############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GenomicFeatures_1.46.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GenomicFeatures.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK * this is package ‘GenomicFeatures’ version ‘1.46.5’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'AnnotationDbi' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GenomicFeatures’ can be installed ... OK * checking installed package size ... OK * 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 ... NOTE ':::' call which should be '::': ‘rtracklayer:::tableNames’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’ ‘rtracklayer:::resourceDescription’ 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘GenomicFeatures-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: makeTxDbFromBiomart > ### Title: Make a TxDb object from annotations available on a BioMart > ### database > ### Aliases: makeTxDbFromBiomart getChromInfoFromBiomart > > ### ** Examples > > ## --------------------------------------------------------------------- > ## A. BASIC USAGE > ## --------------------------------------------------------------------- > > ## We can use listDatasets() from the biomaRt package to list the > ## datasets available in the "ENSEMBL_MART_ENSEMBL" BioMart database: > library(biomaRt) > listMarts(host="www.ensembl.org") Warning: Ensembl will soon enforce the use of https. Ensure the 'host' argument includes "https://" biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 106 2 ENSEMBL_MART_MOUSE Mouse strains 106 3 ENSEMBL_MART_SNP Ensembl Variation 106 4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 106 > mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org") Warning: Ensembl will soon enforce the use of https. Ensure the 'host' argument includes "https://" Ensembl site unresponsive, trying uswest mirror > datasets <- listDatasets(mart) > head(datasets) dataset description 1 abrachyrhynchus_gene_ensembl Pink-footed goose genes (ASM259213v1) 2 acalliptera_gene_ensembl Eastern happy genes (fAstCal1.2) 3 acarolinensis_gene_ensembl Green anole genes (AnoCar2.0v2) 4 acchrysaetos_gene_ensembl Golden eagle genes (bAquChr1.2) 5 acitrinellus_gene_ensembl Midas cichlid genes (Midas_v5) 6 amelanoleuca_gene_ensembl Giant panda genes (ASM200744v2) version 1 ASM259213v1 2 fAstCal1.2 3 AnoCar2.0v2 4 bAquChr1.2 5 Midas_v5 6 ASM200744v2 > subset(datasets, grepl("elegans", dataset, ignore.case=TRUE)) dataset description 29 celegans_gene_ensembl Caenorhabditis elegans (PRJNA13758) genes (WBcel235) version 29 WBcel235 > > ## Retrieve the full transcript dataset for Worm: > txdb1 <- makeTxDbFromBiomart(dataset="celegans_gene_ensembl") Warning: Ensembl will soon enforce the use of https. Ensure the 'host' argument includes "https://" Ensembl site unresponsive, trying asia mirror Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... Ensembl site unresponsive, trying uswest mirror FAILED! (=> skipped) Download and preprocess the 'splicings' data frame ... OK Download and preprocess the 'genes' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... Warning in .infer_chrominfo_from_transcripts_and_splicings(transcripts$tx_chrom, : chromosome lengths and circularity flags are not available for this TxDb object OK > txdb1 TxDb object: # Db type: TxDb # Supporting package: GenomicFeatures # Data source: BioMart # Organism: Caenorhabditis elegans # Taxonomy ID: 6239 # Resource URL: www.ensembl.org:80 # BioMart database: ENSEMBL_MART_ENSEMBL # BioMart database version: Ensembl Genes 105 # BioMart dataset: celegans_gene_ensembl # BioMart dataset description: Caenorhabditis elegans genes (WBcel235) # BioMart dataset version: WBcel235 # Full dataset: yes # miRBase build ID: NA # Nb of transcripts: 59897 # Db created by: GenomicFeatures package from Bioconductor # Creation time: 2022-04-12 07:47:12 -0400 (Tue, 12 Apr 2022) # GenomicFeatures version at creation time: 1.46.5 # RSQLite version at creation time: 2.2.12 # DBSCHEMAVERSION: 1.2 > > ## Retrieve an incomplete transcript dataset for Human: > transcript_ids <- c( + "ENST00000013894", + "ENST00000268655", + "ENST00000313243", + "ENST00000435657", + "ENST00000384428", + "ENST00000478783" + ) > > if (interactive()) { + txdb2 <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl", + transcript_ids=transcript_ids) + txdb2 # note that these annotations match the GRCh38 genome assembly + } > > ## --------------------------------------------------------------------- > ## B. ACCESSING THE EnsemblGenomes MARTS > ## --------------------------------------------------------------------- > > library(biomaRt) > > ## Note that BioMart is not currently available for Ensembl Bacteria. > > ## --------------------- > ## --- Ensembl Fungi --- > > mart <- useMart(biomart="fungi_mart", host="fungi.ensembl.org") Warning: Ensembl will soon enforce the use of https. Ensure the 'host' argument includes "https://" > datasets <- listDatasets(mart) > datasets$dataset [1] "aastaci_eg_gene" "aclavatus_eg_gene" [3] "aflavus_eg_gene" "afumigatus_eg_gene" [5] "afumigatusa1163_eg_gene" "agossypii_eg_gene" [7] "ainvadans_eg_gene" "anidulans_eg_gene" [9] "aniger_eg_gene" "aoryzae_eg_gene" [11] "aterreus_eg_gene" "bbassiana_eg_gene" [13] "bcinerea_eg_gene" "bgraminis_eg_gene" [15] "calbicans_eg_gene" "cauris_eg_gene" [17] "cduobushaemulonis_eg_gene" "cglabrata_eg_gene" [19] "cgloeosporioides_eg_gene" "cgraminicola_eg_gene" [21] "chaemuloni_eg_gene" "chigginsianum_eg_gene" [23] "cneoformans_eg_gene" "corbiculare_eg_gene" [25] "cparapsilosis_eg_gene" "cpseudohaemulonis_eg_gene" [27] "ctropicalis_eg_gene" "dseptosporum_eg_gene" [29] "fculmorum_eg_gene" "ffujikuroi_eg_gene" [31] "fgraminearum_eg_gene" "foxysporum_eg_gene" [33] "fpseudograminearum_eg_gene" "fsolani_eg_gene" [35] "fverticillioides_eg_gene" "ggraminis_eg_gene" [37] "gultimum_eg_gene" "harabidopsidis_eg_gene" [39] "hcapsulatum_eg_gene" "kpastoris_eg_gene" [41] "lmaculans_eg_gene" "mlaricipopulina_eg_gene" [43] "moryzae_eg_gene" "mpoae_eg_gene" [45] "mviolaceum_eg_gene" "ncrassa_eg_gene" [47] "nfischeri_eg_gene" "pchrysosporium_eg_gene" [49] "pgraminis_eg_gene" "pgraminisug99_eg_gene" [51] "pnodorum_eg_gene" "poryzae_eg_gene" [53] "pstriiformis_eg_gene" "pteres_eg_gene" [55] "ptriticina_eg_gene" "ptriticirepentis_eg_gene" [57] "scerevisiae_eg_gene" "scryophilus_eg_gene" [59] "sjaponicus_eg_gene" "soctosporus_eg_gene" [61] "spombe_eg_gene" "sreilianum_eg_gene" [63] "ssclerotiorum_eg_gene" "tmelanosporum_eg_gene" [65] "treesei_eg_gene" "tvirens_eg_gene" [67] "umaydis_eg_gene" "vdahliae_eg_gene" [69] "vdahliaejr2_eg_gene" "ylipolytica_eg_gene" [71] "ztritici_eg_gene" > yeast_txdb <- makeTxDbFromBiomart(biomart="fungi_mart", + dataset="scerevisiae_eg_gene", + host="fungi.ensembl.org") Warning: Ensembl will soon enforce the use of https. Ensure the 'host' argument includes "https://" Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... OK Download and preprocess the 'splicings' data frame ... OK Download and preprocess the 'genes' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK > yeast_txdb TxDb object: # Db type: TxDb # Supporting package: GenomicFeatures # Data source: BioMart # Organism: Saccharomyces cerevisiae # Taxonomy ID: 4932 # Resource URL: fungi.ensembl.org:80 # BioMart database: fungi_mart # BioMart database version: Ensembl Fungi Genes 53 # BioMart dataset: scerevisiae_eg_gene # BioMart dataset description: Saccharomyces cerevisiae genes (R64-1-1) # BioMart dataset version: R64-1-1 # Full dataset: yes # miRBase build ID: NA # Nb of transcripts: 7127 # Db created by: GenomicFeatures package from Bioconductor # Creation time: 2022-04-12 07:47:33 -0400 (Tue, 12 Apr 2022) # GenomicFeatures version at creation time: 1.46.5 # RSQLite version at creation time: 2.2.12 # DBSCHEMAVERSION: 1.2 > > ## Note that the dataset for Yeast on Ensembl Fungi is not necessarily > ## the same as on the main Ensembl database: > yeast_txdb0 <- makeTxDbFromBiomart(dataset="scerevisiae_gene_ensembl") Warning: Ensembl will soon enforce the use of https. Ensure the 'host' argument includes "https://" Ensembl site unresponsive, trying uswest mirror Ensembl site unresponsive, trying asia mirror Ensembl site unresponsive, trying useast mirror Error in curl::curl_fetch_memory(url, handle = handle) : SSL certificate problem: unable to get local issuer certificate Calls: makeTxDbFromBiomart ... request_fetch -> request_fetch.write_memory -> Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ ERROR Running the tests in ‘tests/run_unitTests.R’ failed. Last 13 lines of output: In addition: Warning messages: 1: In .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type exon. This information was ignored. 2: In .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. 3: In .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. 4: In (function (seqlevels, genome, new_style) : cannot switch some of hg19's seqlevels from UCSC to NCBI style 5: In (function (seqlevels, genome, new_style) : cannot switch some of hg19's seqlevels from UCSC to NCBI style Execution halted * 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 ERRORs, 3 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/GenomicFeatures.Rcheck/00check.log’ for details.