Good evening everyone!
I'm experiencing problems with installation of packages and would be grateful for any help. I need a package to enable download of data from TCGA, and I've tried with both TCGAbiolinks and RTCGAToolbox. As described on the software package page, I've written the following to initiate the installation:
if (!requireNamespace("BiocManager", quietly = TRUE)) + install.packages("BiocManager") BiocManager::install("TCGAbiolinks")
But for both TCGAbiolinks and RTCGAToolbox, the same thing happens. Everything seems to work, but then I get this message:
Warning messages: 1: In install.packages(...) : installation of package ‘TCGAbiolinks’ had non-zero exit status 2: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\ju3564li\Documents\R\win-library\4.0\00LOCK\rlang\libs\x64\rlang.dll to C:\Users\ju3564li\Documents\R\win-library\4.0\rlang\libs\x64\rlang.dll: Permission denied
I've tried Tools --> Install Packages --> and change "Install to library" to "R-4.0.0/library", but as I can't select Bioconductor as repository (CRAN and package archive file are the only options), I can't access the libraries this way.
Here is my session info:
sessioninfo() R version 4.0.0 (2020-04-24) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale:  LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C  LC_TIME=Swedish_Sweden.1252 attached base packages:  parallel stats graphics grDevices utils datasets methods base other attached packages:  RJSONIO_1.3-1.4 jsonlite_1.6.1 rjson_0.2.20 readr_1.3.1 doParallel_1.0.15 iterators_1.0.12 foreach_1.5.0 loaded via a namespace (and not attached):  bitops_1.0-6 matrixStats_0.56.0 HiveR_0.3.42 bit64_0.9-7 webshot_0.5.2  RColorBrewer_1.1-2 GenomeInfoDb_1.24.0 tools_4.0.0 utf8_1.1.4 R6_2.4.1  DBI_1.1.0 BiocGenerics_0.34.0 colorspace_1.4-1 manipulateWidget_0.10.1 tidyselect_1.0.0  gridExtra_2.3 bit_1.1-15.2 compiler_4.0.0 RISmed_2.1.7 cli_2.0.2  Biobase_2.48.0 tkrgl_0.9 xml2_1.3.2 DelayedArray_0.14.0 scales_1.1.0  stringr_1.4.0 digest_0.6.25 DOSE_3.14.0 GEOquery_2.56.0 XVector_0.28.0  jpeg_0.1-8.1 pkgconfig_2.0.3 htmltools_0.4.0 limma_3.44.1 fastmap_1.0.1  htmlwidgets_1.5.1 rlang_0.4.5 rstudioapi_0.11 RSQLite_2.2.0 shiny_184.108.40.206  crosstalk_220.127.116.11 BiocParallel_1.22.0 GOSemSim_2.14.0 dplyr_0.8.5 RCurl_1.98-1.2  magrittr_1.5 GO.db_3.11.0 GenomeInfoDbData_1.2.3 Matrix_1.2-18 fansi_0.4.1  Rcpp_18.104.22.168 munsell_0.5.0 S4Vectors_0.26.0 lifecycle_0.2.0 yaml_2.2.1  stringi_1.4.6 SummarizedExperiment_1.18.1 zlibbioc_1.34.0 plyr_1.8.6 qvalue_2.20.0  grid_4.0.0 blob_1.2.1 promises_1.1.0 DO.db_2.9 crayon_1.3.4  miniUI_0.1.1.1 lattice_0.20-41 splines_4.0.0 hms_0.5.3 knitr_1.28  pillar_1.4.4 fgsea_1.14.0 tcltk_4.0.0 GenomicRanges_1.40.0 reshape2_1.4.4  codetools_0.2-16 stats4_4.0.0 fastmatch_1.1-0 glue_1.4.0 data.table_1.12.8  BiocManager_1.30.10 png_0.1-7 vctrs_0.2.4 httpuv_1.5.2 tidyr_1.0.2  gtable_0.3.0 purrr_0.3.4 assertthat_0.2.1 ggplot2_3.3.0 xfun_0.13  mime_0.9 xtable_1.8-4 later_1.0.0 tibble_3.0.1 AnnotationDbi_1.50.0  memoise_1.1.0 IRanges_2.22.1 rgl_0.100.54 ellipsis_0.3.0
Does anyone have any idea of what I can do to fix this problem?
Best regards, Julia