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

Schneper, Lisa M. |we|@ @end|ng |rom pr|nceton@edu
Wed Jun 17 16:08:03 CEST 2020

Dear Lori,

Thank you very much. I checked with our IT team and the server doesn't allow this traffic out for security reasons. Is there a way to create a local directory that has the information that the program is looking for and point the proxy there?

Thank you,

From: Shepherd, Lori <Lori.Shepherd using roswellpark.org>
Sent: Wednesday, June 17, 2020 8:23 AM
To: Schneper, Lisa M. <lweis using princeton.edu>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: Problem installing sesameData on locked down server

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!


        [[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]]

More information about the Bioc-devel mailing list