[Bioc-devel] Problem installing sesameData on locked down server

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Wed Jun 17 14:23:57 CEST 2020

If the institution is behind a proxy there is a different ExperimentHub (and AnnotationHub) option for setting the proxy.

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-bounces using r-project.org> on behalf of Schneper, Lisa M. <lweis using princeton.edu>
Sent: Tuesday, June 16, 2020 6:05 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Problem installing sesameData on locked down server


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


 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C

 [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] 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!


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