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
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