trouble importing data for DEseq2 workflow
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@stanley-yang-12536
Last seen 2.4 years ago

Hi 

I'm trying the latest version of DESeq2 workflow, but have trouble loading "tximport", "tximportData", "pasilla" packages to begin with. 

Here is my error for installing "tximport". Error messages for other packages are the same. 

> BiocManager::install("tximport")

Bioconductor version 3.8 (BiocManager 1.30.2), R 3.5.1 (2018-07-02)

Installing package(s) 'tximport'

trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/macosx/el-capitan/contrib/3.5/tximport_1.9.12.tgz'

Content type 'application/x-gzip' length 247885 bytes (242 KB)

==================================================

downloaded 242 KB



The downloaded binary packages are in

/var/folders/vs/z75wlg1d603_b5qkzs92mhlng7wwqk/T//RtmpxuOhzO/downloaded_packages

installation path not writeable, unable to update packages: foreign, survival

 

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] DESeq2_1.21.22              SummarizedExperiment_1.11.6 DelayedArray_0.7.47         BiocParallel_1.15.15        matrixStats_0.54.0         
 [6] GenomicRanges_1.33.14       GenomeInfoDb_1.17.2         org.Mm.eg.db_3.6.0          AnnotationDbi_1.43.1        IRanges_2.15.18            
[11] S4Vectors_0.19.20           Biobase_2.41.2              BiocGenerics_0.27.1         bindrcpp_0.2.2              forcats_0.3.0              
[16] stringr_1.3.1               dplyr_0.7.6                 purrr_0.2.5                 readr_1.1.1                 tidyr_0.8.1                
[21] tibble_1.4.2                ggplot2_3.0.0               tidyverse_1.2.1             edgeR_3.23.5                limma_3.37.7               

loaded via a namespace (and not attached):
 [1] nlme_3.1-137           bitops_1.0-6           lubridate_1.7.4        bit64_0.9-7            RColorBrewer_1.1-2     httr_1.3.1            
 [7] tools_3.5.1            backports_1.1.2        utf8_1.1.4             R6_2.3.0               rpart_4.1-13           Hmisc_4.1-1           
[13] DBI_1.0.0              lazyeval_0.2.1         colorspace_1.3-2       nnet_7.3-12            withr_2.1.2            gridExtra_2.3         
[19] tidyselect_0.2.4       bit_1.1-14             compiler_3.5.1         cli_1.0.1              rvest_0.3.2            htmlTable_1.12        
[25] xml2_1.2.0             checkmate_1.8.5        scales_1.0.0           genefilter_1.63.2      digest_0.6.17          foreign_0.8-71        
[31] XVector_0.21.4         htmltools_0.3.6        base64enc_0.1-3        pkgconfig_2.0.2        htmlwidgets_1.3        rlang_0.2.2           
[37] readxl_1.1.0           rstudioapi_0.8         RSQLite_2.1.1          bindr_0.1.1            jsonlite_1.5           acepack_1.4.1         
[43] RCurl_1.95-4.11        magrittr_1.5           GenomeInfoDbData_1.2.0 Formula_1.2-3          Matrix_1.2-14          Rcpp_0.12.19          
[49] munsell_0.5.0          fansi_0.4.0            stringi_1.2.4          yaml_2.2.0             zlibbioc_1.27.0        plyr_1.8.4            
[55] grid_3.5.1             blob_1.1.1             crayon_1.3.4           lattice_0.20-35        haven_1.1.2            splines_3.5.1         
[61] annotate_1.59.1        hms_0.4.2              locfit_1.5-9.1         knitr_1.20             pillar_1.3.0           geneplotter_1.59.0    
[67] XML_3.98-1.16          glue_1.3.0             latticeExtra_0.6-28    data.table_1.11.8      BiocManager_1.30.2     modelr_0.1.2          
[73] cellranger_1.1.0       gtable_0.2.0           assertthat_0.2.0       xtable_1.8-3           broom_0.5.0            survival_2.42-3       
[79] memoise_1.1.0          cluster_2.0.7-1        statmod_1.4.30  

Could anyone have any suggestion to fix the issue? 

Thank you in advance! 

deseq2 tximport tximportdata pasilla Tutorial • 338 views
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@mikelove
Last seen 15 hours ago
United States

I don't see an error. 

Have you tried seeing if tximport was installed:

library(tximport)

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Thank you, Michael!!!

Now it works after I typed: 

library(tximport) 

I was worried about the installation was not successful.  Thank you! 

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