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

Fri Jun 19 16:30:22 CEST 2020

Dear Lori,

Thank you. I'll forward your e-mail to our IT team and see if they can help.

If and when you do implement the export function in the Hubs, please let me know.

Best,

Lisa
________________________________
From: Shepherd, Lori <Lori.Shepherd using roswellpark.org>
Sent: Friday, June 19, 2020 7:48 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

It is our understanding that for servers there is normally one main node that has internet access while the other server nodes do not and that all nodes would have access to some shared drive/space.  We suggest asking your IT team to download the resources you need for analysis to the shared space.  There are functions in ExpeirmentHub, as you've explored, that could allow IT to download them to a specific location (by using setExperimentHubOption("CACHE", <location>)  or by using environment variables EXPERIMENT_HUB_CACHE ).  If IT is able to download for you, then you could change the cache location also to where ever that shared drive is and use localhub=TRUE to access the already download resources.

Looking at your original email more closely,  uploading a cache directly might not work because of the hard coded local file paths.  The underlying caching mechanism in ExperimentHub and AnnotationHub is BiocFileCache.  We implemented an exportbfc function but I don't think we ever implemented it in the Hubs.  I will look into implementing this in the hubs but it may take some time.

What I can suggest trying in the meantime is working through something like the following:

# locally
library(ExperimentHub)
eh = ExperimentHub()

# download the sesameData files using experimenthub so they are in your local cache

bfc = BiocFileCache(getExperimentHubOption("CACHE"))

exportbfc(bfc, outputFile="ExperimentHub.tar", outputMethod="tar")
# you could also use zip
exportbfc(bfc, outputFile="ExperimentHub.zip", outputMethod="zip")

You can then try uploading this file to  the server,  untar or unzip and then try pointing to use that location on the server with setExperimentHubOption("CACHE", <location>)

Hope this helps.

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Schneper, Lisa M. <lweis using princeton.edu>
Sent: Wednesday, June 17, 2020 10:08 AM
To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: Problem installing sesameData on locked down server

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,

Lisa
________________________________
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.

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-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

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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