Question: trouble importing data for DEseq2 workflow
0
gravatar for Stanley Yang
7 months ago by
Stanley Yang0 wrote:

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! 

ADD COMMENTlink modified 7 months ago by Michael Love23k • written 7 months ago by Stanley Yang0
Answer: trouble importing data for DEseq2 workflow
1
gravatar for Michael Love
7 months ago by
Michael Love23k
United States
Michael Love23k wrote:

I don't see an error. 

Have you tried seeing if tximport was installed:

library(tximport)

ADD COMMENTlink written 7 months ago by Michael Love23k

Thank you, Michael!!!

Now it works after I typed: 

library(tximport) 

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

ADD REPLYlink written 7 months ago by Stanley Yang0
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