| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:21 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2027/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.26.0 (landing page) Tiago Chedraoui Silva
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK |  | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: TCGAbiolinks |
| Version: 2.26.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TCGAbiolinks_2.26.0.tar.gz |
| StartedAt: 2023-04-11 00:29:59 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 01:09:59 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 2400.0 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TCGAbiolinks_2.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.26.0’
* package encoding: UTF-8
* 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 6.4Mb
sub-directories of 1Mb or more:
R 1.6Mb
data 4.5Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' call not declared from: ‘dplyr’
'library' or 'require' calls in package code:
‘dplyr’ ‘maftools’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GDCprepare_clinic: no visible binding for global variable
‘bcr_patient_barcode’
GDCprepare_clinic: no visible binding for global variable
‘days_to_last_followup’
GDCprepare_clinic: no visible binding for global variable
‘vital_status’
GDCquery : <anonymous>: no visible binding for global variable
‘submitter_id’
GDCquery : <anonymous>: no visible binding for global variable
‘is_ffpe’
GDCquery_clinic : <anonymous>: no visible binding for global variable
‘submitter_id’
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 binding for global variable
‘gene_name’
TCGAvisualize_starburst: no visible binding for global variable
‘geFDR2’
TCGAvisualize_starburst: no visible binding for global variable ‘logFC’
TCGAvisualize_starburst: no visible binding for global variable
‘meFDR2’
TCGAvisualize_starburst: no visible binding for global variable
‘threshold.starburst’
TCGAvisualize_starburst: no visible binding for global variable
‘starburst.status’
colDataPrepare: no visible binding for global variable
‘sample_submitter_id’
colDataPrepare: no visible binding for global variable ‘submitter_id’
colDataPrepare: no visible binding for global variable ‘sample_type’
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’
readSingleCellAnalysis : <anonymous>: no visible global function
definition for ‘Read10X’
Undefined global functions or variables:
Read10X Tumor.purity assay.list barcode bcr_patient_barcode clinical
coordinates days_to_last_followup exon geFDR2 gene_name is_ffpe logFC
meFDR2 rse_gene sample_submitter_id sample_type starburst.status
submitter_id threshold.starburst value vital_status
* 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
GDCquery_clinic 685.271 6.921 723.523
getManifest 11.952 1.465 82.849
TCGAanalyze_DEA 9.977 0.180 10.158
TCGAanalyze_LevelTab 5.503 0.016 5.519
GDCdownload 2.449 0.206 34.803
GDCprepare_clinic 2.374 0.109 56.458
matchedMetExp 0.813 0.080 5.608
getResults 0.657 0.052 5.748
GDCquery 0.543 0.004 5.724
* 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 ...
‘analysis.Rmd’ using ‘UTF-8’... OK
‘casestudy.Rmd’ using ‘UTF-8’... OK
‘classifiers.Rmd’ using ‘UTF-8’... OK
‘clinical.Rmd’ using ‘UTF-8’... OK
‘download_prepare.Rmd’ using ‘UTF-8’... OK
‘extension.Rmd’ using ‘UTF-8’... OK
‘gui.Rmd’ using ‘UTF-8’... OK
‘index.Rmd’ using ‘UTF-8’... OK
‘mutation.Rmd’ using ‘UTF-8’... OK
‘query.Rmd’ using ‘UTF-8’... OK
‘stemness_score.Rmd’ using ‘UTF-8’... OK
‘subtypes.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ...
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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")
| | 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"
[ FAIL 0 | WARN 901 | SKIP 22 | PASS 45 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (22)
[ FAIL 0 | WARN 901 | SKIP 22 | PASS 45 ]
>
> proc.time()
user system elapsed
146.965 5.552 159.761
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
| name | user | system | elapsed | |
| GDCdownload | 2.449 | 0.206 | 34.803 | |
| GDCprepare | 0 | 0 | 0 | |
| GDCprepare_clinic | 2.374 | 0.109 | 56.458 | |
| GDCquery | 0.543 | 0.004 | 5.724 | |
| GDCquery_ATAC_seq | 0.329 | 0.029 | 0.754 | |
| GDCquery_clinic | 685.271 | 6.921 | 723.523 | |
| PanCancerAtlas_subtypes | 0.015 | 0.000 | 0.014 | |
| TCGAVisualize_volcano | 0.494 | 0.004 | 0.498 | |
| TCGA_MolecularSubtype | 0.274 | 0.000 | 0.274 | |
| TCGAanalyze_DEA | 9.977 | 0.180 | 10.158 | |
| TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
| TCGAanalyze_DMC | 0.950 | 0.024 | 0.975 | |
| TCGAanalyze_EA | 0 | 0 | 0 | |
| TCGAanalyze_EAcomplete | 2.27 | 0.08 | 2.35 | |
| TCGAanalyze_Filtering | 3.203 | 0.007 | 3.210 | |
| TCGAanalyze_LevelTab | 5.503 | 0.016 | 5.519 | |
| TCGAanalyze_Normalization | 1.607 | 0.000 | 1.606 | |
| TCGAanalyze_Pathview | 0.001 | 0.000 | 0.000 | |
| TCGAanalyze_Stemness | 1.731 | 0.004 | 1.735 | |
| TCGAanalyze_SurvivalKM | 0.1 | 0.0 | 0.1 | |
| TCGAanalyze_survival | 2.734 | 0.060 | 2.794 | |
| TCGAprepare_Affy | 0 | 0 | 0 | |
| TCGAquery_MatchedCoupledSampleTypes | 0.002 | 0.000 | 0.002 | |
| TCGAquery_SampleTypes | 0.001 | 0.000 | 0.001 | |
| TCGAquery_recount2 | 0.000 | 0.000 | 0.001 | |
| TCGAquery_subtype | 0.007 | 0.000 | 0.007 | |
| TCGAtumor_purity | 0.06 | 0.00 | 0.06 | |
| TCGAvisualize_EAbarplot | 2.171 | 0.008 | 2.179 | |
| TCGAvisualize_Heatmap | 1.766 | 0.004 | 1.770 | |
| TCGAvisualize_PCA | 1.981 | 0.012 | 1.992 | |
| TCGAvisualize_meanMethylation | 2.881 | 0.004 | 2.885 | |
| TCGAvisualize_oncoprint | 0 | 0 | 0 | |
| TCGAvisualize_starburst | 0.001 | 0.000 | 0.001 | |
| UseRaw_afterFilter | 0 | 0 | 0 | |
| colDataPrepare | 0.138 | 0.004 | 0.828 | |
| dmc.non.parametric | 0.090 | 0.008 | 0.097 | |
| dmc.non.parametric.se | 0.193 | 0.000 | 0.193 | |
| gaiaCNVplot | 0.043 | 0.000 | 0.043 | |
| getAdjacencyBiogrid | 0.002 | 0.000 | 0.002 | |
| getDataCategorySummary | 1.155 | 0.016 | 4.611 | |
| getGDCInfo | 0.024 | 0.012 | 0.154 | |
| getGDCprojects | 0.057 | 0.024 | 0.193 | |
| getLinkedOmicsData | 0.001 | 0.000 | 0.001 | |
| getMC3MAF | 0 | 0 | 0 | |
| getManifest | 11.952 | 1.465 | 82.849 | |
| getNbCases | 0 | 0 | 0 | |
| getNbFiles | 0 | 0 | 0 | |
| getProjectSummary | 0.071 | 0.005 | 0.326 | |
| getResults | 0.657 | 0.052 | 5.748 | |
| getSampleFilesSummary | 0.535 | 0.096 | 2.093 | |
| getTSS | 0 | 0 | 0 | |
| gliomaClassifier | 0 | 0 | 0 | |
| isServeOK | 0.026 | 0.000 | 0.158 | |
| matchedMetExp | 0.813 | 0.080 | 5.608 | |