| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-03 11:38:01 -0400 (Fri, 03 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
| 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 | ||||
| Package 2071/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.33.0 (landing page) Tiago Chedraoui Silva
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK |  | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK |  | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the TCGAbiolinks package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: TCGAbiolinks |
| Version: 2.33.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TCGAbiolinks.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.33.0.tar.gz |
| StartedAt: 2024-05-02 05:39:19 -0400 (Thu, 02 May 2024) |
| EndedAt: 2024-05-02 05:48:48 -0400 (Thu, 02 May 2024) |
| EllapsedTime: 569.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TCGAbiolinks.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/TCGAbiolinks.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TCGAbiolinks/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TCGAbiolinks' version '2.33.0'
* 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 whether package 'TCGAbiolinks' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
R 1.6Mb
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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'dnet'
* checking S3 generic/method consistency ... WARNING
print:
function(x, ...)
print.header:
function(text, type)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* 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'
GDCquery_clinic : <anonymous>: no visible global function definition
for 'across'
GDCquery_clinic : <anonymous>: no visible global function definition
for 'everything'
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'
readExonQuantification: no visible binding for global variable 'exon'
readExonQuantification: no visible binding for global variable
'coordinates'
readSingleCellAnalysis : <anonymous>: no visible global function
definition for 'Read10X'
read_gene_expression_quantification : <anonymous>: no visible binding
for '<<-' assignment to 'assay.list'
read_gene_expression_quantification: no visible binding for global
variable 'assay.list'
Undefined global functions or variables:
Read10X Tumor.purity across assay.list barcode bcr_patient_barcode
clinical coordinates days_to_last_followup everything exon geFDR2
gene_name is_ffpe logFC meFDR2 rse_gene sample_submitter_id
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
TCGAanalyze_DEA 12.29 0.58 12.89
getManifest 11.17 0.26 106.81
TCGAanalyze_LevelTab 8.06 0.15 8.22
GDCquery 1.89 0.07 10.90
GDCprepare_clinic 1.02 0.17 30.13
matchedMetExp 1.14 0.03 10.17
getResults 0.78 0.04 6.94
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc/meat/TCGAbiolinks.Rcheck/00check.log'
for details.
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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 0 | SKIP 24 | PASS 32 ]
══ Skipped tests (24) ══════════════════════════════════════════════════════════
• On Bioconductor (24): 'test-prepare-download.R:4:5',
'test-prepare-download.R:49:5', 'test-prepare-download.R:92:5',
'test-prepare-download.R:102:5', 'test-prepare-download.R:124:5',
'test-prepare-download.R:145:5', 'test-prepare-download.R:164:5',
'test-prepare-download.R:183:5', 'test-prepare-download.R:199:5',
'test-prepare-download.R:209:5', 'test-prepare-download.R:221:5',
'test-prepare-download.R:246:5', 'test-prepare-download.R:286:5',
'test-prepare-download.R:316:5', 'test-prepare-download.R:347:5',
'test-prepare-download.R:381:5', 'test-query-clinical.R:13:5',
'test-query-clinical.R:69:5', 'test-query.R:5:5', 'test-query.R:15:5',
'test-query.R:44:5', 'test-query.R:86:5', 'test-query.R:127:5',
'test-query.R:147:5'
[ FAIL 0 | WARN 0 | SKIP 24 | PASS 32 ]
>
> proc.time()
user system elapsed
52.32 2.40 54.71
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
| name | user | system | elapsed | |
| GDCdownload | 0 | 0 | 0 | |
| GDCprepare | 0 | 0 | 0 | |
| GDCprepare_clinic | 1.02 | 0.17 | 30.13 | |
| GDCquery | 1.89 | 0.07 | 10.90 | |
| GDCquery_ATAC_seq | 0.36 | 0.04 | 1.24 | |
| GDCquery_clinic | 0.61 | 0.02 | 2.58 | |
| PanCancerAtlas_subtypes | 0.02 | 0.00 | 0.01 | |
| TCGAVisualize_volcano | 0.35 | 0.01 | 0.74 | |
| TCGA_MolecularSubtype | 0.40 | 0.00 | 0.39 | |
| TCGAanalyze_DEA | 12.29 | 0.58 | 12.89 | |
| TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
| TCGAanalyze_DMC | 1.30 | 0.16 | 1.45 | |
| TCGAanalyze_EA | 0 | 0 | 0 | |
| TCGAanalyze_EAcomplete | 3.58 | 0.14 | 3.72 | |
| TCGAanalyze_Filtering | 3.98 | 0.08 | 4.06 | |
| TCGAanalyze_LevelTab | 8.06 | 0.15 | 8.22 | |
| TCGAanalyze_Normalization | 1.39 | 0.10 | 1.48 | |
| TCGAanalyze_Pathview | 0.02 | 0.00 | 0.00 | |
| TCGAanalyze_Stemness | 1.73 | 0.00 | 1.73 | |
| TCGAanalyze_SurvivalKM | 0.14 | 0.00 | 0.14 | |
| TCGAanalyze_survival | 3.02 | 0.09 | 3.29 | |
| TCGAprepare_Affy | 0 | 0 | 0 | |
| TCGAquery_MatchedCoupledSampleTypes | 0 | 0 | 0 | |
| TCGAquery_SampleTypes | 0 | 0 | 0 | |
| TCGAquery_recount2 | 0 | 0 | 0 | |
| TCGAquery_subtype | 0.01 | 0.00 | 0.02 | |
| TCGAtumor_purity | 0.06 | 0.00 | 0.06 | |
| TCGAvisualize_EAbarplot | 4.38 | 0.06 | 4.44 | |
| TCGAvisualize_Heatmap | 2.20 | 0.78 | 2.00 | |
| TCGAvisualize_PCA | 2.24 | 0.04 | 2.27 | |
| TCGAvisualize_meanMethylation | 3.55 | 0.12 | 3.67 | |
| TCGAvisualize_oncoprint | 0 | 0 | 0 | |
| TCGAvisualize_starburst | 0 | 0 | 0 | |
| UseRaw_afterFilter | 0 | 0 | 0 | |
| colDataPrepare | 0.12 | 0.00 | 0.77 | |
| dmc.non.parametric | 0.15 | 0.03 | 0.17 | |
| dmc.non.parametric.se | 0.23 | 0.02 | 0.25 | |
| gaiaCNVplot | 0.05 | 0.00 | 0.05 | |
| geneInfoHT | 0 | 0 | 0 | |
| getAdjacencyBiogrid | 0 | 0 | 0 | |
| getDataCategorySummary | 1.14 | 0.03 | 2.42 | |
| getGDCInfo | 0.00 | 0.00 | 0.12 | |
| getGDCprojects | 0.03 | 0.00 | 0.13 | |
| getLinkedOmicsData | 0 | 0 | 0 | |
| getMC3MAF | 0 | 0 | 0 | |
| getManifest | 11.17 | 0.26 | 106.81 | |
| getNbCases | 0 | 0 | 0 | |
| getNbFiles | 0 | 0 | 0 | |
| getProjectSummary | 0.05 | 0.00 | 0.27 | |
| getResults | 0.78 | 0.04 | 6.94 | |
| getSampleFilesSummary | 0.44 | 0.07 | 1.40 | |
| getTSS | 0 | 0 | 0 | |
| gliomaClassifier | 0 | 0 | 0 | |
| isServeOK | 0.00 | 0.00 | 0.12 | |
| matchedMetExp | 1.14 | 0.03 | 10.17 | |