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Stanley Yang
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@stanley-yang-12536
Last seen 5.5 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.
![](<a href="https://imgur.com/WR0vwgg"><img src="https://i.imgur.com/WR0vwgg.png" title="source: imgur.com" /></a>)
> 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!
Thank you, Michael!!!
Now it works after I typed:
library(tximport)
I was worried about the installation was not successful. Thank you!