Question

Error: unexpected string constant in "suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE)), when installed the package "Mus.musculus",

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443606623 • 0

@443606623-23755

Last seen 3.9 years ago

When I installed the package "Mus.musculus",

I used the code:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Mus.musculus")

And I had these error below.

Error: unexpected string constant in:
"suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE))
tools:::makeLazyLoading("Mus.musculus", '"
Execution halted
ERROR: lazy loading failed for package 'Mus.musculus'

Hope someone could help me deal with these, thank you very much.

install packages Mus.musculus • 2.2k views

ADD COMMENT • link updated 3.9 years ago by Kevin Blighe ★ 3.9k • written 3.9 years ago by 443606623 • 0

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Please make sure that BiocManager::valid() returns TRUE. Can you please provide the output of traceback() and sessionInfo() ?

ADD REPLY • link 3.9 years ago Martin Morgan 25k

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> traceback()
No traceback available 
> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 
[2] LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6         compiler_4.0.0       RColorBrewer_1.1-2  
 [4] BiocManager_1.30.10  bitops_1.0-6         tools_4.0.0         
 [7] digest_0.6.25        bit_1.1-15.2         jsonlite_1.6.1      
[10] RSQLite_2.2.0        memoise_1.1.0        lattice_0.20-41     
[13] rlang_0.4.6          DBI_1.1.0            parallel_4.0.0      
[16] Glimma_1.17.1        vctrs_0.3.0          S4Vectors_0.27.12   
[19] gtools_3.8.2         caTools_1.18.0       IRanges_2.23.10     
[22] locfit_1.5-9.4       stats4_4.0.0         bit64_0.9-7         
[25] grid_4.0.0           Biobase_2.49.0       AnnotationDbi_1.51.0
[28] gdata_2.18.0         limma_3.44.3         blob_1.2.1          
[31] edgeR_3.30.3         gplots_3.0.3         BiocGenerics_0.35.4 
[34] KernSmooth_2.23-17   RCurl_1.98-1.2

Thank you very much.

ADD REPLY • link updated 3.9 years ago by Martin Morgan 25k • written 3.9 years ago by 443606623 • 0

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> BiocManager::valid()

* sessionInfo()

R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 
[2] LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6         compiler_4.0.0       RColorBrewer_1.1-2  
 [4] BiocManager_1.30.10  bitops_1.0-6         tools_4.0.0         
 [7] digest_0.6.25        bit_1.1-15.2         jsonlite_1.6.1      
[10] RSQLite_2.2.0        memoise_1.1.0        lattice_0.20-41     
[13] rlang_0.4.6          DBI_1.1.0            parallel_4.0.0      
[16] Glimma_1.17.1        vctrs_0.3.0          S4Vectors_0.27.12   
[19] gtools_3.8.2         caTools_1.18.0       IRanges_2.23.10     
[22] locfit_1.5-9.4       stats4_4.0.0         bit64_0.9-7         
[25] grid_4.0.0           Biobase_2.49.0       AnnotationDbi_1.51.0
[28] gdata_2.18.0         limma_3.44.3         blob_1.2.1          
[31] edgeR_3.30.3         gplots_3.0.3         BiocGenerics_0.35.4 
[34] KernSmooth_2.23-17   RCurl_1.98-1.2      

Bioconductor version '3.12'

  * 17 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install(c(
    "backports", "bookdown", "DelayedArray", "DT", "edgeR", "ggforce", "GO.db",
    "gower", "jsonlite", "knitr", "limma", "org.Mm.eg.db", "raster", "RcppParallel",
    "rgdal", "TxDb.Mmusculus.UCSC.mm10.knownGene", "vctrs"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning messages:
1: In readChar(...) : can only read in bytes in a non-UTF-8 MBCS locale
2: In readChar(...) : can only read in bytes in a non-UTF-8 MBCS locale
3: In readChar(...) : can only read in bytes in a non-UTF-8 MBCS locale
4: In readChar(...) : can only read in bytes in a non-UTF-8 MBCS locale
5: In readChar(...) : can only read in bytes in a non-UTF-8 MBCS locale
6: 17 packages out-of-date; 0 packages too new

ADD REPLY • link updated 3.9 years ago by Martin Morgan 25k • written 3.9 years ago by 443606623 • 0

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You could try the suggestion from BiocManager::valid() to run:

BiocManager::install(c(
    "backports", "bookdown", "DelayedArray", "DT", "edgeR", "ggforce", "GO.db",
    "gower", "jsonlite", "knitr", "limma", "org.Mm.eg.db", "raster", "RcppParallel",
    "rgdal", "TxDb.Mmusculus.UCSC.mm10.knownGene", "vctrs"
  ), update = TRUE, ask = FALSE)

ADD REPLY • link 3.9 years ago Kevin Blighe ★ 3.9k