############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:recount3.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings recount3_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/recount3.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘recount3/DESCRIPTION’ ... OK * this is package ‘recount3’ version ‘1.15.0’ * package encoding: UTF-8 * 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 for sufficient/correct file permissions ... OK * checking whether package ‘recount3’ 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 code 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 loading without being on the library search path ... 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 ... 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 ‘recount3-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: create_rse > ### Title: Create a recount3 RangedSummarizedExperiment gene or exon object > ### Aliases: create_rse > > ### ** Examples > > > ## Find all available human projects > human_projects <- available_projects() 2024-10-03 00:41:49.0032 caching file sra.recount_project.MD.gz. 2024-10-03 00:41:49.31123 caching file gtex.recount_project.MD.gz. 2024-10-03 00:41:49.657228 caching file tcga.recount_project.MD.gz. > > ## Find the project you are interested in > proj_info <- subset( + human_projects, + project == "SRP009615" & project_type == "data_sources" + ) > > ## Create a RSE object at the gene level > rse_gene_SRP009615 <- create_rse(proj_info) 2024-10-03 00:41:55.591835 downloading and reading the metadata. 2024-10-03 00:41:55.904537 caching file sra.sra.SRP009615.MD.gz. 2024-10-03 00:41:56.252022 caching file sra.recount_project.SRP009615.MD.gz. 2024-10-03 00:41:56.637174 caching file sra.recount_qc.SRP009615.MD.gz. 2024-10-03 00:41:56.955453 caching file sra.recount_seq_qc.SRP009615.MD.gz. 2024-10-03 00:41:57.256237 caching file sra.recount_pred.SRP009615.MD.gz. 2024-10-03 00:41:57.375685 downloading and reading the feature information. 2024-10-03 00:41:57.639251 caching file human.gene_sums.G026.gtf.gz. 2024-10-03 00:41:58.259706 downloading and reading the counts: 12 samples across 63856 features. 2024-10-03 00:41:58.476765 caching file sra.gene_sums.SRP009615.G026.gz. 2024-10-03 00:41:58.716865 constructing the RangedSummarizedExperiment (rse) object. > > ## Explore the resulting RSE gene object > rse_gene_SRP009615 class: RangedSummarizedExperiment dim: 63856 12 metadata(8): time_created recount3_version ... annotation recount3_url assays(1): raw_counts rownames(63856): ENSG00000278704.1 ENSG00000277400.1 ... ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y rowData names(10): source type ... havana_gene tag colnames(12): SRR387777 SRR387778 ... SRR389077 SRR389078 colData names(175): rail_id external_id ... recount_pred.curated.cell_line BigWigURL > > ## Information about how this RSE object was made > metadata(rse_gene_SRP009615) $time_created [1] "2024-10-03 00:41:58 EDT" $recount3_version package ondiskversion loadedversion recount3 recount3 1.15.0 1.15.0 path recount3 /tmp/Rtmpctxm2j/RLIBS_2244c51da82052/recount3 loadedpath attached is_base recount3 /home/biocbuild/bbs-3.20-bioc/R/site-library/recount3 TRUE FALSE date source md5ok library recount3 2024-10-02 Bioconductor 3.20 (R 4.4.1) NA $project [1] "SRP009615" $project_home [1] "data_sources/sra" $type [1] "gene" $organism [1] "human" $annotation [1] "gencode_v26" $recount3_url [1] "http://duffel.rail.bio/recount3" > > ## Number of genes by number of samples > dim(rse_gene_SRP009615) [1] 63856 12 > > ## Information about the genes > rowRanges(rse_gene_SRP009615) GRanges object with 63856 ranges and 10 metadata columns: seqnames ranges strand | source | ENSG00000278704.1 GL000009.2 56140-58376 - | ENSEMBL ENSG00000277400.1 GL000194.1 53590-115018 - | ENSEMBL ENSG00000274847.1 GL000194.1 53594-115055 - | ENSEMBL ENSG00000277428.1 GL000195.1 37434-37534 - | ENSEMBL ENSG00000276256.1 GL000195.1 42939-49164 - | ENSEMBL ... ... ... ... . ... ENSG00000124334.17_PAR_Y chrY 57184101-57197337 + | HAVANA ENSG00000185203.12_PAR_Y chrY 57201143-57203357 - | HAVANA ENSG00000270726.6_PAR_Y chrY 57190738-57208756 + | HAVANA ENSG00000182484.15_PAR_Y chrY 57207346-57212230 + | HAVANA ENSG00000227159.8_PAR_Y chrY 57212184-57214397 - | HAVANA type bp_length phase gene_id ENSG00000278704.1 gene 2237 ENSG00000278704.1 ENSG00000277400.1 gene 2179 ENSG00000277400.1 ENSG00000274847.1 gene 1599 ENSG00000274847.1 ENSG00000277428.1 gene 101 ENSG00000277428.1 ENSG00000276256.1 gene 2195 ENSG00000276256.1 ... ... ... ... ... ENSG00000124334.17_PAR_Y gene 2504 ENSG00000124334.17_P.. ENSG00000185203.12_PAR_Y gene 1054 ENSG00000185203.12_P.. ENSG00000270726.6_PAR_Y gene 773 ENSG00000270726.6_PA.. ENSG00000182484.15_PAR_Y gene 4618 ENSG00000182484.15_P.. ENSG00000227159.8_PAR_Y gene 1306 ENSG00000227159.8_PA.. gene_type gene_name level ENSG00000278704.1 protein_coding BX004987.1 3 ENSG00000277400.1 protein_coding AC145212.2 3 ENSG00000274847.1 protein_coding AC145212.1 3 ENSG00000277428.1 misc_RNA Y_RNA 3 ENSG00000276256.1 protein_coding AC011043.1 3 ... ... ... ... ENSG00000124334.17_PAR_Y protein_coding IL9R 2 ENSG00000185203.12_PAR_Y antisense WASIR1 2 ENSG00000270726.6_PAR_Y processed_transcript AJ271736.10 2 ENSG00000182484.15_PAR_Y transcribed_unproces.. WASH6P 2 ENSG00000227159.8_PAR_Y unprocessed_pseudogene DDX11L16 2 havana_gene tag ENSG00000278704.1 ENSG00000277400.1 ENSG00000274847.1 ENSG00000277428.1 ENSG00000276256.1 ... ... ... ENSG00000124334.17_PAR_Y OTTHUMG00000022720.1 PAR ENSG00000185203.12_PAR_Y OTTHUMG00000022676.3 PAR ENSG00000270726.6_PAR_Y OTTHUMG00000184987.2 PAR ENSG00000182484.15_PAR_Y OTTHUMG00000022677.5 PAR ENSG00000227159.8_PAR_Y OTTHUMG00000022678.1 PAR ------- seqinfo: 374 sequences from an unspecified genome; no seqlengths > > ## Sample metadata > colnames(colData(rse_gene_SRP009615)) [1] "rail_id" [2] "external_id" [3] "study" [4] "sra.sample_acc.x" [5] "sra.experiment_acc" [6] "sra.submission_acc" [7] "sra.submission_center" [8] "sra.submission_lab" [9] "sra.study_title" [10] "sra.study_abstract" [11] "sra.study_description" [12] "sra.experiment_title" [13] "sra.design_description" [14] "sra.sample_description" [15] "sra.library_name" [16] "sra.library_strategy" [17] "sra.library_source" [18] "sra.library_selection" [19] "sra.library_layout" [20] "sra.paired_nominal_length" [21] "sra.paired_nominal_stdev" [22] "sra.library_construction_protocol" [23] "sra.platform_model" [24] "sra.sample_attributes" [25] "sra.experiment_attributes" [26] "sra.spot_length" [27] "sra.sample_name" [28] "sra.sample_title" [29] "sra.sample_bases" [30] "sra.sample_spots" [31] "sra.run_published" [32] "sra.size" [33] "sra.run_total_bases" [34] "sra.run_total_spots" [35] "sra.num_reads" [36] "sra.num_spots" [37] "sra.read_info" [38] "sra.run_alias" [39] "sra.run_center_name" [40] "sra.run_broker_name" [41] "sra.run_center" [42] "recount_project.project" [43] "recount_project.organism" [44] "recount_project.file_source" [45] "recount_project.metadata_source" [46] "recount_project.date_processed" [47] "recount_qc.aligned_reads%.chrm" [48] "recount_qc.aligned_reads%.chrx" [49] "recount_qc.aligned_reads%.chry" [50] "recount_qc.bc_auc.all_reads_all_bases" [51] "recount_qc.bc_auc.all_reads_annotated_bases" [52] "recount_qc.bc_auc.unique_reads_all_bases" [53] "recount_qc.bc_auc.unique_reads_annotated_bases" [54] "recount_qc.bc_auc.all_%" [55] "recount_qc.bc_auc.unique_%" [56] "recount_qc.bc_frag.count" [57] "recount_qc.bc_frag.kallisto_count" [58] "recount_qc.bc_frag.kallisto_mean_length" [59] "recount_qc.bc_frag.mean_length" [60] "recount_qc.bc_frag.mode_length" [61] "recount_qc.bc_frag.mode_length_count" [62] "recount_qc.exon_fc.all_%" [63] "recount_qc.exon_fc.unique_%" [64] "recount_qc.exon_fc_count_all.total" [65] "recount_qc.exon_fc_count_all.assigned" [66] "recount_qc.exon_fc_count_unique.total" [67] "recount_qc.exon_fc_count_unique.assigned" [68] "recount_qc.gene_fc.all_%" [69] "recount_qc.gene_fc.unique_%" [70] "recount_qc.gene_fc_count_all.total" [71] "recount_qc.gene_fc_count_all.assigned" [72] "recount_qc.gene_fc_count_unique.total" [73] "recount_qc.gene_fc_count_unique.assigned" [74] "recount_qc.intron_sum" [75] "recount_qc.intron_sum_%" [76] "recount_qc.star.%_of_chimeric_reads" [77] "recount_qc.star.%_of_chimeric_reads2" [78] "recount_qc.star.%_of_reads_mapped_to_multiple_loci" [79] "recount_qc.star.%_of_reads_mapped_to_multiple_loci2" [80] "recount_qc.star.%_of_reads_mapped_to_too_many_loci" [81] "recount_qc.star.%_of_reads_mapped_to_too_many_loci2" [82] "recount_qc.star.%_of_reads_unmapped:_other" [83] "recount_qc.star.%_of_reads_unmapped:_other2" [84] "recount_qc.star.%_of_reads_unmapped:_too_many_mismatches" [85] "recount_qc.star.%_of_reads_unmapped:_too_many_mismatches2" [86] "recount_qc.star.%_of_reads_unmapped:_too_short" [87] "recount_qc.star.%_of_reads_unmapped:_too_short2" [88] "recount_qc.star.all_mapped_reads" [89] "recount_qc.star.all_mapped_reads2" [90] "recount_qc.star.average_input_read_length" [91] "recount_qc.star.average_input_read_length2" [92] "recount_qc.star.average_mapped_length" [93] "recount_qc.star.average_mapped_length2" [94] "recount_qc.star.deletion_average_length" [95] "recount_qc.star.deletion_average_length2" [96] "recount_qc.star.deletion_rate_per_base" [97] "recount_qc.star.deletion_rate_per_base2" [98] "recount_qc.star.insertion_average_length" [99] "recount_qc.star.insertion_average_length2" [100] "recount_qc.star.insertion_rate_per_base" [101] "recount_qc.star.insertion_rate_per_base2" [102] "recount_qc.star.mapping_speed,_million_of_reads_per_hour" [103] "recount_qc.star.mapping_speed,_million_of_reads_per_hour2" [104] "recount_qc.star.mismatch_rate_per_base,_%" [105] "recount_qc.star.mismatch_rate_per_base,_%2" [106] "recount_qc.star.number_of_chimeric_reads" [107] "recount_qc.star.number_of_chimeric_reads2" [108] "recount_qc.star.number_of_input_reads" [109] "recount_qc.star.number_of_input_reads2" [110] "recount_qc.star.number_of_reads_mapped_to_multiple_loci" [111] "recount_qc.star.number_of_reads_mapped_to_multiple_loci2" [112] "recount_qc.star.number_of_reads_mapped_to_too_many_loci" [113] "recount_qc.star.number_of_reads_mapped_to_too_many_loci2" [114] "recount_qc.star.number_of_reads_unmapped:_other" [115] "recount_qc.star.number_of_reads_unmapped:_other2" [116] "recount_qc.star.number_of_reads_unmapped:_too_many_mismatches" [117] "recount_qc.star.number_of_reads_unmapped:_too_many_mismatches2" [118] "recount_qc.star.number_of_reads_unmapped:_too_short" [119] "recount_qc.star.number_of_reads_unmapped:_too_short2" [120] "recount_qc.star.number_of_splices:_at/ac" [121] "recount_qc.star.number_of_splices:_at/ac2" [122] "recount_qc.star.number_of_splices:_annotated_(sjdb)" [123] "recount_qc.star.number_of_splices:_annotated_(sjdb)2" [124] "recount_qc.star.number_of_splices:_gc/ag" [125] "recount_qc.star.number_of_splices:_gc/ag2" [126] "recount_qc.star.number_of_splices:_gt/ag" [127] "recount_qc.star.number_of_splices:_gt/ag2" [128] "recount_qc.star.number_of_splices:_non-canonical" [129] "recount_qc.star.number_of_splices:_non-canonical2" [130] "recount_qc.star.number_of_splices:_total" [131] "recount_qc.star.number_of_splices:_total2" [132] "recount_qc.star.uniquely_mapped_reads_%" [133] "recount_qc.star.uniquely_mapped_reads_%2" [134] "recount_qc.star.uniquely_mapped_reads_number" [135] "recount_qc.star.uniquely_mapped_reads_number2" [136] "recount_qc.junction_count" [137] "recount_qc.junction_coverage" [138] "recount_qc.junction_avg_coverage" [139] "recount_qc.star.number_of_input_reads_both" [140] "recount_qc.star.all_mapped_reads_both" [141] "recount_qc.star.number_of_chimeric_reads_both" [142] "recount_qc.star.number_of_reads_mapped_to_multiple_loci_both" [143] "recount_qc.star.number_of_reads_mapped_to_too_many_loci_both" [144] "recount_qc.star.number_of_reads_unmapped:_other_both" [145] "recount_qc.star.number_of_reads_unmapped:_too_many_mismatches_both" [146] "recount_qc.star.number_of_reads_unmapped:_too_short_both" [147] "recount_qc.star.uniquely_mapped_reads_number_both" [148] "recount_qc.star.%_mapped_reads_both" [149] "recount_qc.star.%_chimeric_reads_both" [150] "recount_qc.star.%_reads_mapped_to_multiple_loci_both" [151] "recount_qc.star.%_reads_mapped_to_too_many_loci_both" [152] "recount_qc.star.%_reads_unmapped:_other_both" [153] "recount_qc.star.%_reads_unmapped:_too_many_mismatches_both" [154] "recount_qc.star.%_reads_unmapped:_too_short_both" [155] "recount_qc.star.uniquely_mapped_reads_%_both" [156] "recount_seq_qc.min_len" [157] "recount_seq_qc.max_len" [158] "recount_seq_qc.avg_len" [159] "recount_seq_qc.#distinct_quality_values" [160] "recount_seq_qc.#bases" [161] "recount_seq_qc.%a" [162] "recount_seq_qc.%c" [163] "recount_seq_qc.%g" [164] "recount_seq_qc.%t" [165] "recount_seq_qc.%n" [166] "recount_seq_qc.avgq" [167] "recount_seq_qc.errq" [168] "recount_pred.sample_acc.y" [169] "recount_pred.curated.type" [170] "recount_pred.curated.tissue" [171] "recount_pred.pattern.predict.type" [172] "recount_pred.pred.type" [173] "recount_pred.curated.cell_type" [174] "recount_pred.curated.cell_line" [175] "BigWigURL" > > ## Check how much memory this RSE object uses > pryr::object_size(rse_gene_SRP009615) 24.81 MB > > ## Create an RSE object using gencode_v29 instead of gencode_v26 > rse_gene_SRP009615_gencode_v29 <- create_rse( + proj_info, + annotation = "gencode_v29", + verbose = FALSE + ) > rowRanges(rse_gene_SRP009615_gencode_v29) GRanges object with 64837 ranges and 10 metadata columns: seqnames ranges strand | source | ENSG00000278704.1 GL000009.2 56140-58376 - | ENSEMBL ENSG00000277400.1 GL000194.1 53590-115018 - | ENSEMBL ENSG00000274847.1 GL000194.1 53594-115055 - | ENSEMBL ENSG00000277428.1 GL000195.1 37434-37534 - | ENSEMBL ENSG00000276256.1 GL000195.1 42939-49164 - | ENSEMBL ... ... ... ... . ... ENSG00000124334.17_PAR_Y chrY 57184101-57197337 + | HAVANA ENSG00000185203.12_PAR_Y chrY 57201143-57203357 - | HAVANA ENSG00000270726.6_PAR_Y chrY 57190738-57208756 + | HAVANA ENSG00000182484.15_PAR_Y chrY 57207346-57212230 + | HAVANA ENSG00000227159.8_PAR_Y chrY 57212184-57214397 - | HAVANA type bp_length phase gene_id ENSG00000278704.1 gene 2237 ENSG00000278704.1 ENSG00000277400.1 gene 2179 ENSG00000277400.1 ENSG00000274847.1 gene 1599 ENSG00000274847.1 ENSG00000277428.1 gene 101 ENSG00000277428.1 ENSG00000276256.1 gene 2195 ENSG00000276256.1 ... ... ... ... ... ENSG00000124334.17_PAR_Y gene 2504 ENSG00000124334.17_P.. ENSG00000185203.12_PAR_Y gene 1054 ENSG00000185203.12_P.. ENSG00000270726.6_PAR_Y gene 773 ENSG00000270726.6_PA.. ENSG00000182484.15_PAR_Y gene 4618 ENSG00000182484.15_P.. ENSG00000227159.8_PAR_Y gene 1306 ENSG00000227159.8_PA.. gene_type gene_name level ENSG00000278704.1 protein_coding BX004987.1 3 ENSG00000277400.1 protein_coding AC145212.1 3 ENSG00000274847.1 protein_coding MAFIP 3 ENSG00000277428.1 misc_RNA RF00019 3 ENSG00000276256.1 protein_coding AC011043.1 3 ... ... ... ... ENSG00000124334.17_PAR_Y protein_coding IL9R 2 ENSG00000185203.12_PAR_Y antisense WASIR1 2 ENSG00000270726.6_PAR_Y processed_transcript AJ271736.1 2 ENSG00000182484.15_PAR_Y transcribed_unproces.. WASH6P 2 ENSG00000227159.8_PAR_Y unprocessed_pseudogene DDX11L16 2 havana_gene tag ENSG00000278704.1 ENSG00000277400.1 ENSG00000274847.1 ENSG00000277428.1 ENSG00000276256.1 ... ... ... ENSG00000124334.17_PAR_Y OTTHUMG00000022720.1 PAR ENSG00000185203.12_PAR_Y OTTHUMG00000022676.3 PAR ENSG00000270726.6_PAR_Y OTTHUMG00000184987.2 PAR ENSG00000182484.15_PAR_Y OTTHUMG00000022677.5 PAR ENSG00000227159.8_PAR_Y OTTHUMG00000022678.1 PAR ------- seqinfo: 406 sequences from an unspecified genome; no seqlengths > > ## Create an RSE object using FANTOM6_CAT instead of gencode_v26 > rse_gene_SRP009615_fantom6_cat <- create_rse( + proj_info, + annotation = "fantom6_cat" + ) 2024-10-03 00:42:02.318671 downloading and reading the metadata. 2024-10-03 00:42:02.573701 caching file sra.sra.SRP009615.MD.gz. 2024-10-03 00:42:02.932672 caching file sra.recount_project.SRP009615.MD.gz. 2024-10-03 00:42:03.275173 caching file sra.recount_qc.SRP009615.MD.gz. 2024-10-03 00:42:03.60726 caching file sra.recount_seq_qc.SRP009615.MD.gz. 2024-10-03 00:42:03.943509 caching file sra.recount_pred.SRP009615.MD.gz. 2024-10-03 00:42:04.063164 downloading and reading the feature information. 2024-10-03 00:42:04.314303 caching file human.gene_sums.F006.gtf.gz. 2024-10-03 00:42:04.862681 downloading and reading the counts: 12 samples across 124047 features. 2024-10-03 00:42:05.272102 caching file sra.gene_sums.SRP009615.F006.gz. 2024-10-03 00:42:05.670627 constructing the RangedSummarizedExperiment (rse) object. > rowRanges(rse_gene_SRP009615_fantom6_cat) GRanges object with 124047 ranges and 5 metadata columns: seqnames ranges strand | source type | CATG00000042730 chr1 159537-162485 - | FANTOM6 gene CATG00000042731 chr1 273882-274416 - | FANTOM6 gene ENSG00000223659 chr1 627377-629095 - | FANTOM6 gene ENSG00000225630 chr1 630001-630683 + | FANTOM6 gene ENSG00000225972 chr1 629209-631743 + | FANTOM6 gene ... ... ... ... . ... ... CATG00000114975 chrY 56836712-56851323 + | FANTOM6 gene CATG00000115126 chrY 56855793-56856102 - | FANTOM6 gene CATG00000114976 chrY 56855491-56858320 + | FANTOM6 gene CATG00000114977 chrY 56867675-56882339 + | FANTOM6 gene CATG00000115127 chrY 56884759-56885317 - | FANTOM6 gene bp_length phase gene_id CATG00000042730 2949 CATG00000042730 CATG00000042731 535 CATG00000042731 ENSG00000223659 887 ENSG00000223659 ENSG00000225630 683 ENSG00000225630 ENSG00000225972 438 ENSG00000225972 ... ... ... ... CATG00000114975 4376 CATG00000114975 CATG00000115126 310 CATG00000115126 CATG00000114976 2830 CATG00000114976 CATG00000114977 14665 CATG00000114977 CATG00000115127 559 CATG00000115127 ------- seqinfo: 25 sequences from an unspecified genome; no seqlengths > > ## Create an RSE object using RefSeq instead of gencode_v26 > rse_gene_SRP009615_refseq <- create_rse( + proj_info, + annotation = "refseq" + ) 2024-10-03 00:42:05.718317 downloading and reading the metadata. 2024-10-03 00:42:05.972519 caching file sra.sra.SRP009615.MD.gz. 2024-10-03 00:42:06.286743 caching file sra.recount_project.SRP009615.MD.gz. 2024-10-03 00:42:06.642832 caching file sra.recount_qc.SRP009615.MD.gz. 2024-10-03 00:42:06.967014 caching file sra.recount_seq_qc.SRP009615.MD.gz. 2024-10-03 00:42:07.271254 caching file sra.recount_pred.SRP009615.MD.gz. 2024-10-03 00:42:07.417642 downloading and reading the feature information. 2024-10-03 00:42:07.733296 caching file human.gene_sums.R109.gtf.gz. 2024-10-03 00:42:08.552344 downloading and reading the counts: 12 samples across 54042 features. 2024-10-03 00:42:08.885721 caching file sra.gene_sums.SRP009615.R109.gz. 2024-10-03 00:42:09.435019 constructing the RangedSummarizedExperiment (rse) object. > rowRanges(rse_gene_SRP009615_refseq) GRanges object with 54042 ranges and 25 metadata columns: seqnames ranges strand | source type bp_length | gene14440 GL000008.2 124376-125329 - | RefSeq gene 954 gene14441 GL000008.2 153090-153485 - | RefSeq gene 396 gene14442 GL000008.2 161987-178171 - | RefSeq gene 1744 gene38360 GL000009.2 32290-36345 + | RefSeq gene 1512 gene38362 GL000009.2 43342-56258 + | RefSeq gene 972 ... ... ... ... . ... ... ... gene54245 chrY 57171874-57172771 - | RefSeq gene 898 gene54246 chrY 57184101-57199537 + | RefSeq gene 6193 gene54247 chrY 57201084-57203350 - | RefSeq gene 1231 gene54248 chrY 57208178-57212192 + | RefSeq gene 1570 gene54249 chrY 57212178-57214703 - | RefSeq gene 1643 phase gene_id Dbxref Name gene14440 gene14440 GeneID:100419019,HGN.. SNX18P15 gene14441 gene14441 GeneID:100419020,HGN.. SNX18P16 gene14442 gene14442 GeneID:100874392,Gen.. NR_046228.1 gene38360 gene38360 GeneID:100533720,HGN.. ANKRD20A15P gene38362 gene38362 GeneID:105379272,Gen.. XR_949087.2 ... ... ... ... ... gene54245 gene54245 GeneID:644218,HGNC:H.. TRPC6P gene54246 gene54246 gene54247 gene54247 GeneID:100128260,Gen.. NR_138048.1 gene54248 gene54248 GeneID:653440,HGNC:H.. WASH6P gene54249 gene54249 GeneID:727856,Genban.. NR_110561.1 description gbkey gene_biotype gene_name gene14440 sorting nexin 18 pse.. Gene pseudogene SNX18P15 gene14441 sorting nexin 18 pse.. Gene pseudogene SNX18P16 gene14442 misc_RNA ANKRD20A12P gene38360 ankyrin repeat domai.. Gene pseudogene ANKRD20A15P gene38362 ncRNA LOC105379272 ... ... ... ... ... gene54245 transient receptor p.. Gene pseudogene TRPC6P gene54246 mRNA IL9R gene54247 ncRNA WASIR1 gene54248 WAS protein family h.. Gene pseudogene WASH6P gene54249 misc_RNA DDX11L16 pseudo product model_evidence gene14440 true gene14441 true gene14442 ankyrin repeat domai.. gene38360 true gene38362 uncharacterized LOC1.. Supporting evidence .. ... ... ... ... gene54245 true gene54246 gene54247 WASH and IL9R antise.. gene54248 true gene54249 DEAD/H-box helicase .. exception partial Note inference geneID gene14440 gene14441 gene14442 gene38360 gene38362 ... ... ... ... ... ... gene54245 gene54246 gene54247 gene54248 gene54249 anticodon gene_synonym end_range start_range gene14440 gene14441 gene14442 gene38360 gene38362 ... ... ... ... ... gene54245 TRPC6L gene54246 gene54247 gene54248 CXYorf1,FAM39A,WASH gene54249 standard_name codons gene14440 gene14441 gene14442 gene38360 gene38362 ... ... ... gene54245 gene54246 gene54247 gene54248 gene54249 ------- seqinfo: 436 sequences from an unspecified genome; no seqlengths > > ## Create an RSE object using ERCC instead of gencode_v26 > rse_gene_SRP009615_ercc <- create_rse( + proj_info, + annotation = "ercc" + ) 2024-10-03 00:42:09.481803 downloading and reading the metadata. 2024-10-03 00:42:09.756313 caching file sra.sra.SRP009615.MD.gz. 2024-10-03 00:42:10.109496 caching file sra.recount_project.SRP009615.MD.gz. 2024-10-03 00:42:10.462806 caching file sra.recount_qc.SRP009615.MD.gz. 2024-10-03 00:42:10.770139 caching file sra.recount_seq_qc.SRP009615.MD.gz. 2024-10-03 00:42:11.097935 caching file sra.recount_pred.SRP009615.MD.gz. 2024-10-03 00:42:11.216676 downloading and reading the feature information. 2024-10-03 00:42:11.474055 caching file human.gene_sums.ERCC.gtf.gz. 2024-10-03 00:42:11.600386 downloading and reading the counts: 12 samples across 92 features. 2024-10-03 00:42:11.991655 caching file sra.gene_sums.SRP009615.ERCC.gz. 2024-10-03 00:42:12.154433 constructing the RangedSummarizedExperiment (rse) object. > rowRanges(rse_gene_SRP009615_ercc) GRanges object with 92 ranges and 6 metadata columns: seqnames ranges strand | source type bp_length | ERCC-00002 ERCC-00002 1-1061 + | ERCC gene 1061 ERCC-00003 ERCC-00003 1-1023 + | ERCC gene 1023 ERCC-00004 ERCC-00004 1-523 + | ERCC gene 523 ERCC-00009 ERCC-00009 1-984 + | ERCC gene 984 ERCC-00012 ERCC-00012 1-994 + | ERCC gene 994 ... ... ... ... . ... ... ... ERCC-00164 ERCC-00164 1-1022 + | ERCC gene 1022 ERCC-00165 ERCC-00165 1-872 + | ERCC gene 872 ERCC-00168 ERCC-00168 1-1024 + | ERCC gene 1024 ERCC-00170 ERCC-00170 1-1023 + | ERCC gene 1023 ERCC-00171 ERCC-00171 1-505 + | ERCC gene 505 phase gene_id transcript_id ERCC-00002 ERCC-00002 DQ459430 ERCC-00003 ERCC-00003 DQ516784 ERCC-00004 ERCC-00004 DQ516752 ERCC-00009 ERCC-00009 DQ668364 ERCC-00012 ERCC-00012 DQ883670 ... ... ... ... ERCC-00164 ERCC-00164 DQ516779 ERCC-00165 ERCC-00165 DQ668363 ERCC-00168 ERCC-00168 DQ516776 ERCC-00170 ERCC-00170 DQ516773 ERCC-00171 ERCC-00171 DQ854994 ------- seqinfo: 92 sequences from an unspecified genome; no seqlengths > > ## Create an RSE object using SIRV instead of gencode_v26 > rse_gene_SRP009615_sirv <- create_rse( + proj_info, + annotation = "sirv" + ) 2024-10-03 00:42:12.197198 downloading and reading the metadata. 2024-10-03 00:42:12.466772 caching file sra.sra.SRP009615.MD.gz. 2024-10-03 00:42:12.839371 caching file sra.recount_project.SRP009615.MD.gz. 2024-10-03 00:42:13.214729 caching file sra.recount_qc.SRP009615.MD.gz. 2024-10-03 00:42:13.550132 caching file sra.recount_seq_qc.SRP009615.MD.gz. 2024-10-03 00:42:13.870481 caching file sra.recount_pred.SRP009615.MD.gz. 2024-10-03 00:42:14.008686 downloading and reading the feature information. 2024-10-03 00:42:14.259999 caching file human.gene_sums.SIRV.gtf.gz. 2024-10-03 00:42:14.406356 downloading and reading the counts: 12 samples across 7 features. 2024-10-03 00:42:14.726173 caching file sra.gene_sums.SRP009615.SIRV.gz. 2024-10-03 00:42:14.903756 constructing the RangedSummarizedExperiment (rse) object. > rowRanges(rse_gene_SRP009615_sirv) GRanges object with 7 ranges and 5 metadata columns: seqnames ranges strand | source type bp_length | SIRV1 SIRV1 1001-11643 * | LexogenSIRVData gene NA SIRV2 SIRV2 1001-5911 * | LexogenSIRVData gene NA SIRV3 SIRV3 1001-9943 * | LexogenSIRVData gene NA SIRV4 SIRV4 1001-15122 * | LexogenSIRVData gene NA SIRV5 SIRV5 1001-13606 * | LexogenSIRVData gene NA SIRV6 SIRV6 1001-11837 * | LexogenSIRVData gene NA SIRV7 SIRV7 1001-147957 * | LexogenSIRVData gene NA phase gene_id SIRV1 0 SIRV1 SIRV2 0 SIRV2 SIRV3 0 SIRV3 SIRV4 0 SIRV4 SIRV5 0 SIRV5 SIRV6 0 SIRV6 SIRV7 0 SIRV7 ------- seqinfo: 7 sequences from an unspecified genome; no seqlengths > > ## Obtain a list of RSE objects for all gene annotations > rses_gene <- lapply(annotation_options(), function(x) { + create_rse(proj_info, type = "gene", annotation = x) + }) 2024-10-03 00:42:14.941224 downloading and reading the metadata. 2024-10-03 00:42:15.207002 caching file sra.sra.SRP009615.MD.gz. 2024-10-03 00:42:15.597556 caching file sra.recount_project.SRP009615.MD.gz. 2024-10-03 00:42:15.989378 caching file sra.recount_qc.SRP009615.MD.gz. 2024-10-03 00:42:16.319367 caching file sra.recount_seq_qc.SRP009615.MD.gz. 2024-10-03 00:42:16.714427 caching file sra.recount_pred.SRP009615.MD.gz. 2024-10-03 00:42:16.871504 downloading and reading the feature information. 2024-10-03 00:42:17.109418 caching file human.gene_sums.G026.gtf.gz. 2024-10-03 00:42:17.890803 downloading and reading the counts: 12 samples across 63856 features. 2024-10-03 00:42:18.121136 caching file sra.gene_sums.SRP009615.G026.gz. 2024-10-03 00:42:18.352364 constructing the RangedSummarizedExperiment (rse) object. 2024-10-03 00:42:18.386964 downloading and reading the metadata. 2024-10-03 00:42:18.674479 caching file sra.sra.SRP009615.MD.gz. 2024-10-03 00:42:19.071449 caching file sra.recount_project.SRP009615.MD.gz. 2024-10-03 00:42:19.449987 caching file sra.recount_qc.SRP009615.MD.gz. 2024-10-03 00:42:19.780993 caching file sra.recount_seq_qc.SRP009615.MD.gz. 2024-10-03 00:42:20.094846 caching file sra.recount_pred.SRP009615.MD.gz. 2024-10-03 00:42:20.209183 downloading and reading the feature information. 2024-10-03 00:42:20.469043 caching file human.gene_sums.G029.gtf.gz. 2024-10-03 00:42:21.17391 downloading and reading the counts: 12 samples across 64837 features. 2024-10-03 00:42:21.445754 caching file sra.gene_sums.SRP009615.G029.gz. 2024-10-03 00:42:21.803784 constructing the RangedSummarizedExperiment (rse) object. 2024-10-03 00:42:21.872009 downloading and reading the metadata. 2024-10-03 00:42:22.113493 caching file sra.sra.SRP009615.MD.gz. 2024-10-03 00:42:22.464983 caching file sra.recount_project.SRP009615.MD.gz. 2024-10-03 00:42:22.849179 caching file sra.recount_qc.SRP009615.MD.gz. 2024-10-03 00:42:23.147153 caching file sra.recount_seq_qc.SRP009615.MD.gz. 2024-10-03 00:42:23.473845 caching file sra.recount_pred.SRP009615.MD.gz. 2024-10-03 00:42:23.590785 downloading and reading the feature information. 2024-10-03 00:42:23.816847 caching file human.gene_sums.F006.gtf.gz. 2024-10-03 00:42:24.35905 downloading and reading the counts: 12 samples across 124047 features. 2024-10-03 00:42:24.671501 caching file sra.gene_sums.SRP009615.F006.gz. 2024-10-03 00:42:26.579309 constructing the RangedSummarizedExperiment (rse) object. 2024-10-03 00:42:26.608748 downloading and reading the metadata. 2024-10-03 00:42:26.905896 caching file sra.sra.SRP009615.MD.gz. 2024-10-03 00:42:27.28486 caching file sra.recount_project.SRP009615.MD.gz. 2024-10-03 00:42:27.67641 caching file sra.recount_qc.SRP009615.MD.gz. 2024-10-03 00:42:27.97737 caching file sra.recount_seq_qc.SRP009615.MD.gz. 2024-10-03 00:42:28.367782 caching file sra.recount_pred.SRP009615.MD.gz. 2024-10-03 00:42:28.476548 downloading and reading the feature information. 2024-10-03 00:42:28.760823 caching file human.gene_sums.R109.gtf.gz. 2024-10-03 00:42:29.441067 downloading and reading the counts: 12 samples across 54042 features. 2024-10-03 00:42:29.741665 caching file sra.gene_sums.SRP009615.R109.gz. 2024-10-03 00:42:29.953829 constructing the RangedSummarizedExperiment (rse) object. 2024-10-03 00:42:29.986382 downloading and reading the metadata. 2024-10-03 00:42:30.220448 caching file sra.sra.SRP009615.MD.gz. 2024-10-03 00:42:30.557773 caching file sra.recount_project.SRP009615.MD.gz. 2024-10-03 00:42:30.936225 caching file sra.recount_qc.SRP009615.MD.gz. 2024-10-03 00:42:31.2858 caching file sra.recount_seq_qc.SRP009615.MD.gz. 2024-10-03 00:42:31.626441 caching file sra.recount_pred.SRP009615.MD.gz. 2024-10-03 00:42:31.86217 downloading and reading the feature information. 2024-10-03 00:42:32.090228 caching file human.gene_sums.ERCC.gtf.gz. 2024-10-03 00:42:32.193658 downloading and reading the counts: 12 samples across 92 features. 2024-10-03 00:42:32.523872 caching file sra.gene_sums.SRP009615.ERCC.gz. 2024-10-03 00:42:32.657683 constructing the RangedSummarizedExperiment (rse) object. 2024-10-03 00:42:32.68698 downloading and reading the metadata. 2024-10-03 00:42:32.925802 caching file sra.sra.SRP009615.MD.gz. 2024-10-03 00:42:33.307835 caching file sra.recount_project.SRP009615.MD.gz. 2024-10-03 00:42:33.638124 caching file sra.recount_qc.SRP009615.MD.gz. 2024-10-03 00:42:33.971668 caching file sra.recount_seq_qc.SRP009615.MD.gz. 2024-10-03 00:42:34.292306 caching file sra.recount_pred.SRP009615.MD.gz. 2024-10-03 00:42:34.407721 downloading and reading the feature information. 2024-10-03 00:42:34.634189 caching file human.gene_sums.SIRV.gtf.gz. 2024-10-03 00:42:34.747686 downloading and reading the counts: 12 samples across 7 features. 2024-10-03 00:42:35.05108 caching file sra.gene_sums.SRP009615.SIRV.gz. 2024-10-03 00:42:35.207052 constructing the RangedSummarizedExperiment (rse) object. > names(rses_gene) <- annotation_options() > rses_gene $gencode_v26 class: RangedSummarizedExperiment dim: 63856 12 metadata(8): time_created recount3_version ... annotation recount3_url assays(1): raw_counts rownames(63856): ENSG00000278704.1 ENSG00000277400.1 ... ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y rowData names(10): source type ... havana_gene tag colnames(12): SRR387777 SRR387778 ... SRR389077 SRR389078 colData names(175): rail_id external_id ... recount_pred.curated.cell_line BigWigURL $gencode_v29 class: RangedSummarizedExperiment dim: 64837 12 metadata(8): time_created recount3_version ... annotation recount3_url assays(1): raw_counts rownames(64837): ENSG00000278704.1 ENSG00000277400.1 ... ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y rowData names(10): source type ... havana_gene tag colnames(12): SRR387777 SRR387778 ... SRR389077 SRR389078 colData names(175): rail_id external_id ... recount_pred.curated.cell_line BigWigURL $fantom6_cat class: RangedSummarizedExperiment dim: 124047 12 metadata(8): time_created recount3_version ... annotation recount3_url assays(1): raw_counts rownames(124047): CATG00000042730 CATG00000042731 ... CATG00000114977 CATG00000115127 rowData names(5): source type bp_length phase gene_id colnames(12): SRR387777 SRR387778 ... SRR389077 SRR389078 colData names(175): rail_id external_id ... recount_pred.curated.cell_line BigWigURL $refseq class: RangedSummarizedExperiment dim: 54042 12 metadata(8): time_created recount3_version ... annotation recount3_url assays(1): raw_counts rownames(54042): gene14440 gene14441 ... gene54248 gene54249 rowData names(25): source type ... standard_name codons colnames(12): SRR387777 SRR387778 ... SRR389077 SRR389078 colData names(175): rail_id external_id ... recount_pred.curated.cell_line BigWigURL $ercc class: RangedSummarizedExperiment dim: 92 12 metadata(8): time_created recount3_version ... annotation recount3_url assays(1): raw_counts rownames(92): ERCC-00002 ERCC-00003 ... ERCC-00170 ERCC-00171 rowData names(6): source type ... gene_id transcript_id colnames(12): SRR387777 SRR387778 ... SRR389077 SRR389078 colData names(175): rail_id external_id ... recount_pred.curated.cell_line BigWigURL $sirv class: RangedSummarizedExperiment dim: 7 12 metadata(8): time_created recount3_version ... annotation recount3_url assays(1): raw_counts rownames(7): SIRV1 SIRV2 ... SIRV6 SIRV7 rowData names(5): source type bp_length phase gene_id colnames(12): SRR387777 SRR387778 ... SRR389077 SRR389078 colData names(175): rail_id external_id ... recount_pred.curated.cell_line BigWigURL > > ## Create a RSE object at the exon level > rse_exon_SRP009615 <- create_rse( + proj_info, + type = "exon" + ) 2024-10-03 00:42:35.325456 downloading and reading the metadata. 2024-10-03 00:42:35.604543 caching file sra.sra.SRP009615.MD.gz. 2024-10-03 00:42:35.957705 caching file sra.recount_project.SRP009615.MD.gz. 2024-10-03 00:42:36.350358 caching file sra.recount_qc.SRP009615.MD.gz. 2024-10-03 00:42:36.702767 caching file sra.recount_seq_qc.SRP009615.MD.gz. 2024-10-03 00:42:37.053597 caching file sra.recount_pred.SRP009615.MD.gz. 2024-10-03 00:42:37.197948 downloading and reading the feature information. 2024-10-03 00:42:37.428899 caching file human.exon_sums.G026.gtf.gz. 2024-10-03 00:43:05.797486 downloading and reading the counts: 12 samples across 1299686 features. 2024-10-03 00:43:06.13981 caching file sra.exon_sums.SRP009615.G026.gz. Warning in writeBin(bfr, con = out, size = 1L) : problem writing to connection Warning in writeBin(bfr, con = out, size = 1L) : problem writing to connection Warning in writeBin(bfr, con = out, size = 1L) : problem writing to connection Warning in writeBin(bfr, con = out, size = 1L) : problem writing to connection Warning in writeBin(bfr, con = out, size = 1L) : problem writing to connection Warning in writeBin(bfr, con = out, size = 1L) : problem writing to connection Warning in data.table::fread(counts_file, skip = 2, colClasses = c("character", : Stopped early on line 470825. Expected 13 fields but found 7. Consider fill=TRUE and comment.char=. First discarded non-empty line: <> 2024-10-03 00:43:07.213936 constructing the RangedSummarizedExperiment (rse) object. Error in create_rse_manual(project = project_info$project, project_home = project_info$project_home, : Exon names and count rownames are not matching. Calls: create_rse -> create_rse_manual -> stopifnot Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘recount3-quickstart.Rmd’ using rmarkdown Quitting from lines 416-427 [rse_exon] (recount3-quickstart.Rmd) Error: processing vignette 'recount3-quickstart.Rmd' failed with diagnostics: Exon names and count rownames are not matching. --- failed re-building ‘recount3-quickstart.Rmd’ SUMMARY: processing the following file failed: ‘recount3-quickstart.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs See ‘/home/biocbuild/bbs-3.20-bioc/meat/recount3.Rcheck/00check.log’ for details.