metage problem with DESeq
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0
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GM ▴ 10
@gm
Last seen 3 days ago
Sint-Martens-Latem

Hello,

I 'm trying to use the packages metagene and metagene2 but I 'm getting the following error.

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

When I 'm trying to install DESeq I get the following error.

package ‘DESeq’ is not available for this version of R

Any idea how to proceed?

R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocParallel_1.24.1  GenomicRanges_1.42.0 GenomeInfoDb_1.26.2  IRanges_2.24.1       S4Vectors_0.28.1     BiocGenerics_0.36.0  R6_2.5.0            
[8] BiocManager_1.30.10 

loaded via a namespace (and not attached):
 [1] locfit_1.5-9.4              Rcpp_1.0.6                  lattice_0.20-41             Rsamtools_2.6.0             Biostrings_2.58.0          
 [6] assertthat_0.2.1            digest_0.6.27               utf8_1.1.4                  evaluate_0.14               ggplot2_3.3.3              
[11] pillar_1.5.0                zlibbioc_1.36.0             rlang_0.4.10                rstudioapi_0.13             Matrix_1.3-2               
[16] rmarkdown_2.7               readr_1.4.0                 RCurl_1.98-1.2              munsell_0.5.0               tinytex_0.30               
[21] DelayedArray_0.16.2         compiler_4.0.4              xfun_0.21                   pkgconfig_2.0.3             tidygenomics_0.1.2         
[26] htmltools_0.5.1.1           tidyselect_1.1.0            SummarizedExperiment_1.20.0 tibble_3.1.0                GenomeInfoDbData_1.2.4     
[31] edgeR_3.32.1                matrixStats_0.58.0          fansi_0.4.2                 crayon_1.4.1                dplyr_1.0.4                
[36] GenomicAlignments_1.26.0    bitops_1.0-6                grid_4.0.4                  gtable_0.3.0                lifecycle_1.0.0            
[41] DBI_1.1.1                   magrittr_2.0.1              scales_1.1.1                XVector_0.30.0              limma_3.46.0               
[46] ellipsis_0.3.1              generics_0.1.0              vctrs_0.3.6                 tools_4.0.4                 Biobase_2.50.0             
[51] glue_1.4.2                  purrr_0.3.4                 hms_1.0.0                   MatrixGenerics_1.2.1        yaml_2.2.1                 
[56] colorspace_2.0-0            knitr_1.31
DESeq metagene2 metagene • 236 views
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Entering edit mode

I also encountered this problem, and have contacted the package maintainer. I will post any resolution to the problem on my thread.

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Entering edit mode
@0f19c65e
Last seen 6 months ago

Hi,

I'm the maintener of metagene2. Sorry for not catching your post sooner.

The dependency for DESeq was removed in the devl version of metagene2, but not for the release version. This was a mistake, and I've pushed a fix to the release branch of Bioconductor (metagene2 version 1.6.1) which should make metagene2 install correctly. The package should be updated in the next Bioconductor build, which I believe occurs nightly.

I'll update this answer once I've validated the fix did publish correctly. In the meantime, you can fix this issue by installing the devel version of metagene2.

Cheers, -Eric

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