I cannot install "microbiome"
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kikiki • 0
@61191329
Last seen 8 weeks ago
Japan

Hi there, i cannot install package "microbiome" in R (ver 4.2.1),

when i input the code, it seems OK,

BiocManager::install("microbiome", force = TRUE)


'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Installing package(s) 'microbiome'
trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/windows/contrib/4.2/microbiome_1.18.0.zip'
Content type 'application/zip' length 1044918 bytes (1020 KB)
downloaded 1020 KB

package ‘microbiome’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\work\AppData\Local\Temp\RtmpklUZ1g\downloaded_packages

but...

library(microbiome)

Loading required package: phyloseq
Error: package or namespace load failed for ‘phyloseq’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GenomeInfoDbData’
Error: package ‘phyloseq’ could not be loaded

So, i tried to install "phyloseq",

BiocManager::install("phyloseq", force = TRUE)

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Installing package(s) 'phyloseq'
trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/windows/contrib/4.2/phyloseq_1.40.0.zip'
Content type 'application/zip' length 4630961 bytes (4.4 MB)
downloaded 4.4 MB

package ‘phyloseq’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\work\AppData\Local\Temp\RtmpklUZ1g\downloaded_packages

but...

library(phyloseq)

Error: package or namespace load failed for ‘phyloseq’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GenomeInfoDbData’

then, i tried to install "GenomeInfoDbData", but...

BiocManager::install("GenomeInfoDbData", force = TRUE)

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Installing package(s) 'GenomeInfoDbData'
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GenomeInfoDbData_1.2.8.tar.gz'
Content type 'application/x-gzip' length 11512907 bytes (11.0 MB)
downloaded 11.0 MB


The downloaded source packages are in
    ‘C:\Users\work\AppData\Local\Temp\RtmpklUZ1g\downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status

i checked the library, there is no "GenomeInfoDbData" there,

remove.packages("GenomeInfoDbData", lib = "C:/Users/work/AppData/Local/R/win-library/4.2")
Error in remove.packages : there is no package called ‘GenomeInfoDbData’
remove.packages("GenomeInfoDbData", lib = "C:/Program Files/R/R-4.2.1/library")
Error in remove.packages : there is no package called ‘GenomeInfoDbData’

how can i resolve this error? Thank you !

GenomeInfoDbData microbiome phyloseq • 198 views
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Is there any additional output / ERROR when you try

BiocManager::install("GenomeInfoDbData")
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Thank you for reply~

enter image description here

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Hi @61191329 ,

Unfortunately, I am unable to reproduce the issue on Windows. Please provide additional information, namely BiocManager::valid(), .libPaths(), and sessionInfo().

sessionInfo()

R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

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

other attached packages:
[1] microbiome_1.18.0   ggplot2_3.3.6       phyloseq_1.40.0     BiocManager_1.30.18

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.2       reshape2_1.4.4         purrr_0.3.4            splines_4.2.1          lattice_0.20-45        rhdf5_2.40.0           colorspace_2.0-3      
 [8] vctrs_0.4.1            generics_0.1.3         stats4_4.2.1           mgcv_1.8-40            utf8_1.2.2             survival_3.3-1         rlang_1.0.4           
[15] pillar_1.8.0           withr_2.5.0            DBI_1.1.3              glue_1.6.2             BiocGenerics_0.42.0    GenomeInfoDbData_1.2.8 foreach_1.5.2         
[22] lifecycle_1.0.1        plyr_1.8.7             stringr_1.4.0          zlibbioc_1.42.0        Biostrings_2.64.0      munsell_0.5.0          gtable_0.3.0          
[29] codetools_0.2-18       Biobase_2.56.0         permute_0.9-7          IRanges_2.30.0         GenomeInfoDb_1.32.3    biomformat_1.24.0      parallel_4.2.1        
[36] fansi_1.0.3            Rcpp_1.0.9             scales_1.2.0           vegan_2.6-2            S4Vectors_0.34.0       jsonlite_1.8.0         XVector_0.36.0        
[43] Rtsne_0.16             stringi_1.7.8          dplyr_1.0.9            grid_4.2.1             ade4_1.7-19            cli_3.3.0              tools_4.2.1           
[50] rhdf5filters_1.8.0     bitops_1.0-7           magrittr_2.0.3         RCurl_1.98-1.8         tibble_3.1.8           cluster_2.1.3          tidyr_1.2.0           
[57] crayon_1.5.1           ape_5.6-2              pkgconfig_2.0.3        MASS_7.3-57            Matrix_1.4-1           data.table_1.14.2      iterators_1.0.14      
[64] Rhdf5lib_1.18.2        R6_2.5.1               multtest_2.52.0        igraph_1.3.4           nlme_3.1-157           compiler_4.2.1

Best,

Marcel

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