| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:55 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the TCGAbiolinks package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TCGAbiolinks.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1899/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.20.1 (landing page) Tiago Chedraoui Silva
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: TCGAbiolinks |
| Version: 2.20.1 |
| 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_2.20.1.tar.gz |
| StartedAt: 2021-10-15 00:37:07 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 00:47:27 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 619.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: 1 |
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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_2.20.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.20.1’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 : <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 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 LazyData ... 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
TCGAanalyze_LevelTab 18.665 2.134 20.810
GDCquery_clinic 19.552 0.336 37.488
TCGAanalyze_DEA 13.692 0.278 13.982
TCGAanalyze_Filtering 10.229 0.106 10.341
TCGAvisualize_PCA 6.080 0.082 6.167
TCGAanalyze_Stemness 5.274 0.046 5.327
TCGAanalyze_Normalization 4.988 0.038 5.029
GDCdownload 4.434 0.199 39.519
GDCprepare_clinic 3.050 0.137 51.248
getDataCategorySummary 1.978 0.029 5.344
GDCquery 0.848 0.019 6.079
getManifest 0.831 0.011 7.134
getResults 0.735 0.011 5.951
matchedMetExp 0.676 0.019 5.778
* 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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.13-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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
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
62.731 2.126 70.628
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
| name | user | system | elapsed | |
| GDCdownload | 4.434 | 0.199 | 39.519 | |
| GDCprepare | 0.001 | 0.001 | 0.001 | |
| GDCprepare_clinic | 3.050 | 0.137 | 51.248 | |
| GDCquery | 0.848 | 0.019 | 6.079 | |
| GDCquery_ATAC_seq | 0.597 | 0.025 | 1.397 | |
| GDCquery_Maf | 0.000 | 0.000 | 0.001 | |
| GDCquery_clinic | 19.552 | 0.336 | 37.488 | |
| PanCancerAtlas_subtypes | 0.022 | 0.002 | 0.024 | |
| TCGAVisualize_volcano | 0.357 | 0.011 | 0.369 | |
| TCGA_MolecularSubtype | 0.533 | 0.003 | 0.535 | |
| TCGAanalyze_DEA | 13.692 | 0.278 | 13.982 | |
| TCGAanalyze_DEA_Affy | 0.000 | 0.000 | 0.001 | |
| TCGAanalyze_DMC | 1.542 | 0.065 | 1.652 | |
| TCGAanalyze_EA | 0.000 | 0.001 | 0.001 | |
| TCGAanalyze_EAcomplete | 3.629 | 0.076 | 3.707 | |
| TCGAanalyze_Filtering | 10.229 | 0.106 | 10.341 | |
| TCGAanalyze_LevelTab | 18.665 | 2.134 | 20.810 | |
| TCGAanalyze_Normalization | 4.988 | 0.038 | 5.029 | |
| TCGAanalyze_Pathview | 0.000 | 0.000 | 0.001 | |
| TCGAanalyze_Stemness | 5.274 | 0.046 | 5.327 | |
| TCGAanalyze_SurvivalKM | 0.178 | 0.008 | 0.187 | |
| TCGAanalyze_survival | 3.883 | 0.149 | 4.040 | |
| TCGAprepare_Affy | 0.000 | 0.000 | 0.001 | |
| TCGAquery_MatchedCoupledSampleTypes | 0.003 | 0.000 | 0.004 | |
| TCGAquery_SampleTypes | 0.002 | 0.001 | 0.002 | |
| TCGAquery_recount2 | 0 | 0 | 0 | |
| TCGAquery_subtype | 0.009 | 0.001 | 0.009 | |
| TCGAtumor_purity | 0.09 | 0.00 | 0.09 | |
| TCGAvisualize_EAbarplot | 3.771 | 0.087 | 3.862 | |
| TCGAvisualize_Heatmap | 3.094 | 0.062 | 3.160 | |
| TCGAvisualize_PCA | 6.080 | 0.082 | 6.167 | |
| TCGAvisualize_meanMethylation | 3.288 | 0.048 | 3.343 | |
| TCGAvisualize_oncoprint | 0.000 | 0.001 | 0.001 | |
| TCGAvisualize_starburst | 0.000 | 0.002 | 0.002 | |
| UseRaw_afterFilter | 0.000 | 0.001 | 0.001 | |
| colDataPrepare | 0.187 | 0.005 | 0.785 | |
| dmc.non.parametric | 0.196 | 0.040 | 0.237 | |
| dmc.non.parametric.se | 0.326 | 0.016 | 0.342 | |
| gaiaCNVplot | 0.039 | 0.002 | 0.041 | |
| getAdjacencyBiogrid | 0.002 | 0.001 | 0.003 | |
| getDataCategorySummary | 1.978 | 0.029 | 5.344 | |
| getGDCInfo | 0.025 | 0.002 | 0.246 | |
| getGDCprojects | 0.038 | 0.002 | 0.221 | |
| getLinkedOmicsData | 0 | 0 | 0 | |
| getMC3MAF | 0 | 0 | 0 | |
| getManifest | 0.831 | 0.011 | 7.134 | |
| getNbCases | 0 | 0 | 0 | |
| getNbFiles | 0 | 0 | 0 | |
| getProjectSummary | 0 | 0 | 0 | |
| getResults | 0.735 | 0.011 | 5.951 | |
| getSampleFilesSummary | 0.447 | 0.008 | 1.707 | |
| getTSS | 0 | 0 | 0 | |
| gliomaClassifier | 0.000 | 0.001 | 0.000 | |
| isServeOK | 0.025 | 0.002 | 0.251 | |
| matchedMetExp | 0.676 | 0.019 | 5.778 | |