Installation Failure

[ndjayne]

So I installed ~2 days ago, no major issues. However, today, while helping a colleague I got this error then got it myself trying the same install:

Error: Failed to install 'depmap' from GitHub: (converted from warning) installation of package ‘C:/Users/username/AppData/Local/Temp/Rtmp4uHAOP/file2b249ff41c2/depmap_0.99.5.tar.gz’ had non-zero exit status

[lgatto]

I suspect that's because yesterday we pushed a update with the 19_Q3 data. You will need the development version of Bioconductor to use that.

[lgatto]

Also, to be able to help, developers need the actual error message and the output of sessionInfo().

[ndjayne]

[lgatto]

No, that only tells that installation failed, but not why it fails. Here is the kind of output we need.

Here is an example output that tells us that the installation fails because data 19_Q2 is missing, which is the result of this computer running the release version of Bioconductor (i.e 3.9).

> BiocManager::install("UCLouvain-CBIO/depmap")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 RC (2019-04-21 r76417)
Installing github package(s) 'UCLouvain-CBIO/depmap'
Downloading GitHub repo UCLouvain-CBIO/depmap@master
✔  checking for file ‘/tmp/RtmpkAfKvU/remotes27e27a28b491/UCLouvain-CBIO-depmap-9492961/DESCRIPTION’
─  preparing ‘depmap’:
✔  checking DESCRIPTION meta-information
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘depmap_0.99.5.tar.gz’

* installing *source* package ‘depmap’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Using temporary cache /tmp/RtmpntHGKv/BiocFileCache
snapshotDate(): 2019-04-29
Using temporary cache /tmp/RtmpntHGKv/BiocFileCache
Using temporary cache /tmp/RtmpntHGKv/BiocFileCache
Using temporary cache /tmp/RtmpntHGKv/BiocFileCache
snapshotDate(): 2019-04-29
Using temporary cache /tmp/RtmpntHGKv/BiocFileCache
Using temporary cache /tmp/RtmpntHGKv/BiocFileCache
Error: package or namespace load failed for ‘depmap’:
 .onLoad failed in loadNamespace() for 'depmap', details:
  call: FUN(X[[i]], ...)
  error: ‘rnai_19Q2’ not found in ExperimentHub
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/lgatto/R/x86_64-pc-linux-gnu-library/3.6/depmap’
Error: Failed to install 'depmap' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmpkAfKvU/file27e241230b88/depmap_0.99.5.tar.gz’ had non-zero exit status
> sessionInfo()
R version 3.6.0 RC (2019-04-21 r76417)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/libf77blas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
 [1] ps_1.3.0           prettyunits_1.0.2  withr_2.1.2        crayon_1.3.4      
 [5] rprojroot_1.3-2    assertthat_0.2.1   R6_2.4.0           backports_1.1.4   
 [9] magrittr_1.5       cli_1.1.0          curl_4.0           remotes_2.1.0     
[13] callr_3.3.1        tools_3.6.0        compiler_3.6.0     processx_3.4.1    
[17] pkgbuild_1.0.3     BiocManager_1.30.4
> BiocManager::version()
[1] ‘3.9’

[lgatto]

To learn about Bioconductor devel, see http://bioconductor.org/developers/how-to/useDevel/.

[ndjayne]

Sorry, I am new to this sort of stuff. I got the devel version and got this error afterward:

BiocManager::install("uclouvain-cbio/depmap") Bioconductor version 3.10 (BiocManager 1.30.4), R 3.6.1 (2019-07-05) Installing github package(s) 'uclouvain-cbio/depmap' Downloading GitHub repo uclouvain-cbio/depmap@master These packages have more recent versions available. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: Biobase (2.44.0 -> 2.45.0 ) [CRAN] 5: IRanges (2.18.1 -> 2.19.10) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1 S4Vectors (NA -> 0.23.17) [CRAN] Biobase (2.44.0 -> 2.45.0 ) [CRAN] IRanges (2.18.1 -> 2.19.10) [CRAN] Installing 3 packages: S4Vectors, Biobase, IRanges Installing packages into ‘C:/Users/Nathan/Documents/Programs/R_lib’ (as ‘lib’ is unspecified) trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/S4Vectors_0.23.17.zip' Content type 'application/zip' length 2117901 bytes (2.0 MB) downloaded 2.0 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/Biobase_2.45.0.zip' Content type 'application/zip' length 2422505 bytes (2.3 MB) downloaded 2.3 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/IRanges_2.19.10.zip' Content type 'application/zip' length 2358995 bytes (2.2 MB) downloaded 2.2 MB

package ‘S4Vectors’ successfully unpacked and MD5 sums checked Error: Failed to install 'depmap' from GitHub: (converted from warning) cannot remove prior installation of package ‘S4Vectors’

[ndjayne]

sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252

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

other attached packages: [1] dbplyr_1.4.2

loaded via a namespace (and not attached): Error in x[["Version"]] : subscript out of bounds In addition: Warning message: In FUN(X[[i]], ...) : DESCRIPTION file of package 'S4Vectors' is missing or broken

[ndjayne]

After fixing that package issue I successfully installed and loaded depmap, thank you.

[lgatto]

Excellent!