"Permission denied" when installing TCGAbiolinks and RTCGAToolbox
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@juliatutzauer-23483
Last seen 8 months ago

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:
[1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252    LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C                   
[5] LC_TIME=Swedish_Sweden.1252    

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

other attached packages:
[1] 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):
 [1] bitops_1.0-6                matrixStats_0.56.0          HiveR_0.3.42                bit64_0.9-7                 webshot_0.5.2              
 [6] RColorBrewer_1.1-2          GenomeInfoDb_1.24.0         tools_4.0.0                 utf8_1.1.4                  R6_2.4.1                   
[11] DBI_1.1.0                   BiocGenerics_0.34.0         colorspace_1.4-1            manipulateWidget_0.10.1     tidyselect_1.0.0           
[16] gridExtra_2.3               bit_1.1-15.2                compiler_4.0.0              RISmed_2.1.7                cli_2.0.2                  
[21] Biobase_2.48.0              tkrgl_0.9                   xml2_1.3.2                  DelayedArray_0.14.0         scales_1.1.0               
[26] stringr_1.4.0               digest_0.6.25               DOSE_3.14.0                 GEOquery_2.56.0             XVector_0.28.0             
[31] jpeg_0.1-8.1                pkgconfig_2.0.3             htmltools_0.4.0             limma_3.44.1                fastmap_1.0.1              
[36] htmlwidgets_1.5.1           rlang_0.4.5                 rstudioapi_0.11             RSQLite_2.2.0               shiny_1.4.0.2              
[41] crosstalk_1.1.0.1           BiocParallel_1.22.0         GOSemSim_2.14.0             dplyr_0.8.5                 RCurl_1.98-1.2             
[46] magrittr_1.5                GO.db_3.11.0                GenomeInfoDbData_1.2.3      Matrix_1.2-18               fansi_0.4.1                
[51] Rcpp_1.0.4.6                munsell_0.5.0               S4Vectors_0.26.0            lifecycle_0.2.0             yaml_2.2.1                 
[56] stringi_1.4.6               SummarizedExperiment_1.18.1 zlibbioc_1.34.0             plyr_1.8.6                  qvalue_2.20.0              
[61] grid_4.0.0                  blob_1.2.1                  promises_1.1.0              DO.db_2.9                   crayon_1.3.4               
[66] miniUI_0.1.1.1              lattice_0.20-41             splines_4.0.0               hms_0.5.3                   knitr_1.28                 
[71] pillar_1.4.4                fgsea_1.14.0                tcltk_4.0.0                 GenomicRanges_1.40.0        reshape2_1.4.4             
[76] codetools_0.2-16            stats4_4.0.0                fastmatch_1.1-0             glue_1.4.0                  data.table_1.12.8          
[81] BiocManager_1.30.10         png_0.1-7                   vctrs_0.2.4                 httpuv_1.5.2                tidyr_1.0.2                
[86] gtable_0.3.0                purrr_0.3.4                 assertthat_0.2.1            ggplot2_3.3.0               xfun_0.13                  
[91] mime_0.9                    xtable_1.8-4                later_1.0.0                 tibble_3.0.1                AnnotationDbi_1.50.0       
[96] 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

installation permission denied RTCGAToolbox TCGAbiolinks • 503 views
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Simplify the problem by (trying to) install only the problematic package

BiocManager::install("rlang")

If this fails, make sure that there are no other R processes running on your computer, remove rlang

remove.packages("rlang")

(perhaps issuing the command several times) and then try installing again.

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0
Entering edit mode

Hi Julia,

Have you checked your installation of Bioconductor by doing BiocManager::valid()?

What does the packageVersion("BiocVersion") say?

The permission denied issues may happen when you have a package library that resides in a Windows partition. I am not sure but it would be helpful if you can provide the full error message (for RTCGAToolbox) as well as the result of above commands. Thank you.

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Entering edit mode

Hi Martin and Marcel!

I'm really grateful for all this help!

I tried to reinstall rlang, but still got error messages when trying to install TCGAbiolinks.

packageVersion("BiocVersion") says ‘3.11.1’ and BiocManager::valid() gives:

* 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:
[1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252    LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C                   
[5] LC_TIME=Swedish_Sweden.1252    

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

other attached packages:
[1] doParallel_1.0.15 iterators_1.0.12  foreach_1.5.0    

loaded via a namespace (and not attached):
......
.....

Bioconductor version '3.11'

  * 5 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install(c(
    "git2r", "openxlsx", "rlang", "tidyr", "zoo"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
5 packages out-of-date; 0 packages too new 

So apparently 5 packages are too old. I tried to re-install them separately. and tried again with BiocManager::install("TCGAbiolinks"), and it worked!

Thank you again, this has really been worth a lot to me!

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