| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:45 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 2044/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.29.4 (landing page) Tiago Chedraoui Silva
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: TCGAbiolinks |
| Version: 2.29.4 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings TCGAbiolinks_2.29.4.tar.gz |
| StartedAt: 2023-05-30 21:08:48 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 21:29:36 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 1247.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings TCGAbiolinks_2.29.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.29.4’
* 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 loading without being on the library search path ... 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 14.240 0.752 14.993
getManifest 12.499 1.036 96.221
TCGAanalyze_LevelTab 7.420 0.220 7.642
GDCprepare_clinic 3.026 0.347 38.950
matchedMetExp 2.926 0.192 30.036
GDCquery_clinic 2.118 0.203 18.183
getResults 1.630 0.120 16.086
getDataCategorySummary 1.566 0.164 7.306
GDCquery 1.443 0.196 14.093
GDCquery_ATAC_seq 0.986 0.089 5.034
getSampleFilesSummary 0.836 0.044 7.800
* 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
‘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 ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 0 | SKIP 19 | PASS 32 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (19)
[ FAIL 0 | WARN 0 | SKIP 19 | PASS 32 ]
>
> proc.time()
user system elapsed
56.662 1.478 58.129
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
| name | user | system | elapsed | |
| GDCdownload | 0 | 0 | 0 | |
| GDCprepare | 0 | 0 | 0 | |
| GDCprepare_clinic | 3.026 | 0.347 | 38.950 | |
| GDCquery | 1.443 | 0.196 | 14.093 | |
| GDCquery_ATAC_seq | 0.986 | 0.089 | 5.034 | |
| GDCquery_clinic | 2.118 | 0.203 | 18.183 | |
| PanCancerAtlas_subtypes | 0.007 | 0.012 | 0.019 | |
| TCGAVisualize_volcano | 0.409 | 0.060 | 0.468 | |
| TCGA_MolecularSubtype | 0.477 | 0.040 | 0.517 | |
| TCGAanalyze_DEA | 14.240 | 0.752 | 14.993 | |
| TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
| TCGAanalyze_DMC | 1.269 | 0.040 | 1.309 | |
| TCGAanalyze_EA | 0 | 0 | 0 | |
| TCGAanalyze_EAcomplete | 3.272 | 0.160 | 3.432 | |
| TCGAanalyze_Filtering | 4.009 | 0.052 | 4.062 | |
| TCGAanalyze_LevelTab | 7.420 | 0.220 | 7.642 | |
| TCGAanalyze_Normalization | 2.859 | 0.096 | 2.955 | |
| TCGAanalyze_Pathview | 0 | 0 | 0 | |
| TCGAanalyze_Stemness | 2.065 | 0.096 | 2.160 | |
| TCGAanalyze_SurvivalKM | 0.189 | 0.023 | 0.212 | |
| TCGAanalyze_survival | 3.701 | 0.244 | 3.945 | |
| TCGAprepare_Affy | 0 | 0 | 0 | |
| TCGAquery_MatchedCoupledSampleTypes | 0.000 | 0.003 | 0.003 | |
| TCGAquery_SampleTypes | 0.001 | 0.000 | 0.001 | |
| TCGAquery_recount2 | 0 | 0 | 0 | |
| TCGAquery_subtype | 0.009 | 0.000 | 0.008 | |
| TCGAtumor_purity | 0.08 | 0.00 | 0.08 | |
| TCGAvisualize_EAbarplot | 3.212 | 0.108 | 3.320 | |
| TCGAvisualize_Heatmap | 2.592 | 0.092 | 2.685 | |
| TCGAvisualize_PCA | 2.072 | 0.052 | 2.124 | |
| TCGAvisualize_meanMethylation | 3.847 | 0.100 | 3.947 | |
| TCGAvisualize_oncoprint | 0 | 0 | 0 | |
| TCGAvisualize_starburst | 0 | 0 | 0 | |
| UseRaw_afterFilter | 0.001 | 0.000 | 0.000 | |
| colDataPrepare | 0.461 | 0.008 | 3.315 | |
| dmc.non.parametric | 0.146 | 0.016 | 0.162 | |
| dmc.non.parametric.se | 0.241 | 0.012 | 0.253 | |
| gaiaCNVplot | 0.036 | 0.004 | 0.041 | |
| getAdjacencyBiogrid | 0.002 | 0.000 | 0.002 | |
| getDataCategorySummary | 1.566 | 0.164 | 7.306 | |
| getGDCInfo | 0.157 | 0.004 | 1.233 | |
| getGDCprojects | 0.181 | 0.008 | 1.167 | |
| getLinkedOmicsData | 0 | 0 | 0 | |
| getMC3MAF | 0 | 0 | 0 | |
| getManifest | 12.499 | 1.036 | 96.221 | |
| getNbCases | 0 | 0 | 0 | |
| getNbFiles | 0.001 | 0.000 | 0.000 | |
| getProjectSummary | 0.335 | 0.015 | 2.283 | |
| getResults | 1.630 | 0.120 | 16.086 | |
| getSampleFilesSummary | 0.836 | 0.044 | 7.800 | |
| getTSS | 0 | 0 | 0 | |
| gliomaClassifier | 0.000 | 0.000 | 0.001 | |
| isServeOK | 0.151 | 0.004 | 1.213 | |
| matchedMetExp | 2.926 | 0.192 | 30.036 | |