BSgenome.Tgondii.ToxoDB.7.0 package installation problem
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Entering edit mode
ms_toxo • 0
@ms_toxo
Last seen 16 months 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                  
>
BSgenome.Tgondii.ToxoDB.7.0 • 224 views
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Entering edit mode
@herve-pages-1542
Last seen 20 hours ago
Seattle, WA, United States

Should be fixed in BSgenome.Tgondii.ToxoDB.7.0 version 0.99.1 (will became available via BiocManager::install() in the next 2-3 hours). Sorry for the delay.

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