Tiago Chedraoui Silva
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/TCGAbiolinks |
| Branch: RELEASE_3_12 |
| Last Commit: df6b579 |
| Last Changed Date: 2020-10-27 11:07:19 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:37:08 -0400 (Thu, 06 May 2021).
|
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 1842/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.18.0 (landing page) Tiago Chedraoui Silva
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: TCGAbiolinks |
| Version: 2.18.0 |
| 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_2.18.0.tar.gz |
| StartedAt: 2021-05-06 06:47:57 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:57:53 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 596.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_2.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.18.0’
* 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 6.7Mb
sub-directories of 1Mb or more:
R 2.4Mb
data 4.0Mb
* 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 : <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’
getMetPlatInfo: no visible global function definition for
‘sesameDataCacheAll’
getMetPlatInfo: no visible global function definition for
‘sesameDataGet’
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 coordinates exon is_ffpe
rse_gene sesameDataCacheAll sesameDataGet 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 20.214 0.325 36.034
TCGAanalyze_LevelTab 17.522 1.375 18.915
TCGAanalyze_DEA 13.324 0.224 13.567
GDCdownload 9.995 0.481 38.921
TCGAanalyze_Filtering 9.859 0.084 9.955
TCGAvisualize_PCA 5.645 0.058 5.709
GDCprepare_clinic 2.786 0.116 42.379
GDCquery 0.584 0.014 5.209
getManifest 0.573 0.010 5.044
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.12-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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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"
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (21)
[ FAIL 0 | WARN 4 | SKIP 21 | PASS 45 ]
>
> proc.time()
user system elapsed
59.816 1.880 68.534
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
| name | user | system | elapsed | |
| GDCdownload | 9.995 | 0.481 | 38.921 | |
| GDCprepare | 0.001 | 0.000 | 0.000 | |
| GDCprepare_clinic | 2.786 | 0.116 | 42.379 | |
| GDCquery | 0.584 | 0.014 | 5.209 | |
| GDCquery_ATAC_seq | 3.208 | 0.267 | 4.087 | |
| GDCquery_Maf | 0.001 | 0.000 | 0.000 | |
| GDCquery_clinic | 20.214 | 0.325 | 36.034 | |
| PanCancerAtlas_subtypes | 0.018 | 0.002 | 0.020 | |
| TCGAVisualize_volcano | 0.331 | 0.007 | 0.338 | |
| TCGA_MolecularSubtype | 0.646 | 0.003 | 0.650 | |
| TCGAanalyze_DEA | 13.324 | 0.224 | 13.567 | |
| TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
| TCGAanalyze_DMC | 1.457 | 0.064 | 1.522 | |
| TCGAanalyze_EA | 0.000 | 0.001 | 0.001 | |
| TCGAanalyze_EAcomplete | 3.616 | 0.094 | 3.718 | |
| TCGAanalyze_Filtering | 9.859 | 0.084 | 9.955 | |
| TCGAanalyze_LevelTab | 17.522 | 1.375 | 18.915 | |
| TCGAanalyze_Normalization | 4.666 | 0.054 | 4.725 | |
| TCGAanalyze_Pathview | 0.001 | 0.000 | 0.000 | |
| TCGAanalyze_Stemness | 4.787 | 0.056 | 4.879 | |
| TCGAanalyze_SurvivalKM | 0.170 | 0.006 | 0.176 | |
| TCGAanalyze_survival | 3.585 | 0.118 | 3.715 | |
| TCGAprepare_Affy | 0 | 0 | 0 | |
| TCGAquery_MatchedCoupledSampleTypes | 0.003 | 0.001 | 0.004 | |
| TCGAquery_SampleTypes | 0.001 | 0.000 | 0.001 | |
| TCGAquery_recount2 | 0 | 0 | 0 | |
| TCGAquery_subtype | 0.012 | 0.001 | 0.013 | |
| TCGAtumor_purity | 0.146 | 0.001 | 0.147 | |
| TCGAvisualize_EAbarplot | 3.307 | 0.075 | 3.385 | |
| TCGAvisualize_Heatmap | 2.691 | 0.079 | 2.772 | |
| TCGAvisualize_PCA | 5.645 | 0.058 | 5.709 | |
| TCGAvisualize_meanMethylation | 3.337 | 0.058 | 3.404 | |
| TCGAvisualize_oncoprint | 0.001 | 0.001 | 0.002 | |
| TCGAvisualize_starburst | 0.000 | 0.001 | 0.002 | |
| UseRaw_afterFilter | 0.000 | 0.001 | 0.001 | |
| colDataPrepare | 0.178 | 0.005 | 0.626 | |
| dmc.non.parametric | 0.224 | 0.042 | 0.267 | |
| dmc.non.parametric.se | 0.303 | 0.016 | 0.319 | |
| gaiaCNVplot | 0.044 | 0.002 | 0.046 | |
| getAdjacencyBiogrid | 0.001 | 0.000 | 0.002 | |
| getDataCategorySummary | 1.809 | 0.019 | 4.964 | |
| getGDCInfo | 0.017 | 0.001 | 0.172 | |
| getGDCprojects | 0.029 | 0.001 | 0.164 | |
| getLinkedOmicsData | 0.001 | 0.000 | 0.000 | |
| getMC3MAF | 0.000 | 0.001 | 0.000 | |
| getManifest | 0.573 | 0.010 | 5.044 | |
| getNbCases | 0 | 0 | 0 | |
| getNbFiles | 0 | 0 | 0 | |
| getProjectSummary | 0.000 | 0.001 | 0.001 | |
| getResults | 0.664 | 0.012 | 4.920 | |
| getSampleFilesSummary | 0.479 | 0.007 | 1.429 | |
| getTSS | 0.001 | 0.000 | 0.000 | |
| gliomaClassifier | 0.000 | 0.000 | 0.001 | |
| isServeOK | 0.017 | 0.001 | 0.170 | |
| matchedMetExp | 0.578 | 0.017 | 4.509 | |