If the institution is behind a proxy there is a different ExperimentHub (and
AnnotationHub) option for setting the proxy.
try:
setExperimentHubOption("PROXY", <value>)
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Schneper, Lisa
M. <lw...@princeton.edu>
Sent: Tuesday, June 16, 2020 6:05 PM
To: bioc-devel@r-project.org <bioc-devel@r-project.org>
Subject: [Bioc-devel] Problem installing sesameData on locked down server
Hi,
I would like to use the SeSAMe package to analyze methylation data that we've
generated. Unfortunately, I'm having difficulty installing the sesameData
package on our server. The server does not access the internet due to security.
I think I've installed all the dependencies. I was able to download the cache
using a version of R on my local computer and tried to put the downloaded files
on the server.
I'm getting an error b/c ExperimentHub Caching can't connect to the server and
can't figure out how to fix it (or if it is possible):
> setExperimentHubOption("CACHE","/home/geneticData/R-3.6.2/library/CACHE/ExperimentHub/")
> library(AnnotationHub)
> setAnnotationHubOption("CACHE","/home/geneticData/R-3.6.2/library/CACHE/AnnotationHub/")
> setExperimentHubOption("LOCAL",TRUE)
> setAnnotationHubOption("LOCAL",TRUE)
> library(sesameData)
Loading sesameData.
ExperimentHub Caching causes a warning:
URL
'https://secure-web.cisco.com/1QG4CRZR1UJL2pjbyFBDtIKGCM9boQZgRQNA9uuIfL7QL5omF1je_lr4TopC9SabxnI2MLq_kTv5GemLFqTJg1NCuoSOWkSNLxBZ7DwK2RMZY5V0CPEwbef9xO0RV0kvTpDf0z59UZWsq2Ib4kNFhV4a6D5POCywJGgV4F_s1xSWbghThfdStnIBx3dTXPavNBfdeEkWH3ZSsRdj8sg2bbDIN8jiuA3oW54IrOi6AXYvxG5GpZcfi6t0fJTeKnwMLzVXPlv-0jP9kHaqiSjLOPRukH9w4IusNozuFnU-wcBB3sd8CkvL-R70_ftObQE_G87aDJl-DPwh7ckLPvJ4JMObL9wOdIMsMW6fnfG0rcSI/https%3A%2F%2Fbioconductor.org%2Fconfig.yaml':
status was 'Couldn't connect to server'Warning message:
In message(cond, appendLF = TRUE) :
additional arguments ignored in message()
This is my sessionInfo()
> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Springdale Linux 7.8 (Verona)
Matrix products: default
BLAS: /home/geneticData/R-3.6.2/lib/libRblas.so
LAPACK: /home/geneticData/R-3.6.2/lib/libRlapack.so
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] curl_4.3 sesameData_1.4.0 ExperimentHub_1.12.0
[4] AnnotationHub_2.18.0 BiocFileCache_1.10.2 dbplyr_1.4.3
[7] BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 pillar_1.4.3
[3] compiler_3.6.2 BiocManager_1.30.10
[5] later_1.0.0 digest_0.6.23
[7] bit_1.1-15.2 RSQLite_2.2.0
[9] memoise_1.1.0 lifecycle_0.2.0
[11] tibble_3.0.1 pkgconfig_2.0.3
[13] rlang_0.4.5 shiny_1.4.0.2
[15] DBI_1.1.0 yaml_2.2.1
[17] fastmap_1.0.1 dplyr_0.8.5
[19] httr_1.4.1 IRanges_2.20.2
[21] S4Vectors_0.24.4 vctrs_0.2.4
[23] rappdirs_0.3.1 stats4_3.6.2
[25] bit64_0.9-7 tidyselect_1.0.0
[27] Biobase_2.46.0 glue_1.3.1
[29] R6_2.4.1 AnnotationDbi_1.48.0
[31] purrr_0.3.4 blob_1.2.1
[33] magrittr_1.5 promises_1.1.0
[35] ellipsis_0.3.0 htmltools_0.4.0
[37] assertthat_0.2.1 mime_0.9
[39] interactiveDisplayBase_1.26.0 xtable_1.8-4
[41] httpuv_1.5.2 crayon_1.3.4
[43] BiocVersion_3.10.1
Here are the list of files in my CACHE:
> list.files("/home/geneticData/R-3.6.2/library/CACHE/ExperimentHub/")
[1] "656b10a5788d_1673"
[2] "656b13963d2e_1682"
[3] "656b14d8873b_1681"
[4] "656b1539427_1684"
[5] "656b16238d1f_1685"
[6] "656b21dde7c0_1670"
[7] "656b27f30d6e_1667"
[8] "656b2ce156bc_1679"
[9] "656b2d083cf2_1664"
[10] "656b321fe953_1677"
[11] "656b38d6e1d7_1688"
[12] "656b4124fa1e_1675"
[13] "656b45f6c53f_1668"
[14] "656b4c0fcefb_1669"
[15] "656b4d0f61da_1678"
[16] "656b4ef9a36a_experimenthub.sqlite3"
[17] "656b50445f74_1687"
[18] "656b5ac899f2_1666"
[19] "656b5f8d7984_1674"
[20] "656b62a0e8fb_1676"
[21] "656b6757aca7_656b6757aca7_hub_index.rds"
[22] "656b675d174f_1672"
[23] "656b6c8aa10d_1683"
[24] "656b6f99ff9e_1671"
[25] "656b77d94af6_1665"
[26] "656b7805f993_1686"
[27] "656b7e0567a8_1680"
[28] "BiocFileCache.sqlite"
If I try ignoring the message, and try loading data into sesame, I get the
following error:
> library(sesame)
> betas<-openSesame("Plate45")
Error: failed to connect to local data base
database:
�/home/geneticData/R-3.6.2/library/CACHE/ExperimentHub//656b4ef9a36a_experimenthub.sqlite3�
reason: invalid version specification �Bioconductor version cannot be
validated; no internet connection?�
In addition: Warning messages:
1: In file(con, "r") :
URL
'https://secure-web.cisco.com/1QG4CRZR1UJL2pjbyFBDtIKGCM9boQZgRQNA9uuIfL7QL5omF1je_lr4TopC9SabxnI2MLq_kTv5GemLFqTJg1NCuoSOWkSNLxBZ7DwK2RMZY5V0CPEwbef9xO0RV0kvTpDf0z59UZWsq2Ib4kNFhV4a6D5POCywJGgV4F_s1xSWbghThfdStnIBx3dTXPavNBfdeEkWH3ZSsRdj8sg2bbDIN8jiuA3oW54IrOi6AXYvxG5GpZcfi6t0fJTeKnwMLzVXPlv-0jP9kHaqiSjLOPRukH9w4IusNozuFnU-wcBB3sd8CkvL-R70_ftObQE_G87aDJl-DPwh7ckLPvJ4JMObL9wOdIMsMW6fnfG0rcSI/https%3A%2F%2Fbioconductor.org%2Fconfig.yaml':
status was 'Couldn't connect to server'
2: In file(con, "r") :
URL
'http://secure-web.cisco.com/1YPi7mlJoD5thyD0geTwSTc1Bmv03_3iT4l5zgjefT5BgIRxpM_HD8g2dBTCjs5n0cLBIhv0jgq5A8s1Uz1cZXxb9qKiP5JCCUoB8nqAoa5tTQVUutbPDaTOMuSWBRIgaRtftkDcvv2QaLTtIsLahfDou8NlBC3KjgWQY1orJUBxODX1AALUf0sCZf2U_vGjFoF8qagMkzMnU-nbeYtEYrvcMTiiH3q1He1Hh3-sQUFciT43gySIlpu0QrGmEkAmlSxMnM7wlfc88ntE85rIsBETB2645zOfMpJfxHo7IK5qsIS1mUHzCYVxCPGEFMM1uw9KKQ8TzKRoNKjAOVAslda_rtHcZvi2tCxN01XZBxy4/http%3A%2F%2Fbioconductor.org%2Fconfig.yaml':
status was 'Couldn't connect to server'
Do you have any suggestions? Sorry if this is basic.
Thank you in advance for your help!
Lisa
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