* using log directory 'd:/RCompile/CRANincoming/R-devel/geneNR.Rcheck' * using R Under development (unstable) (2025-02-20 r87772 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'geneNR/DESCRIPTION' ... OK * this is package 'geneNR' version '0.0.0.9000' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Rajamani Nirmalaruban ' New submission Version contains large components (0.0.0.9000) Possibly misspelled words in DESCRIPTION: GWAS (3:14, 17:54, 17:236) SNPs (17:157) geneNR (17:18) * 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 'geneNR' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 use of S3 registration ... 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 line widths ... 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [17s] ERROR Running examples in 'geneNR-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: geneNR > ### Title: Automated Candidate Gene Identification and Retrieval for > ### Post-GWAS Analysis > ### Aliases: geneNR > > ### ** Examples > > result <- geneNR("sample_data_wheat", 10000, 10000, crop="wheat") [1] "SNP" "Chr" "Pos" "traits" # A tibble: 6 × 9 SNP Chr Pos traits start stop search_window url file_name 1 AX-94490431 7A 93007534 FarmCP… 9.30e7 9.30e7 7A:92997534-… http… FarmCPU.… 2 AX-94695736 7B 41798403 FarmCP… 4.18e7 4.18e7 7B:41788403-… http… FarmCPU.… 3 AX-95170264 7B 44136480 FarmCP… 4.41e7 4.41e7 7B:44126480-… http… FarmCPU.… 4 AX-94652542 7D 90573370 FarmCP… 9.06e7 9.06e7 7D:90563370-… http… FarmCPU.… 5 AX-95133422 7D 90578465 FarmCP… 9.06e7 9.06e7 7D:90568465-… http… FarmCPU.… 6 AX-94883629 7D 90952858 FarmCP… 9.09e7 9.10e7 7D:90942858-… http… FarmCPU.… [1] "Error processing URL: https://plants.ensembl.org/Triticum_aestivum/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=7D:90563370-90583370;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Triticum_aestivum/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=7D:90568465-90588465;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Triticum_aestivum/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=7D:90942858-90962858;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Triticum_aestivum/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=2A:746959222-746979222;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Triticum_aestivum/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=3A:657925147-657945147;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Triticum_aestivum/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=4A:69258323-69278323;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" Rows: 0 Columns: 18 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (18): seqname, source, feature, start, end, score, strand, frame, hid, h... ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 0 Columns: 18 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (18): seqname, source, feature, start, end, score, strand, frame, hid, h... ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 0 Columns: 18 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (18): seqname, source, feature, start, end, score, strand, frame, hid, h... ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. # A tibble: 0 × 6 # ℹ 6 variables: traits , SNP , search_window , gene_size , # gene_id , gene_type [1] "Filtered gene IDs saved to D:\\temp\\2025_02_21_17_15_17_18683\\RtmpyK3zmI\\filtered_gene_idbee446722cb3.xlsx" > result <- geneNR("sample_data_rice", 10000, 10000, crop="rice") [1] "traits" "SNP" "Chr" "Pos" # A tibble: 6 × 9 traits SNP Chr Pos start stop search_window url file_name 1 Vg AX76094365 2 32823442 3.28e7 3.28e7 2:32813442-3… http… Vg_AX760… 2 Vg AX259141729 8 17112201 1.71e7 1.71e7 8:17102201-1… http… Vg_AX259… 3 Vg AX295828591 10 2343321 2.33e6 2.35e6 10:2333321-2… http… Vg_AX295… 4 Vg AX327352384 11 10659827 1.06e7 1.07e7 11:10649827-… http… Vg_AX327… 5 Vg AX367573681 12 21860018 2.19e7 2.19e7 12:21850018-… http… Vg_AX367… 6 AGR AX109131000 3 29922827 2.99e7 2.99e7 3:29912827-2… http… AGR_AX10… [1] "Error processing URL: https://plants.ensembl.org/Oryza_sativa/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=2:32813442-32833442;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Oryza_sativa/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=8:17102201-17122201;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Oryza_sativa/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=10:2333321-2353321;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Oryza_sativa/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=11:10649827-10669827;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Oryza_sativa/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=12:21850018-21870018;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Oryza_sativa/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=3:29912827-29932827;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Oryza_sativa/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=7:20176986-20196986;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Oryza_sativa/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=8:20009565-20029565;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Oryza_sativa/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=9:11715818-11735818;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Oryza_sativa/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=2:18349158-18369158;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Oryza_sativa/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=7:24076549-24096549;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" [1] "Error processing URL: https://plants.ensembl.org/Oryza_sativa/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=csv;r=9:12417777-12437777;strand=feature;param=gene;_format=Text Error: Error in open.connection(x, \"rb\"): cannot open the connection\n" Error in geneNR("sample_data_rice", 10000, 10000, crop = "rice") : The data does not contain the expected columns. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [16s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE