############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAbiolinks.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.20.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/TCGAbiolinks.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '2.20.1' * 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 ... NOTE Found the following non-portable file paths: TCGAbiolinks/vignettes/GDCdata/TCGA-ACC/harmonized/Clinical/Clinical_Supplement/4612e74a-f374-459a-a14f-8cecdb1c14f8/nationwidechildrens.org_clinical_radiation_acc.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/22656b71-476a-4b5f-9f3b-82afb29a34bc/nationwidechildrens.org_biospecimen_portion_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/41fd4c6c-2932-4c6b-914f-7abaea9dc8a0/nationwidechildrens.org_ssf_tumor_samples_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/43569ab9-5a32-45ef-a07e-e93f45416a16/nationwidechildrens.org_biospecimen_shipment_portion_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/5907be67-69f6-4339-8264-952a2462bea5/nationwidechildrens.org_ssf_normal_controls_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/950ee56c-df20-4b39-867e-c73f17d0f4f6/nationwidechildrens.org_biospecimen_aliquot_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/a24d7574-e419-47ce-9293-b9b29f854a10/nationwidechildrens.org_biospecimen_protocol_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/c10090b8-fa42-4e32-86a0-9dedceb5b605/nationwidechildrens.org_biospecimen_slide_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/c5039e7e-14d8-4e59-ba20-0d3fa38b86df/nationwidechildrens.org_biospecimen_sample_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/d0c967b5-78ee-4bc4-9493-3cbe44af1bf5/nationwidechildrens.org_biospecimen_analyte_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/edbb5de2-d0b5-4a07-a0e1-19e952a5117d/nationwidechildrens.org_biospecimen_diagnostic_slides_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/0a40467f-9495-4c5b-b56e-3347a3ee0572/nationwidechildrens.org_clinical_radiation_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/1e6b79ff-9787-4cbe-b19d-ebabb6b43589/nationwidechildrens.org_clinical_drug_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/22f38342-3f1a-47e5-9025-c19719fa21d0/nationwidechildrens.org_clinical_follow_up_v1.5_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/403b5cef-8173-47c7-b56a-cc94dcfbb2e3/nationwidechildrens.org_clinical_follow_up_v2.1_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/62d4515f-a30b-4b1a-b2dd-c8bf9476e803/nationwidechildrens.org_clinical_follow_up_v4.0_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/8162d394-8b64-4da2-9f5b-d164c54b9608/nationwidechildrens.org_clinical_patient_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/a88c168e-4bba-4bd2-9c0c-77934444cc1c/nationwidechildrens.org_clinical_nte_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/a9baecf0-5549-4396-8805-a6d1681d11cd/nationwidechildrens.org_clinical_follow_up_v4.0_nte_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/f434b393-9e32-4ca2-aa1a-3b0de36b5ffe/nationwidechildrens.org_clinical_omf_v4.0_brca.txt TCGAbiolinks/vignettes/GDCdata/TCGA-ACC/harmonized/Clinical/Clinical_Supplement/4612e74a-f374-459a-a14f-8cecdb1c14f8 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/22656b71-476a-4b5f-9f3b-82afb29a34bc TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/41fd4c6c-2932-4c6b-914f-7abaea9dc8a0 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/43569ab9-5a32-45ef-a07e-e93f45416a16 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/5907be67-69f6-4339-8264-952a2462bea5 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/950ee56c-df20-4b39-867e-c73f17d0f4f6 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/a24d7574-e419-47ce-9293-b9b29f854a10 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/c10090b8-fa42-4e32-86a0-9dedceb5b605 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/c5039e7e-14d8-4e59-ba20-0d3fa38b86df TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/d0c967b5-78ee-4bc4-9493-3cbe44af1bf5 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Biospecimen/Biospecimen_Supplement/edbb5de2-d0b5-4a07-a0e1-19e952a5117d TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/0a40467f-9495-4c5b-b56e-3347a3ee0572 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/1e6b79ff-9787-4cbe-b19d-ebabb6b43589 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/22f38342-3f1a-47e5-9025-c19719fa21d0 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/403b5cef-8173-47c7-b56a-cc94dcfbb2e3 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/62d4515f-a30b-4b1a-b2dd-c8bf9476e803 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/8162d394-8b64-4da2-9f5b-d164c54b9608 TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/a88c168e-4bba-4bd2-9c0c-77934444cc1c TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/a9baecf0-5549-4396-8805-a6d1681d11cd TCGAbiolinks/vignettes/GDCdata/TCGA-BRCA/harmonized/Clinical/Clinical_Supplement/f434b393-9e32-4ca2-aa1a-3b0de36b5ffe Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section 'Package structure' in the 'Writing R Extensions' manual. * checking whether package 'TCGAbiolinks' can be installed ... OK * checking installed package size ... NOTE installed size is 6.1Mb 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 ... WARNING '::' or ':::' import not declared from: 'sesameData' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GDCquery : : no visible binding for global variable 'submitter_id' GDCquery : : 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 : : 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 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed TCGAanalyze_LevelTab 16.91 0.58 17.49 GDCquery_clinic 14.29 0.67 31.05 TCGAanalyze_DEA 14.39 0.31 14.71 TCGAanalyze_Filtering 11.45 0.25 11.70 TCGAvisualize_PCA 5.48 0.17 5.65 TCGAanalyze_Normalization 5.36 0.03 5.39 TCGAanalyze_Stemness 5.27 0.00 5.26 GDCdownload 3.39 0.08 35.90 GDCprepare_clinic 2.58 0.78 49.04 getDataCategorySummary 1.83 0.00 6.16 getResults 0.63 0.01 5.69 getManifest 0.59 0.00 7.29 matchedMetExp 0.56 0.02 5.75 GDCquery 0.55 0.01 5.75 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed TCGAanalyze_LevelTab 17.23 0.03 17.26 GDCquery_clinic 16.51 0.20 33.13 TCGAanalyze_DEA 14.12 0.22 14.35 TCGAanalyze_Filtering 13.22 0.00 13.24 TCGAanalyze_Normalization 7.27 0.00 7.27 TCGAanalyze_Stemness 6.61 0.00 6.61 TCGAvisualize_PCA 6.57 0.00 6.56 GDCdownload 3.20 0.11 34.59 GDCprepare_clinic 2.42 0.23 65.15 getDataCategorySummary 1.77 0.00 5.85 getManifest 0.61 0.01 7.43 getResults 0.59 0.00 6.57 matchedMetExp 0.54 0.02 5.72 GDCquery 0.50 0.00 5.75 * 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: 1 WARNING, 3 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/TCGAbiolinks.Rcheck/00check.log' for details.