Question: Cannot install GO.db for R 3.6.1
0
gravatar for Quinten
21 days ago by
Quinten0
Quinten0 wrote:

Hi all,

I've recently updated my R to the newest version (3.6.1) and updated all my packages. However, one of the functions which previously worked perfectly fine, now produces an error, as the GO.db package is not available. For some reason I cannot install the GO.db package, I've tried multiple things and visited other webpages for problems with this package. So, I have compatible Rtools (v3.5) and RSQLite (which seemed to give problems with other people, e.g. https://www.biostars.org/p/133369/. So, when I run BiocManager::install("GO.db") I get the following error.

Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
Installing package(s) 'GO.db'
cannot open URL 'https://bioconductor.org/packages/3.9/data/experiment/bin/windows/contrib/3.6/PACKAGES.rds': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.9/workflows/bin/windows/contrib/3.6/PACKAGES.rds': HTTP status was '404 Not Found'installing the source package �GO.db�

trying URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GO.db_3.8.2.tar.gz'
Content type 'application/x-gzip' length 31820866 bytes (30.3 MB)
downloaded 30.3 MB

* installing *source* package 'GO.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in findpack(package, lib.loc) : there is no package called 'GO.db'
Calls: <Anonymous> -> findpack
Execution halted
ERROR: lazy loading failed for package 'GO.db'

I subsequently tried to install the package by downloading GO.db_3.8.2.tar.gz to my local computer, and then install from source, which also didn't work. I'm a bit at a loss now, and would very much appreciate any help!

Best, Quinten

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252   
[3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C                      
[5] LC_TIME=Dutch_Netherlands.1252    

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

other attached packages:
[1] devtools_2.1.0 usethis_1.5.1 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1         rstudioapi_0.10    knitr_1.23         magrittr_1.5      
 [5] pkgload_1.0.2      tidyselect_0.2.5   R6_2.4.0           rlang_0.4.0       
 [9] dplyr_0.8.3        tools_3.6.1        pkgbuild_1.0.3     xfun_0.8          
[13] sessioninfo_1.1.1  cli_1.1.0          withr_2.1.2        remotes_2.1.0     
[17] rprojroot_1.3-2    assertthat_0.2.1   digest_0.6.20      tibble_2.1.3      
[21] crayon_1.3.4       processx_3.4.1     BiocManager_1.30.4 purrr_0.3.2       
[25] callr_3.3.1        fs_1.3.1           ps_1.3.0           testthat_2.1.1    
[29] memoise_1.1.0      glue_1.3.1         compiler_3.6.1     pillar_1.4.2      
[33] backports_1.1.4    desc_1.2.0         prettyunits_1.0.2  pkgconfig_2.0.2
ADD COMMENTlink modified 21 days ago by Martin Morgan ♦♦ 23k • written 21 days ago by Quinten0

Are there other versions of GO.db already installed ("GO.db" %in% rownames(installed.packages())? If so remove them with remove.packages("GO.db").

Is the temporary directory tempdir() on a network share or in a location with a space in the path name?

ADD REPLYlink written 21 days ago by Martin Morgan ♦♦ 23k

Dear Martin,

Thanks for your extremely quick reply

GO.db has not been installed yet (only GOstats). tempdir() is on the C:: drive of the PC, and no space in present in the path name, see below

> tempdir()  
[1] "C:\\Users\\QRDUCA~1\\AppData\\Local\\Temp\\RtmpOwYY6B"
One more thing I did not add in the previous post, although I am not sure if it is related, as nothing of the sort displays in the error message: 

Bioconductor version '3.9'

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

create a valid installation with

  BiocManager::install(c(
    "bayesm", "BiocParallel", "curl", "foreach", "iterators", "quantreg", "Rcpp",
    "testthat", "xml2"
  ), update = TRUE, ask = FALSE)

  There are binary versions available but the source versions are later:

  Binaries will be installed

Not all of these packages could be successfully updated. Could this be related to GO.db (even though it does not seem to pop up in the error message)? Or something completely different?

Best, Quinten

ADD REPLYlink written 21 days ago by Quinten0
Answer: Cannot install GO.db for R 3.6.1
0
gravatar for Martin Morgan
21 days ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

I don't really understand the source of this problem. I think a work-around is

BiocManager::install("GO.db", INSTALL_opts="--no-test-load")
ADD COMMENTlink written 21 days ago by Martin Morgan ♦♦ 23k

Dear Martin,

Thanks again for the quick reply. It doesn't work.... I get the same error message, see below =(. Any other ideas? Just out of curiosity, what was the idea behind INSTALL_opts="--no-test-load" ?

> BiocManager::install("GO.db", INSTALL_opts="--no-test-load")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
Installing package(s) 'GO.db'
installing the source package ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GO.db_3.8.2.tar.gz'
Content type 'application/x-gzip' length 31820866 bytes (30.3 MB)
downloaded 30.3 MB

* installing *source* package 'GO.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in findpack(package, lib.loc) : there is no package called 'GO.db'
Calls: <Anonymous> -> findpack
Execution halted
ERROR: lazy loading failed for package 'GO.db'
* removing '\\vf-lumc-home/lumc-home$/qrducarmon/MyDocs/R/win-library/3.6/GO.db'

The downloaded source packages are in
    ‘C:\Users\qrducarmon\AppData\Local\Temp\Rtmp4ClTj0\downloaded_packages’
installation path not writeable, unable to update packages: boot
Update old packages: 'bayesm', 'BiocParallel', 'foreach', 'iterators', 'quantreg', 'xml2'
Update all/some/none? [a/s/n]:

Best, Quinten

ADD REPLYlink written 21 days ago by Quinten0

Please take a second to format your code chunks (select the code chunk and choose the icon with 101/010); I've been cleaning up after you.

The error message is different or you've provided more info, in particular

* removing '\\vf-lumc-home/lumc-home$/qrducarmon/MyDocs/R/win-library/3.6/GO.db'

which is a network drive; can you map this network drive to a non-network drive, and use that or another path to define .libPaths() so that the first entry (e.g., .libPaths(c("c:/non/network/ilbrary", .libPaths())) is a non-network drive?

ADD REPLYlink written 21 days ago by Martin Morgan ♦♦ 23k
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