There are system environment variables that can be set that ExperimentHub/AnnotationHub will grab automatically from the environment.
If a computer has the system environment variable EXPERIMENT_HUB_PROXY (ANNOTATION_HUB_PROXY) the hubs recognize these and set them automatically rather than having to call the constructor with the proxy. The User that is operating through a proxy should set these values on their machine. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Lucas A. Salas Diaz <lucas.a.salas.d...@dartmouth.edu> Sent: Monday, June 24, 2019 3:19:09 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Error No internet connection using 'localHub=TRUE' during FlowSorted.CordBloodCombined.450k package installation Hi, One of the users of our FlowSorted.CordBloodCombined.450k package contacted me for advice about an issue during installation using either Bioconductor 3.9 and 3.10. The issue appears when trying to access the ExperimentHub and dealing with a proxy. A similar error was previously reported by Tim Triche and lead to an interesting discussion with the Bioconductor group: https://support.bioconductor.org/p/111958/ However, in this case the problem appears during the .onLoad instead of during the .onAttach. I was not able to reproduce the problem locally. Thus, I believe this is a problem that I should solve for future users. Do you have any advice on how to solve this problem from the BiocManager::install or from the FlowSorted.CordBloodCombined.450k:::.onLoad? Your advice will be really appreciated. Lucas Below a fragment of the issue and potential problematic areas: > library(BiocManager) � > BiocManager::install("FlowSorted.CordBloodCombined.450k") Bioconductor version 3.10 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing package(s) 'FlowSorted.CordBloodCombined.450k' trying URL 'https://bioconductor.org/packages/3.10/data/experiment/src/contrib/FlowSorted.CordBloodCombined.450k_1.1.0.tar.gz' Content type 'application/x-gzip' length 57511 bytes (56 KB) ================================================== downloaded 56 KB * installing *source* package �FlowSorted.CordBloodCombined.450k� ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package �FlowSorted.CordBloodCombined.450k� finding HTML links ... done FlowSorted.CordBloodCombined.450K html FlowSorted.CordBloodCombined.450k.compTable html IDOLOptimizedCpGsCordBlood html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No internet connection using 'localHub=TRUE' snapshotDate(): 2019-06-20 Error: package or namespace load failed for �FlowSorted.CordBloodCombined.450k�: .onLoad failed in loadNamespace() for 'FlowSorted.CordBloodCombined.450k', details: call: FUN(X[[i]], ...) error: �FlowSorted.CordBloodCombined.450k� not found in ExperimentHub Error: loading failed Execution halted ERROR: loading failed * removing �/usr/local/apps/R/3.6/site-library_3.6.0/FlowSorted.CordBloodCombined.450k� * restoring previous �/usr/local/apps/R/3.6/site-library_3.6.0/FlowSorted.CordBloodCombined.450k� The .onLoad here calls to createHubAccessors: > FlowSorted.CordBloodCombined.450k:::.onLoad function (libname = find.package("FlowSorted.CordBloodCombined.450k"), pkgname = "FlowSorted.CordBloodCombined.450k") { fl <- system.file("extdata", "metadata.csv", package = pkgname) titles <- read.csv(fl, stringsAsFactors = FALSE)$Title createHubAccessors(pkgname, titles) } In the meantime they were able to access the database using the following commands: > library(ExperimentHub) � > hub <- ExperimentHub(proxy=Sys.getenv("http_proxy")) Cannot determine internet connection. If you experience connection issues consider using 'localHub=TRUE' snapshotDate(): 2019-06-20 > query(hub, "FlowSorted.CordBloodCombined.450k") ExperimentHub with 1 record # snapshotDate(): 2019-06-20 # names(): EH2256 # package(): FlowSorted.CordBloodCombined.450k # $dataprovider: Bioconductor, Bioconductor, GEO, karnanilab # $species: Homo sapiens # $rdataclass: RGChannelSet # $rdatadateadded: 2019-01-25 # $title: FlowSorted.CordBloodCombined.450k # $description: The FlowSorted.CordBloodCombined.450k package contains data ... # $taxonomyid: 9606 # $genome: hg19 # $sourcetype: tar.gz # $sourceurl: https://bit.ly/2UaTNSi, https://bit.ly/2RQ1nVF, https://bit.ly... # $sourcesize: NA # $tags: c("ExperimentData", "Homo_sapiens_Data", "Tissue", # "MicroarrayData", "Genome", "TissueMicroarrayData", # "MethylationArrayData", "ExperimentHub") # retrieve record with 'object[["EH2256"]]' His sessionInfo > sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /usr/local/intel/compilers_and_libraries_2019.1.144/linux/mkl/lib/intel64_lin/libmkl_rt.so Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ExperimentHub_1.11.1 AnnotationHub_2.17.3 BiocFileCache_1.9.1 [4] dbplyr_1.4.2 BiocGenerics_0.31.4 BiocManager_1.30.4 loaded via a namespace (and not attached): [1] Rcpp_1.0.1 pillar_1.4.1 [3] compiler_3.6.0 later_0.8.0 [5] tools_3.6.0 digest_0.6.19 [7] bit_1.1-14 RSQLite_2.1.1 [9] memoise_1.1.0 tibble_2.1.3 [11] pkgconfig_2.0.2 rlang_0.3.4 [13] shiny_1.3.2 DBI_1.0.0 [15] curl_3.3 yaml_2.2.0 [17] dplyr_0.8.1 httr_1.4.0 [19] IRanges_2.19.10 S4Vectors_0.23.13 [21] rappdirs_0.3.1 stats4_3.6.0 [23] bit64_0.9-7 tidyselect_0.2.5 [25] Biobase_2.45.0 glue_1.3.1 [27] R6_2.4.0 AnnotationDbi_1.47.0 [29] purrr_0.3.2 blob_1.1.1 [31] magrittr_1.5 promises_1.0.1 [33] htmltools_0.3.6 assertthat_0.2.1 [35] mime_0.7 interactiveDisplayBase_1.23.0 [37] xtable_1.8-4 httpuv_1.5.1 [39] crayon_1.3.4 [[alternative HTML version deleted]] This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
