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ms_toxo
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@ms_toxo
Last seen 3.3 years ago
Hi there!
I'm having trouble installing the BSgenome.Tgondii.ToxoDB.7.0 package. I can install other BSgenomes ok (e.g. BSgenome.Scerevisiae.UCSC.sacCer2 as shown) just not the Toxoplasma one. Can anybody point me in the right direction? I've included the R inputs/session info below.
Thanks in advance!
> if (!requireNamespace("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
> BiocManager::install("BSgenome.Tgondii.ToxoDB.7.0")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'BSgenome.Tgondii.ToxoDB.7.0'
installing the source package 'BSgenome.Tgondii.ToxoDB.7.0'
trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/BSgenome.Tgondii.ToxoDB.7.0_0.99.0.tar.gz'
Content type 'application/x-gzip' length 18178436 bytes (17.3 MB)
==================================================
downloaded 17.3 MB
* installing *source* package ‘BSgenome.Tgondii.ToxoDB.7.0’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'BSgenome(organism = "Toxoplasma gondii", ': unused arguments (nmask_per_seq = .nmask_per_seq, masks_pkgname = pkgname, masks_dir = extdata_dir)
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘BSgenome.Tgondii.ToxoDB.7.0’:
.onLoad failed in loadNamespace() for 'BSgenome.Tgondii.ToxoDB.7.0', details:
call: BSgenome(organism = "Toxoplasma gondii", species = "Toxoplasma gondii",
error: unused arguments (nmask_per_seq = .nmask_per_seq, masks_pkgname = pkgname, masks_dir = extdata_dir)
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BSgenome.Tgondii.ToxoDB.7.0’
The downloaded source packages are in
'/private/var/folders/1h/rvmwv33940vf3rfb8y80mz2m0000gn/T/RtmpgOSmmY/downloaded_packages'
Warning message:
In install.packages(...) :
installation of package 'BSgenome.Tgondii.ToxoDB.7.0' had non-zero exit status
> BiocManager::install("BSgenome.Scerevisiae.UCSC.sacCer2")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'BSgenome.Scerevisiae.UCSC.sacCer2'
installing the source package ‘BSgenome.Scerevisiae.UCSC.sacCer2’
trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz'
Content type 'application/x-gzip' length 2967843 bytes (2.8 MB)
==================================================
downloaded 2.8 MB
* installing *source* package ‘BSgenome.Scerevisiae.UCSC.sacCer2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BSgenome.Scerevisiae.UCSC.sacCer2)
The downloaded source packages are in
‘/private/var/folders/1h/rvmwv33940vf3rfb8y80mz2m0000gn/T/RtmpgOSmmY/downloaded_packages’
sessionInfo( )
> sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] IsoformSwitchAnalyzeR_1.12.0 ggplot2_3.3.3 DEXSeq_1.36.0 RColorBrewer_1.1-2 AnnotationDbi_1.52.0 DESeq2_1.30.0
[7] SummarizedExperiment_1.20.0 MatrixGenerics_1.2.0 matrixStats_0.57.0 Biobase_2.50.0 BiocParallel_1.24.1 limma_3.46.0
[13] BSgenome_1.58.0 rtracklayer_1.50.0 Biostrings_2.58.0 XVector_0.30.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.2
[19] IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.0
loaded via a namespace (and not attached):
[1] colorspace_2.0-0 hwriter_1.3.2 ellipsis_0.3.1 futile.logger_1.4.3 rstudioapi_0.13 bit64_4.0.5
[7] fansi_0.4.1 interactiveDisplayBase_1.28.0 xml2_1.3.2 splines_4.0.3 tximport_1.18.0 geneplotter_1.68.0
[13] jsonlite_1.7.2 Rsamtools_2.6.0 annotate_1.68.0 dbplyr_2.0.0 shiny_1.5.0 readr_1.4.0
[19] BiocManager_1.30.10 compiler_4.0.3 httr_1.4.2 assertthat_0.2.1 Matrix_1.3-2 fastmap_1.0.1
[25] lazyeval_0.2.2 cli_2.2.0 later_1.1.0.1 formatR_1.7 htmltools_0.5.0 prettyunits_1.1.1
[31] tools_4.0.3 gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.4 reshape2_1.4.4 dplyr_1.0.2
[37] rappdirs_0.3.1 Rcpp_1.0.5 DRIMSeq_1.18.0 vctrs_0.3.6 stringr_1.4.0 ps_1.5.0
[43] mime_0.9 lifecycle_0.2.0 ensembldb_2.14.0 statmod_1.4.35 XML_3.99-0.5 edgeR_3.32.0
[49] AnnotationHub_2.22.0 zlibbioc_1.36.0 scales_1.1.1 hms_0.5.3 promises_1.1.1 ProtGenerics_1.22.0
[55] AnnotationFilter_1.14.0 lambda.r_1.2.4 yaml_2.2.1 curl_4.3 memoise_1.1.0 gridExtra_2.3
[61] biomaRt_2.46.0 stringi_1.5.3 RSQLite_2.2.1 BiocVersion_3.12.0 genefilter_1.72.0 GenomicFeatures_1.42.1
[67] rlang_0.4.10 pkgconfig_2.0.3 bitops_1.0-6 lattice_0.20-41 purrr_0.3.4 GenomicAlignments_1.26.0
[73] bit_4.0.4 tidyselect_1.1.0 plyr_1.8.6 magrittr_2.0.1 R6_2.5.0 generics_0.1.0
[79] DelayedArray_0.16.0 DBI_1.1.0 pillar_1.4.7 withr_2.3.0 survival_3.2-7 RCurl_1.98-1.2
[85] tibble_3.0.4 tximeta_1.8.3 crayon_1.3.4 futile.options_1.0.1 BiocFileCache_1.14.0 progress_1.2.2
[91] locfit_1.5-9.4 grid_4.0.3 blob_1.2.1 digest_0.6.27 xtable_1.8-4 VennDiagram_1.6.20
[97] httpuv_1.5.4 openssl_1.4.3 munsell_0.5.0 askpass_1.1
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