[Bioc-devel] Error No internet connection using 'localHub=TRUE' during FlowSorted.CordBloodCombined.450k package installation

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Tue Jun 25 14:31:02 CEST 2019

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-bounces using r-project.org> on behalf of Lucas A. Salas Diaz <Lucas.A.Salas.Diaz using dartmouth.edu>
Sent: Monday, June 24, 2019 3:19:09 PM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] Error No internet connection using 'localHub=TRUE' during FlowSorted.CordBloodCombined.450k package installation


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.


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
    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

[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=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

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