| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:50 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1942/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.23.5 (landing page) Tiago Chedraoui Silva
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: TCGAbiolinks |
| Version: 2.23.5 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TCGAbiolinks.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.23.5.tar.gz |
| StartedAt: 2022-03-17 20:27:20 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:35:24 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 483.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TCGAbiolinks.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.23.5.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/TCGAbiolinks.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TCGAbiolinks/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TCGAbiolinks' version '2.23.5'
* 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 5.9Mb
sub-directories of 1Mb or more:
R 1.6Mb
data 3.4Mb
* 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 dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
'Seurat' 'SeuratDisk' 'sesameData'
':::' call which should be '::': 'stringr:::str_split'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GDCquery : <anonymous>: no visible binding for global variable
'submitter_id'
GDCquery : <anonymous>: no visible binding for global variable
'is_ffpe'
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 global function definition for
'values'
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 clinical coordinates exon
is_ffpe rse_gene submitter_id value values
* 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 15.43 0.19 35.36
TCGAanalyze_DEA 13.08 0.25 13.33
TCGAanalyze_Filtering 10.19 0.10 10.30
TCGAanalyze_LevelTab 7.91 0.16 8.06
TCGAvisualize_PCA 5.18 0.03 5.21
GDCdownload 2.55 0.23 33.00
GDCprepare_clinic 1.75 0.13 41.36
getDataCategorySummary 1.15 0.02 5.90
GDCquery 0.46 0.00 5.32
getResults 0.38 0.01 5.97
matchedMetExp 0.39 0.00 5.58
getManifest 0.37 0.00 6.44
* 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: 1 WARNING, 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/TCGAbiolinks.Rcheck/00check.log'
for details.
TCGAbiolinks.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL TCGAbiolinks
###
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* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'TCGAbiolinks'
finding HTML links ... done
BRCA_rnaseqv2 html
GDCdownload html
GDCprepare html
GDCprepare_clinic html
GDCquery html
GDCquery_ATAC_seq html
GDCquery_Maf html
GDCquery_clinic html
GeneSplitRegulon html
GenesCutID html
PCBC_stemSig html
PanCancerAtlas_subtypes html
TCGAVisualize_volcano html
TCGA_MolecularSubtype html
TCGAanalyze_Clustering html
TCGAanalyze_DEA html
TCGAanalyze_DEA_Affy html
TCGAanalyze_DMC html
TCGAanalyze_EA html
TCGAanalyze_EAcomplete html
TCGAanalyze_Filtering html
TCGAanalyze_LevelTab html
TCGAanalyze_Normalization html
TCGAanalyze_Pathview html
TCGAanalyze_Preprocessing html
TCGAanalyze_Stemness html
TCGAanalyze_SurvivalKM html
TCGAanalyze_analyseGRN html
TCGAanalyze_networkInference html
TCGAanalyze_survival html
TCGAbatch_Correction html
TCGAbiolinks html
TCGAprepare_Affy html
TCGAquery_MatchedCoupledSampleTypes html
TCGAquery_SampleTypes html
TCGAquery_recount2 html
TCGAquery_subtype html
TCGAtumor_purity html
TCGAvisualize_BarPlot html
TCGAvisualize_EAbarplot html
TCGAvisualize_Heatmap html
TCGAvisualize_PCA html
TCGAvisualize_SurvivalCoxNET html
TCGAvisualize_meanMethylation html
TCGAvisualize_oncoprint html
TCGAvisualize_starburst html
TabSubtypesCol_merged html
Tumor.purity html
UseRaw_afterFilter html
batch.info html
bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf
html
chol_maf html
classification html
clinBRCA html
clinical.biotab html
colDataPrepare html
dataBRCA html
dataDEGsFiltLevel html
dataREAD html
dataREAD_df html
dmc.non.parametric html
dmc.non.parametric.se html
gaiaCNVplot html
gbm.exp.harmonized html
gbm.exp.legacy html
geneInfo html
geneInfoHT html
get.GRCh.bioMart html
getAdjacencyBiogrid html
getDataCategorySummary html
getGDCInfo html
getGDCprojects html
getGistic html
getLinkedOmicsData html
getMC3MAF html
getManifest html
getNbCases html
getNbFiles html
getProjectSummary html
getResults html
getSampleFilesSummary html
getTSS html
get_IDs html
ggbiplot html
gliomaClassifier html
isServeOK html
matchedMetExp html
met.gbm.27k html
msi_results html
pancan2018 html
splitAPICall html
tabSurvKMcompleteDEGs html
** 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)
Making 'packages.html' ... done
TCGAbiolinks.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 4 | SKIP 22 | PASS 45 ]
== Skipped tests ===============================================================
* On Bioconductor (22)
[ FAIL 0 | WARN 4 | SKIP 22 | PASS 45 ]
>
> proc.time()
user system elapsed
51.89 3.34 66.56
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
| name | user | system | elapsed | |
| GDCdownload | 2.55 | 0.23 | 33.00 | |
| GDCprepare | 0 | 0 | 0 | |
| GDCprepare_clinic | 1.75 | 0.13 | 41.36 | |
| GDCquery | 0.46 | 0.00 | 5.32 | |
| GDCquery_ATAC_seq | 0.34 | 0.03 | 1.14 | |
| GDCquery_Maf | 0 | 0 | 0 | |
| GDCquery_clinic | 15.43 | 0.19 | 35.36 | |
| PanCancerAtlas_subtypes | 0.02 | 0.01 | 0.03 | |
| TCGAVisualize_volcano | 0.42 | 0.02 | 0.44 | |
| TCGA_MolecularSubtype | 0.2 | 0.0 | 0.2 | |
| TCGAanalyze_DEA | 13.08 | 0.25 | 13.33 | |
| TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
| TCGAanalyze_DMC | 0.88 | 0.01 | 0.89 | |
| TCGAanalyze_EA | 0 | 0 | 0 | |
| TCGAanalyze_EAcomplete | 2.18 | 0.04 | 2.22 | |
| TCGAanalyze_Filtering | 10.19 | 0.10 | 10.30 | |
| TCGAanalyze_LevelTab | 7.91 | 0.16 | 8.06 | |
| TCGAanalyze_Normalization | 4.51 | 0.06 | 4.58 | |
| TCGAanalyze_Pathview | 0 | 0 | 0 | |
| TCGAanalyze_Stemness | 4.64 | 0.08 | 4.72 | |
| TCGAanalyze_SurvivalKM | 0.08 | 0.00 | 0.08 | |
| TCGAanalyze_survival | 1.96 | 0.05 | 2.00 | |
| TCGAprepare_Affy | 0 | 0 | 0 | |
| TCGAquery_MatchedCoupledSampleTypes | 0 | 0 | 0 | |
| TCGAquery_SampleTypes | 0 | 0 | 0 | |
| TCGAquery_recount2 | 0 | 0 | 0 | |
| TCGAquery_subtype | 0 | 0 | 0 | |
| TCGAtumor_purity | 0.06 | 0.00 | 0.06 | |
| TCGAvisualize_EAbarplot | 2.33 | 0.05 | 2.37 | |
| TCGAvisualize_Heatmap | 1.86 | 0.09 | 1.96 | |
| TCGAvisualize_PCA | 5.18 | 0.03 | 5.21 | |
| TCGAvisualize_meanMethylation | 2.46 | 0.02 | 2.58 | |
| TCGAvisualize_oncoprint | 0.01 | 0.00 | 0.02 | |
| TCGAvisualize_starburst | 0 | 0 | 0 | |
| UseRaw_afterFilter | 0 | 0 | 0 | |
| colDataPrepare | 0.10 | 0.01 | 1.28 | |
| dmc.non.parametric | 0.17 | 0.00 | 4.33 | |
| dmc.non.parametric.se | 0.17 | 0.00 | 3.67 | |
| gaiaCNVplot | 0.05 | 0.00 | 0.05 | |
| getAdjacencyBiogrid | 0 | 0 | 0 | |
| getDataCategorySummary | 1.15 | 0.02 | 5.90 | |
| getGDCInfo | 0.00 | 0.00 | 0.24 | |
| getGDCprojects | 0.05 | 0.00 | 0.20 | |
| getLinkedOmicsData | 0 | 0 | 0 | |
| getMC3MAF | 0 | 0 | 0 | |
| getManifest | 0.37 | 0.00 | 6.44 | |
| getNbCases | 0 | 0 | 0 | |
| getNbFiles | 0 | 0 | 0 | |
| getProjectSummary | 0 | 0 | 0 | |
| getResults | 0.38 | 0.01 | 5.97 | |
| getSampleFilesSummary | 0.31 | 0.00 | 1.64 | |
| getTSS | 0 | 0 | 0 | |
| gliomaClassifier | 0 | 0 | 0 | |
| isServeOK | 0.00 | 0.00 | 0.23 | |
| matchedMetExp | 0.39 | 0.00 | 5.58 | |