| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:56 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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 2112/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.30.0 (landing page) Tiago Chedraoui Silva
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 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: 2.30.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TCGAbiolinks_2.30.0.tar.gz |
| StartedAt: 2024-03-03 23:53:45 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-04 00:02:49 -0500 (Mon, 04 Mar 2024) |
| EllapsedTime: 543.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TCGAbiolinks_2.30.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.30.0’
* 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 startup messages can be suppressed ... 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
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 10.698 0.532 11.294
getManifest 9.655 0.248 90.419
GDCquery 1.581 0.051 9.050
GDCprepare_clinic 1.227 0.136 26.982
matchedMetExp 1.057 0.040 9.228
getResults 0.703 0.024 6.338
* 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-3.18-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 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
48.710 2.561 51.553
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
| name | user | system | elapsed | |
| GDCdownload | 0.000 | 0.001 | 0.001 | |
| GDCprepare | 0.000 | 0.000 | 0.001 | |
| GDCprepare_clinic | 1.227 | 0.136 | 26.982 | |
| GDCquery | 1.581 | 0.051 | 9.050 | |
| GDCquery_ATAC_seq | 0.346 | 0.030 | 3.884 | |
| GDCquery_clinic | 0.835 | 0.052 | 3.630 | |
| PanCancerAtlas_subtypes | 0.015 | 0.002 | 0.018 | |
| TCGAVisualize_volcano | 0.338 | 0.017 | 0.359 | |
| TCGA_MolecularSubtype | 0.424 | 0.008 | 0.434 | |
| TCGAanalyze_DEA | 10.698 | 0.532 | 11.294 | |
| TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
| TCGAanalyze_DMC | 1.074 | 0.070 | 1.151 | |
| TCGAanalyze_EA | 0 | 0 | 0 | |
| TCGAanalyze_EAcomplete | 2.978 | 0.090 | 3.087 | |
| TCGAanalyze_Filtering | 4.557 | 0.108 | 4.691 | |
| TCGAanalyze_LevelTab | 4.603 | 0.178 | 4.810 | |
| TCGAanalyze_Normalization | 1.695 | 0.041 | 1.745 | |
| TCGAanalyze_Pathview | 0 | 0 | 0 | |
| TCGAanalyze_Stemness | 3.018 | 0.131 | 3.170 | |
| TCGAanalyze_SurvivalKM | 0.165 | 0.009 | 0.175 | |
| TCGAanalyze_survival | 2.838 | 0.135 | 2.997 | |
| TCGAprepare_Affy | 0 | 0 | 0 | |
| TCGAquery_MatchedCoupledSampleTypes | 0.002 | 0.001 | 0.003 | |
| TCGAquery_SampleTypes | 0.001 | 0.000 | 0.001 | |
| TCGAquery_recount2 | 0 | 0 | 0 | |
| TCGAquery_subtype | 0.005 | 0.001 | 0.006 | |
| TCGAtumor_purity | 0.053 | 0.000 | 0.053 | |
| TCGAvisualize_EAbarplot | 2.475 | 0.092 | 2.584 | |
| TCGAvisualize_Heatmap | 1.958 | 0.115 | 2.082 | |
| TCGAvisualize_PCA | 1.989 | 0.034 | 2.033 | |
| TCGAvisualize_meanMethylation | 3.075 | 0.057 | 3.151 | |
| TCGAvisualize_oncoprint | 0.000 | 0.001 | 0.002 | |
| TCGAvisualize_starburst | 0.001 | 0.001 | 0.001 | |
| UseRaw_afterFilter | 0.000 | 0.001 | 0.000 | |
| colDataPrepare | 0.142 | 0.007 | 0.758 | |
| dmc.non.parametric | 0.150 | 0.031 | 0.182 | |
| dmc.non.parametric.se | 0.181 | 0.013 | 0.194 | |
| gaiaCNVplot | 0.028 | 0.002 | 0.031 | |
| getAdjacencyBiogrid | 0.002 | 0.001 | 0.002 | |
| getDataCategorySummary | 1.144 | 0.022 | 3.067 | |
| getGDCInfo | 0.017 | 0.002 | 0.132 | |
| getGDCprojects | 0.018 | 0.003 | 0.119 | |
| getLinkedOmicsData | 0 | 0 | 0 | |
| getMC3MAF | 0 | 0 | 0 | |
| getManifest | 9.655 | 0.248 | 90.419 | |
| getNbCases | 0.000 | 0.000 | 0.001 | |
| getNbFiles | 0.000 | 0.001 | 0.000 | |
| getProjectSummary | 0.039 | 0.004 | 0.295 | |
| getResults | 0.703 | 0.024 | 6.338 | |
| getSampleFilesSummary | 0.540 | 0.044 | 2.147 | |
| getTSS | 0.000 | 0.001 | 0.001 | |
| gliomaClassifier | 0 | 0 | 0 | |
| isServeOK | 0.022 | 0.001 | 0.141 | |
| matchedMetExp | 1.057 | 0.040 | 9.228 | |