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Code should be placed in three backticks as shown below
# Correcting the file path and ensuring proper quoting
BSgenomeForge::forgeBSgenomeDataPkgFromNCBI(
assembly_accession = "GCF_000841925.1",
pkg_maintainer = "Jabez Battu <jabezbattu@gmail.com>",
organism = "Helicoverpa zea Nudivirus-2",
circ_seqs = "NC_004156.2",
destdir = "E:/PhD data/RNAseq/TSS")
This ran succesfully showing this "Creating package in E:/PhD data/RNAseq/TSS/BSgenome.Hnudivirus-2.NCBI.ViralProj14215"
include your problematic code here with any corresponding output
install.packages("E:/PhD data/RNAseq/TSS/BSgenome.Hnudivirus-2.NCBI.ViralProj14215", type ="source")
Installing package into 'C:/Users/bunny/AppData/Local/R/win-library/4.3'
(as 'lib' is unspecified)
Error in install.packages : error reading from connection
# please also include the results of running the following in an R session
sessionInfo( )
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 26100)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_2.4.5 usethis_3.1.0 TSSr_0.99.6 BSgenomeForge_1.2.3
[5] BiocManager_1.30.25 BSgenome_1.70.2 rtracklayer_1.62.0 BiocIO_1.12.0
[9] Biostrings_2.70.3 XVector_0.42.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.8
[13] IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.17.1
[3] magrittr_2.0.3 GenomicFeatures_1.54.4
[5] farver_2.1.2 rmarkdown_2.29
[7] fs_1.6.6 zlibbioc_1.48.2
[9] vctrs_0.6.5 memoise_2.0.1
[11] Rsamtools_2.18.0 RCurl_1.98-1.17
[13] base64enc_0.1-3 htmltools_0.5.8.1
[15] S4Arrays_1.2.1 progress_1.2.3
[17] curl_6.2.2 SparseArray_1.2.4
[19] Formula_1.2-5 htmlwidgets_1.6.4
[21] Gviz_1.46.1 cachem_1.1.0
[23] GenomicAlignments_1.38.2 mime_0.13
[25] lifecycle_1.0.4 pkgconfig_2.0.3
[27] Matrix_1.6-1.1 R6_2.6.1
[29] fastmap_1.2.0 shiny_1.10.0
[31] GenomeInfoDbData_1.2.11 MatrixGenerics_1.14.0
[33] digest_0.6.37 colorspace_2.1-1
[35] AnnotationDbi_1.64.1 DESeq2_1.42.1
[37] pkgload_1.4.0 Hmisc_5.2-3
[39] RSQLite_2.3.9 filelock_1.0.3
[41] httr_1.4.7 abind_1.4-8
[43] compiler_4.3.1 remotes_2.5.0
[45] bit64_4.6.0-1 htmlTable_2.4.3
[47] backports_1.5.0 BiocParallel_1.36.0
[49] DBI_1.2.3 pkgbuild_1.4.7
[51] biomaRt_2.58.2 MASS_7.3-60
[53] sessioninfo_1.2.3 rappdirs_0.3.3
[55] DelayedArray_0.28.0 rjson_0.2.23
[57] tools_4.3.1 foreign_0.8-84
[59] httpuv_1.6.16 nnet_7.3-19
[61] glue_1.8.0 restfulr_0.0.15
[63] promises_1.3.2 grid_4.3.1
[65] checkmate_2.3.2 cluster_2.1.4
[67] generics_0.1.3 gtable_0.3.6
[69] tidyr_1.3.1 ensembldb_2.26.1
[71] data.table_1.17.0 hms_1.1.3
[73] xml2_1.3.8 pillar_1.10.2
[75] stringr_1.5.1 later_1.4.2
[77] dplyr_1.1.4 BiocFileCache_2.10.2
[79] lattice_0.21-8 bit_4.6.0
[81] deldir_2.0-4 biovizBase_1.50.0
[83] tidyselect_1.2.1 locfit_1.5-9.12
[85] miniUI_0.1.2 knitr_1.50
[87] BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0 gridExtra_2.3
[89] ProtGenerics_1.34.0 SummarizedExperiment_1.32.0
[91] xfun_0.52 Biobase_2.62.0
[93] matrixStats_1.5.0 stringi_1.8.7
[95] lazyeval_0.2.2 yaml_2.3.10
[97] evaluate_1.0.3 codetools_0.2-19
[99] interp_1.1-6 tibble_3.2.1
[101] cli_3.6.5 rpart_4.1.19
[103] xtable_1.8-4 dichromat_2.0-0.1
[105] Rcpp_1.0.14 dbplyr_2.5.0
[107] png_0.1-8 XML_3.99-0.18
[109] parallel_4.3.1 ggfortify_0.4.17
[111] ellipsis_0.3.2 ggplot2_3.5.2
[113] blob_1.2.4 prettyunits_1.2.0
[115] profvis_0.4.0 latticeExtra_0.6-30
[117] calibrate_1.7.7 jpeg_0.1-11
[119] urlchecker_1.0.1 AnnotationFilter_1.26.0
[121] bitops_1.0-9 VariantAnnotation_1.48.1
[123] scales_1.4.0 purrr_1.0.4
[125] crayon_1.5.3 rlang_1.1.6
[127] KEGGREST_1.42.0
install.packages("E:/PhD data/RNAseq/TSS/BSgenome.Hnudivirus-2.NCBI.ViralProj14215", repos = NULL, type = "source") Installing package into C:/Users/bunny/AppData/Local/R/win-library/4.3 (as lib is unspecified)
Malformed package name
See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ERROR: installing package DESCRIPTION failed for package 'BSgenome.Hnudivirus-2.NCBI.ViralProj14215'
R doesn't like the name of your package. I would bet that it's the minus sign, so maybe remove that from the name of the package and from the Package line in the DESCRIPTION file and see if it will install.
Hi, I did that and it accepted it now. Thank you very much!
inputFiles <- "wildtype_samples.bam"
Reading in file: wildtype_samples.bam... Error in value[3L] : 'R_Realloc' could not re-allocate memory (293601280 bytes) file: wildtype_samples.bam index: NA
What does this mean?
It means you are running out of memory. You need to install more RAM or get a computer with more RAM