Tiago Chedraoui Silva
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/TCGAbiolinks |
| Branch: RELEASE_3_12 |
| Last Commit: df6b579 |
| Last Changed Date: 2020-10-27 11:07:19 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:55 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the TCGAbiolinks package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1842/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.18.0 (landing page) Tiago Chedraoui Silva
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: TCGAbiolinks |
| Version: 2.18.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAbiolinks.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.18.0.tar.gz |
| StartedAt: 2021-05-06 07:28:25 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 07:44:53 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 987.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAbiolinks.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/TCGAbiolinks.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '2.18.0'
* 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 6.0Mb
sub-directories of 1Mb or more:
R 1.6Mb
data 3.6Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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'
getMetPlatInfo: no visible global function definition for
'sesameDataCacheAll'
getMetPlatInfo: no visible global function definition for
'sesameDataGet'
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'
Undefined global functions or variables:
Tumor.purity assay.list barcode clinical coordinates exon is_ffpe
rse_gene sesameDataCacheAll sesameDataGet 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
TCGAanalyze_LevelTab 22.01 0.00 22.01
GDCquery_clinic 19.70 1.17 36.05
TCGAanalyze_DEA 17.08 0.45 17.53
TCGAanalyze_Filtering 14.28 0.06 14.35
TCGAvisualize_PCA 8.39 0.00 8.39
TCGAanalyze_Stemness 7.67 0.00 7.68
TCGAanalyze_Normalization 6.54 0.00 6.53
GDCdownload 3.75 0.03 31.14
GDCprepare_clinic 2.98 0.16 43.40
getDataCategorySummary 2.06 0.01 5.54
getManifest 0.48 0.00 5.32
GDCquery 0.45 0.00 5.64
matchedMetExp 0.39 0.02 5.43
getResults 0.37 0.00 5.41
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GDCquery_clinic 19.54 0.19 35.27
TCGAanalyze_LevelTab 19.39 0.02 19.41
TCGAanalyze_DEA 17.89 0.16 18.04
TCGAanalyze_Filtering 14.15 0.03 14.19
TCGAvisualize_PCA 6.30 0.00 6.30
TCGAanalyze_Stemness 5.78 0.00 5.78
TCGAanalyze_Normalization 5.74 0.00 5.73
GDCdownload 5.08 0.15 33.23
GDCprepare_clinic 2.56 0.07 43.20
getDataCategorySummary 2.39 0.03 5.47
getResults 0.71 0.03 5.15
getManifest 0.57 0.00 5.18
matchedMetExp 0.57 0.00 5.30
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/TCGAbiolinks.Rcheck/00check.log'
for details.
TCGAbiolinks.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/TCGAbiolinks_2.18.0.tar.gz && rm -rf TCGAbiolinks.buildbin-libdir && mkdir TCGAbiolinks.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAbiolinks.buildbin-libdir TCGAbiolinks_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL TCGAbiolinks_2.18.0.zip && rm TCGAbiolinks_2.18.0.tar.gz TCGAbiolinks_2.18.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 6490k 100 6490k 0 0 78.9M 0 --:--:-- --:--:-- --:--:-- 80.2M
install for i386
* 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
install for x64
* installing *source* package 'TCGAbiolinks' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCGAbiolinks' as TCGAbiolinks_2.18.0.zip
* DONE (TCGAbiolinks)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'TCGAbiolinks' successfully unpacked and MD5 sums checked
|
TCGAbiolinks.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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"
== Skipped tests ===============================================================
* On Bioconductor (21)
[ FAIL 0 | WARN 4 | SKIP 21 | PASS 45 ]
>
> proc.time()
user system elapsed
66.45 4.20 77.48
|
TCGAbiolinks.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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"
== Skipped tests ===============================================================
* On Bioconductor (21)
[ FAIL 0 | WARN 4 | SKIP 21 | PASS 45 ]
>
> proc.time()
user system elapsed
73.64 1.53 84.93
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TCGAbiolinks.Rcheck/examples_i386/TCGAbiolinks-Ex.timings
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TCGAbiolinks.Rcheck/examples_x64/TCGAbiolinks-Ex.timings
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