Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:33:51 -0400 (Wed, 16 Oct 2019).
Package 1631/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
TCGAbiolinks 2.12.6 Antonio Colaprico
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: TCGAbiolinks |
Version: 2.12.6 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAbiolinks.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.12.6.tar.gz |
StartedAt: 2019-10-16 07:30:35 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 08:04:10 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 2015.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TCGAbiolinks.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAbiolinks.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.12.6.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/TCGAbiolinks.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '2.12.6' * 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 3.6Mb * 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 ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: 'move' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GDCquery_clinic: no visible binding for global variable 'portions' TCGAanalyze_DEA: no visible binding for global variable 'barcode' TCGAanalyze_DEA: no visible binding for global variable 'clinical' TCGAanalyze_DEA_Affy: no visible global function definition for 'limmamakeContrasts' TCGAanalyze_DEA_Affy: no visible global function definition for 'limmacontrasts.fit' TCGAanalyze_analyseGRN: no visible global function definition for 'knnmi.cross' TCGAanalyze_networkInference: no visible global function definition for 'c3net' TCGAanalyze_networkInference: no visible global function definition for 'minet' TCGAquery_recount2: no visible binding for global variable 'rse_gene' TCGAtumor_purity: no visible binding for global variable 'Tumor.purity' TCGAvisualize_SurvivalCoxNET: no visible global function definition for 'dNetInduce' TCGAvisualize_SurvivalCoxNET: no visible global function definition for 'dNetPipeline' TCGAvisualize_SurvivalCoxNET: no visible global function definition for 'dCommSignif' TCGAvisualize_SurvivalCoxNET: no visible global function definition for 'visNet' TCGAvisualize_oncoprint: no visible binding for global variable 'value' readExonQuantification: no visible binding for global variable 'exon' readExonQuantification: no visible binding for global variable 'coordinates' readIDATDNAmethylation: no visible global function definition for 'openSesame' Undefined global functions or variables: Tumor.purity barcode c3net clinical coordinates dCommSignif dNetInduce dNetPipeline exon knnmi.cross limmacontrasts.fit limmamakeContrasts minet openSesame portions rse_gene value visNet * 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 or elapsed time > 5s user system elapsed TCGAanalyze_DMR 21.42 0.49 21.91 TCGAanalyze_LevelTab 20.25 0.02 20.26 TCGAanalyze_DEA 14.10 0.34 14.44 TCGAanalyze_Filtering 10.90 0.00 10.91 GDCprepare_clinic 10.36 0.31 57.76 GDCdownload 6.06 0.18 40.44 TCGAvisualize_PCA 5.37 0.01 5.39 TCGAanalyze_Stemness 5.36 0.00 5.36 TCGAanalyze_Normalization 5.10 0.00 5.10 getSampleFilesSummary 3.47 0.09 8.57 getManifest 3.32 0.01 7.65 GDCquery 2.69 0.00 7.21 matchedMetExp 2.59 0.02 7.68 getResults 2.40 0.02 6.30 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed TCGAanalyze_DMR 34.78 0.11 35.66 TCGAanalyze_LevelTab 20.77 0.10 20.95 TCGAanalyze_DEA 14.78 0.06 16.18 TCGAanalyze_Filtering 13.18 0.00 13.19 GDCprepare_clinic 11.78 0.17 60.86 TCGAvisualize_PCA 6.18 0.00 6.17 TCGAanalyze_Stemness 5.45 0.00 5.46 TCGAanalyze_Normalization 5.42 0.00 5.42 GDCdownload 4.87 0.13 38.39 matchedMetExp 3.44 0.04 9.23 getManifest 3.35 0.00 8.37 getSampleFilesSummary 3.02 0.06 8.28 GDCquery 2.95 0.03 7.45 getResults 2.97 0.00 8.69 getDataCategorySummary 2.20 0.06 6.42 * 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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/TCGAbiolinks.Rcheck/00check.log' for details.
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/TCGAbiolinks_2.12.6.tar.gz && rm -rf TCGAbiolinks.buildbin-libdir && mkdir TCGAbiolinks.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAbiolinks.buildbin-libdir TCGAbiolinks_2.12.6.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL TCGAbiolinks_2.12.6.zip && rm TCGAbiolinks_2.12.6.tar.gz TCGAbiolinks_2.12.6.zip ### ############################################################################## ############################################################################## % 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 6477k 100 6477k 0 0 43.8M 0 --:--:-- --:--:-- --:--:-- 45.8M 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_DMR 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 calculate.pvalues html chol_maf html clinBRCA html clinical.biotab html colDataPrepare html dataBRCA html dataDEGsFiltLevel html dataREAD html dataREAD_df html diffmean 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 getManifest html getResults html getSampleFilesSummary html getTSS html get_IDs html ggbiplot html isServeOK html matchedMetExp html met.gbm.27k html msi_results html pancan2018 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_2.12.6.zip * DONE (TCGAbiolinks) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'TCGAbiolinks' successfully unpacked and MD5 sums checked
TCGAbiolinks.Rcheck/tests_i386/testthat.Rout R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |== | 3% | |==== | 6% | |======= | 9% | |========= | 13% | |============= | 19% | |================== | 26% | |======================= | 32% | |============================= | 41% | |=============================== | 45% | |============================================= | 64% | |=============================================== | 67% | |============================================================= | 87% | |=============================================================== | 90% | |======================================================================| 100% | | 0% |====================================================|100% ~0 s remaining |====================================================|100% Completed after 0 s | | | 0% | |= | 2% | |== | 3% | |==== | 6% | |========= | 13% | |================ | 22% | |================================ | 45% | |================================== | 48% | |==================================== | 51% | |============================================================= | 87% | |==================================================================== | 97% | |======================================================================| 100% | | | 0% | |= | 2% | |== | 3% | |==== | 6% | |======= | 10% | |============================ | 39% | |=================================== | 49% | |===================================== | 53% | |============================================================== | 89% | |=============================================================== | 90% | |==================================================================== | 97% | |======================================================================| 100% | | 0% |================= |33.33333% ~0 s remaining |================================== |66.66667% ~0 s remaining |====================================================|100% ~0 s remaining |====================================================|100% Completed after 1 s | | | 0% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 8% | |====== | 9% | |=========== | 15% | |============= | 19% | |=============== | 21% | |=============== | 22% | |===================== | 30% | |=========================== | 39% | |============================ | 40% | |=================================== | 50% | |========================================= | 59% | |========================================== | 59% | |================================================ | 69% | |======================================================= | 79% | |======================================================== | 79% | |============================================================== | 88% | |============================================================== | 89% | |================================================================= | 93% | |================================================================== | 94% | |======================================================================| 100% |
TCGAbiolinks.Rcheck/tests_x64/testthat.Rout R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |= | 2% | |== | 3% | |==== | 6% | |======= | 10% | |========= | 13% | |=========== | 16% | |============== | 19% | |================ | 23% | |================== | 26% | |==================== | 29% | |========================= | 36% | |======================================= | 55% | |========================================= | 58% | |======================================================================| 100% | | 0% |====================================================|100% ~0 s remaining |====================================================|100% Completed after 0 s | | | 0% | |= | 2% | |=== | 5% | |======== | 11% | |============== | 20% | |======================= | 33% | |=================================== | 50% | |========================================== | 59% | |============================================ | 63% | |===================================================== | 75% | |========================================================= | 82% | |=========================================================== | 85% | |======================================================================| 100% | | | 0% | |= | 2% | |== | 3% | |==== | 6% | |======= | 10% | |=========== | 16% | |================ | 23% | |========================= | 36% | |============================== | 43% | |=================================== | 49% | |===================================== | 53% | |============================================ | 63% | |============================================================ | 86% | |============================================================== | 89% | |======================================================================| 100% | | 0% |================= |33.33333% ~0 s remaining |================================== |66.66667% ~1 s remaining |====================================================|100% ~0 s remaining |====================================================|100% Completed after 2 s | | | 0% | | | 1% | |= | 1% | |== | 2% | |== | 3% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 9% | |======= | 10% | |========= | 12% | |========== | 14% | |============ | 17% | |============== | 19% | |=============== | 21% | |================ | 23% | |================== | 26% | |=================== | 27% | |==================== | 28% | |====================== | 31% | |======================= | 33% | |======================== | 34% | |======================== | 35% | |========================= | 35% | |=========================== | 38% | |============================ | 40% | |============================= | 42% | |=============================== | 44% | |================================ | 45% | |================================= | 47% | |================================== | 49% | |==================================== | 51% | |===================================== | 52% | |===================================== | 53% | |======================================= | 56% | |========================================= | 58% | |========================================== | 60% | |=========================================== | 61% | |============================================ | 63% | |============================================= | 64% | |============================================== | 66% | |================================================ | 69% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 72% | |==================================================== | 74% | |====================================================== | 77% | |======================================================= | 78% | |======================================================== | 80% | |========================================================= | 81% | |========================================================== | 82% | |========================================================== | 83% | |========================================================== | 84% | |=========================================================== | 85% | |============================================================ | 86% | |============================================================= | 87% | |================================================================ | 92% | |================================================================= | 93% | |==================================================================== | 97% | |======================================================================| 100% |
TCGAbiolinks.Rcheck/examples_i386/TCGAbiolinks-Ex.timings
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TCGAbiolinks.Rcheck/examples_x64/TCGAbiolinks-Ex.timings
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