| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:37 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 2076/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.28.4 (landing page) Tiago Chedraoui Silva
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / 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: 2.28.4 |
| 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_2.28.4.tar.gz |
| StartedAt: 2023-10-16 07:56:47 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 08:13:22 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 995.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_2.28.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.28.4’
* 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
getManifest 20.608 0.388 100.051
TCGAanalyze_DEA 17.432 0.471 23.769
TCGAanalyze_LevelTab 8.425 0.129 11.202
TCGAanalyze_Filtering 6.613 0.087 9.493
TCGAvisualize_meanMethylation 6.295 0.087 8.447
TCGAanalyze_survival 6.023 0.171 8.113
TCGAanalyze_EAcomplete 5.316 0.105 7.158
TCGAvisualize_EAbarplot 5.177 0.106 6.931
TCGAvisualize_Heatmap 4.581 0.127 6.188
getResults 2.522 0.050 8.964
GDCprepare_clinic 2.234 0.221 27.687
matchedMetExp 1.940 0.070 11.050
GDCquery_clinic 1.716 0.052 5.402
GDCquery 1.480 0.124 7.980
GDCquery_ATAC_seq 0.657 0.042 7.489
* 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-3.17-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
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
77.535 2.985 105.901
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
| name | user | system | elapsed | |
| GDCdownload | 0.000 | 0.001 | 0.002 | |
| GDCprepare | 0.000 | 0.000 | 0.001 | |
| GDCprepare_clinic | 2.234 | 0.221 | 27.687 | |
| GDCquery | 1.480 | 0.124 | 7.980 | |
| GDCquery_ATAC_seq | 0.657 | 0.042 | 7.489 | |
| GDCquery_clinic | 1.716 | 0.052 | 5.402 | |
| PanCancerAtlas_subtypes | 0.025 | 0.004 | 0.037 | |
| TCGAVisualize_volcano | 0.645 | 0.020 | 0.852 | |
| TCGA_MolecularSubtype | 1.011 | 0.015 | 1.355 | |
| TCGAanalyze_DEA | 17.432 | 0.471 | 23.769 | |
| TCGAanalyze_DEA_Affy | 0.000 | 0.001 | 0.000 | |
| TCGAanalyze_DMC | 2.148 | 0.199 | 3.176 | |
| TCGAanalyze_EA | 0.001 | 0.000 | 0.000 | |
| TCGAanalyze_EAcomplete | 5.316 | 0.105 | 7.158 | |
| TCGAanalyze_Filtering | 6.613 | 0.087 | 9.493 | |
| TCGAanalyze_LevelTab | 8.425 | 0.129 | 11.202 | |
| TCGAanalyze_Normalization | 2.467 | 0.030 | 3.296 | |
| TCGAanalyze_Pathview | 0.000 | 0.000 | 0.001 | |
| TCGAanalyze_Stemness | 2.798 | 0.052 | 3.768 | |
| TCGAanalyze_SurvivalKM | 0.307 | 0.013 | 0.424 | |
| TCGAanalyze_survival | 6.023 | 0.171 | 8.113 | |
| TCGAprepare_Affy | 0 | 0 | 0 | |
| TCGAquery_MatchedCoupledSampleTypes | 0.004 | 0.000 | 0.005 | |
| TCGAquery_SampleTypes | 0.002 | 0.001 | 0.003 | |
| TCGAquery_recount2 | 0.001 | 0.000 | 0.000 | |
| TCGAquery_subtype | 0.012 | 0.001 | 0.015 | |
| TCGAtumor_purity | 0.115 | 0.001 | 0.156 | |
| TCGAvisualize_EAbarplot | 5.177 | 0.106 | 6.931 | |
| TCGAvisualize_Heatmap | 4.581 | 0.127 | 6.188 | |
| TCGAvisualize_PCA | 3.081 | 0.036 | 4.076 | |
| TCGAvisualize_meanMethylation | 6.295 | 0.087 | 8.447 | |
| TCGAvisualize_oncoprint | 0.000 | 0.002 | 0.002 | |
| TCGAvisualize_starburst | 0.000 | 0.002 | 0.008 | |
| UseRaw_afterFilter | 0.001 | 0.000 | 0.000 | |
| colDataPrepare | 0.242 | 0.008 | 0.891 | |
| dmc.non.parametric | 0.278 | 0.065 | 0.448 | |
| dmc.non.parametric.se | 0.372 | 0.033 | 0.538 | |
| gaiaCNVplot | 0.068 | 0.003 | 0.091 | |
| getAdjacencyBiogrid | 0.003 | 0.001 | 0.004 | |
| getDataCategorySummary | 2.388 | 0.024 | 4.799 | |
| getGDCInfo | 0.032 | 0.003 | 0.256 | |
| getGDCprojects | 0.044 | 0.014 | 0.157 | |
| getLinkedOmicsData | 0.000 | 0.001 | 0.001 | |
| getMC3MAF | 0.000 | 0.000 | 0.001 | |
| getManifest | 20.608 | 0.388 | 100.051 | |
| getNbCases | 0.001 | 0.000 | 0.001 | |
| getNbFiles | 0.000 | 0.001 | 0.001 | |
| getProjectSummary | 0.075 | 0.018 | 0.545 | |
| getResults | 2.522 | 0.050 | 8.964 | |
| getSampleFilesSummary | 0.837 | 0.035 | 2.363 | |
| getTSS | 0.000 | 0.001 | 0.000 | |
| gliomaClassifier | 0.000 | 0.001 | 0.001 | |
| isServeOK | 0.029 | 0.003 | 0.517 | |
| matchedMetExp | 1.94 | 0.07 | 11.05 | |