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:
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.
... 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 ...
* 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:  LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8  LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8  LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C  LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  reactome.db_1.70.0 AnnotationDbi_1.52.0 IRanges_2.22.2 S4Vectors_0.26.1  Biobase_2.48.0 BiocGenerics_0.34.0 loaded via a namespace (and not attached):  Rcpp_1.0.6 DBI_1.1.1 RSQLite_2.2.3 cachem_1.0.4  rlang_0.4.10 curl_4.3 remotes_2.2.0 blob_1.2.1  vctrs_0.3.6 tools_4.0.3 bit64_4.0.5 bit_4.0.4  fastmap_1.1.0 compiler_4.0.3 pkgconfig_2.0.3 BiocManager_1.30.10  memoise_2.0.0