 0.001 | 0.001 | 0.001 | |
| TCGAvisualize_starburst | 0.000 | 0.002 | 0.002 | |
| UseRaw_afterFilter | 0.000 | 0.001 | 0.001 | |
| colDataPrepare | 0.197 | 0.004 | 1.026 | |
| dmc.non.parametric | 0.254 | 0.041 | 0.296 | |
| dmc.non.parametric.se | 0.342 | 0.018 | 0.361 | |
| gaiaCNVplot | 0.051 | 0.002 | 0.053 | |
| getAdjacencyBiogrid | 0.002 | 0.001 | 0.002 | |
| getDataCategorySummary | 2.500 | 0.020 | 5.374 | |
| getGDCInfo | 0.017 | 0.001 | 0.180 | |
| getGDCprojects | 0.025 | 0.002 | 0.214 | |
| getLinkedOmicsData | 0.001 | 0.001 | 0.000 | |
| getMC3MAF | 0.000 | 0.000 | 0.001 | |
| getManifest | 0.632 | 0.009 | 7.179 | |
| getNbCases | 0 | 0 | 0 | |
| getNbFiles | 0.000 | 0.000 | 0.001 | |
| getProjectSummary | 0.001 | 0.000 | 0.000 | |
| getResults | 0.792 | 0.011 | 5.308 | |
| getSampleFilesSummary | 0.504 | 0.008 | 1.602 | |
| getTSS | 0.000 | 0.001 | 0.000 | |
| gliomaClassifier | 0.000 | 0.001 | 0.001 | |
| isServeOK | 0.018 | 0.001 | 0.173 | |
| matchedMetExp | 1.589 | 0.024 | 5.644 | |