Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
0
Entering edit mode
florianjt • 0
@user-24576
Last seen 10 days ago

Hello !

I need some help to build my package using reactome.db for reactomePA functions.

In fact, builds and remote downloads have failed for Ubuntu but not for Windows 10 at reactome.db downloading. The same appears when I try to download reactome.db alone.

Archive downloading url works manually from Bioconductor page.

With this command:

BiocManager::install("reactome.db")

I get these messages:

Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'reactome.db'
essai de l'URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/reactome.db_1.70.0.tar.gz'
Content type 'application/x-gzip' length 454979427 bytes (433.9 MB)
========================================
downloaded 348.9 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/reactome.db_1.70.0.tar.gz' failed
De plus : Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 365895769 != reported length 454979427
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/reactome.db_1.70.0.tar.gz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘reactome.db’ failed
Installation path not writeable, unable to update packages: littler, boot, class, cluster,
  codetools, foreign, KernSmooth, MASS, Matrix, mgcv, nlme, nnet, spatial

[EDIT] But in case of package building, this warning is an issue, so how should we manage it ? For CRAN checks for instance.

I get:

...
trying URL 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/reactome.db_1.74.0.tar.gz'
Content type 'application/x-gzip' length 430092992 bytes (410.2 MB)
==================================================
downloaded 410.2 MB
...

Then:

* installing *source* package ‘reactome.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* creating tarball
Build timed out (after 20 minutes). Marking the build as failed.
Build was aborted

Again a question of time, so my question is, how to manage this ? Or this package could be a part of Bioconductor despite this warning ?

Any ideas ? Thanks !

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8       
 [4] LC_COLLATE=fr_FR.UTF-8     LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] reactome.db_1.70.0   AnnotationDbi_1.52.0 IRanges_2.22.2       S4Vectors_0.26.1    
[5] Biobase_2.48.0       BiocGenerics_0.34.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6          DBI_1.1.1           RSQLite_2.2.3       cachem_1.0.4       
 [5] rlang_0.4.10        curl_4.3            remotes_2.2.0       blob_1.2.1         
 [9] vctrs_0.3.6         tools_4.0.3         bit64_4.0.5         bit_4.0.4          
[13] fastmap_1.1.0       compiler_4.0.3      pkgconfig_2.0.3     BiocManager_1.30.10
[17] memoise_2.0.0  
reactome.db ReactomePA • 77 views
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2
Entering edit mode
@martin-morgan-1513
Last seen 1 day ago
United States

Note the warning

Timeout of 60 seconds was reached

and change the timeout option

options(timeout = 300)  # five minutes
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0
Entering edit mode

Thanks !

But in case of package building, this warning is an issue, so how should we manage it ? For CRAN checks for instance.

I get:

...
trying URL 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/reactome.db_1.74.0.tar.gz'
Content type 'application/x-gzip' length 430092992 bytes (410.2 MB)
==================================================
downloaded 410.2 MB
...

Then:

* installing *source* package ‘reactome.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* creating tarball
Build timed out (after 20 minutes). Marking the build as failed.
Build was aborted

Again a question of time, so my question is, how to manage this ? Or this package could be a part of Bioconductor despite this warning ?

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1
Entering edit mode

I don't know what you mean by 'package building'. If you're talking about submitting a package to Bioconductor, then please address questions to the bioc-devel mailing list.

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0
Entering edit mode

Yes I'm talking about this, about CRAN checks actually, thank you for your answers, I will do it.

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