Installation cBioPortalData error

[de Leeuw, Renee]

Good afternoon,

Thank you for the excellent webinar series the past month. I have been using cBioportal for a while and learnt a lot of new ways to modify my queries and explore the data further.

I started working with R recently and thought I'd install the data locally. I made sure to update R to 4.0.0 and copied and ran the code below:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

if (!requireNamespace("cBioPortalData", quietly = TRUE))
    BiocManager::install("cBioPortalData")

library(cBioPortalData)

Unfortunately, after loading and installing it finished with the following error after the last prompt  libary(cBioPortalData):

Error: package or namespace load failed for 'cBioportalData' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'rtracklayer'

Am I doing something wrong or have others run into this issue? Looking forward to hearing from you.

Sincerely,

Renée

--

Renée de Leeuw, PhD

Assistant Professor

UIC - Department of Pathology

6095 COMRB

840 S Wood St, Suite 130 CSN, (MC 847)

Chicago, IL, 60612-4325

Phone: (312) 355-4154

E-mail: rdel...@uic.edu

Twitter: @deLeeuwRenee

Pronouns: she/her/hers

[JJ Gao]

Hi Renée,

Thank you for your feedback!

I am cc'ing Marcel and Levin, the authors of cBioPortalData, and see if they have any insights.

Best,

-JJ

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[Levi Waldron]

Dear Renée,

it looks like you have an broken installation for some reason. Could you send the output of:

BiocManager::version()

BiocManager::valid()

Also it may be worth trying this and sending the output as well:

BiocManager::install()

so we can see what issues there may be with your installation?

--

Levi Waldron                                                

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io

[mohammed imran Khan]

Please install the missing package using this script hopefully it will resolve your problem.

install.packages("rtracklayer")

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

if (!requireNamespace("cBioPortalData", quietly = TRUE))
    BiocManager::install("cBioPortalData")

library(cBioPortalData)

if you still have a problem run this script to see if you have required packages to work in R session.

sessionInfo()

Best regards--
Mohammed Imran Khan, PhD

imrankha...@gmail.com

mkha...@uwo.ca

Postdoctoral Associate (PDA)

Department of Otolaryngology-Head & Neck Surgery,

Western University, London, ON, Canada

https://www.researchgate.net/profile/Mohammed_Khan41

https://scholar.google.com/citations?hl=en&user=K3hnREYAAAAJ

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/CAOUXvx5Gv9zEZsaSj80mRxHsf79AvsY2Px90WNKqTfpcHfcL6Q%40mail.gmail.com.

[Levi Waldron]

I'm sorry to shunt your question off, but would you mind posting it to support.bioconductor.org? I ask because I actually don't know the answer, and it seems to have to do with rtracklayer rather than cBioPortalData directly. It should get a quick response there. I'm just not sure why rtracklayer would not have installed automatically for you, as dependencies (indirect in this case, I assume, since it's not a direct dependency of cBioPortal) normally do. 

On Mon, Jun 1, 2020 at 8:02 PM de Leeuw, Renee <rdel...@uic.edu> wrote:

Hi,

Thank you for your quick responses. Unfortunately this did not resolve my issue, I still got the same error.

This is the output re: Bioconductor and R versions:

> BiocManager::version()

[1] ‘3.11’

> BiocManager::valid()

[1] TRUE

> BiocManager::install()

Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)

As for the error and session info, see here:

Error: package or namespace load failed for ‘cBioPortalData’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

 there is no package called ‘rtracklayer’

>

>

> sessionInfo()

R version 4.0.0 (2020-04-24)

Platform: x86_64-apple-darwin17.0 (64-bit)

Running under: macOS Catalina 10.15.4

Matrix products: default

BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:

 [1] MultiAssayExperiment_1.14.0 SummarizedExperiment_1.18.1 DelayedArray_0.14.0         matrixStats_0.56.0          Biobase_2.48.0              GenomicRanges_1.40.0      

 [7] GenomeInfoDb_1.24.0         IRanges_2.22.2              S4Vectors_0.26.1            BiocGenerics_0.34.0         AnVIL_1.0.3                 dplyr_1.0.0                

loaded via a namespace (and not attached):

 [1] httr_1.4.1                bit64_0.9-7               jsonlite_1.6.1            splines_4.0.0             assertthat_0.2.1          askpass_1.1              

 [7] BiocManager_1.30.10       BiocFileCache_1.12.0      blob_1.2.1                GenomeInfoDbData_1.2.3    RTCGAToolbox_2.18.0       progress_1.2.2          

[13] yaml_2.2.1                pillar_1.4.4              RSQLite_2.2.0             lattice_0.20-41           glue_1.4.1                limma_3.44.1            

[19] digest_0.6.25             XVector_0.28.0            swirl_2.4.5               Matrix_1.2-18             XML_3.99-0.3              pkgconfig_2.0.3          

[25] biomaRt_2.44.0            zlibbioc_1.34.0           purrr_0.3.4               RCircos_1.2.1             rapiclient_0.1.3          openssl_1.4.1            

[31] tibble_3.0.1              generics_0.0.2            ellipsis_0.3.1            survival_3.1-12           RJSONIO_1.3-1.4           magrittr_1.5            

[37] crayon_1.3.4              memoise_1.1.0             xml2_1.3.2                prettyunits_1.1.1         tools_4.0.0               data.table_1.12.8        

[43] hms_0.5.3                 formatR_1.7               lifecycle_0.2.0           stringr_1.4.0             Biostrings_2.56.0         AnnotationDbi_1.50.0    

[49] lambda.r_1.2.4            compiler_4.0.0            rlang_0.4.6               futile.logger_1.4.3       grid_4.0.0                GenomicDataCommons_1.12.0

[55] RCurl_1.98-1.2            rstudioapi_0.11           rappdirs_0.3.1            bitops_1.0-6              testthat_2.3.2            DBI_1.1.0                

[61] curl_4.3                  R6_2.4.1                  bit_1.1-15.2              futile.options_1.0.1      readr_1.3.1               stringi_1.4.6            

[67] RaggedExperiment_1.12.0   Rcpp_1.0.4.6              vctrs_0.3.0               dbplyr_1.4.4              tidyselect_1.1.0      

Hope this helps and thanks for helping me troubleshoot!

Renée

---

From: mohammed imran Khan <imrankha...@gmail.com>
Sent: Sunday, May 31, 2020 8:37 PM
To: Levi Waldron <lwaldron...@gmail.com>
Cc: JJ Gao <jianji...@gmail.com>; Marcel Ramos <mram...@gmail.com>; cbiop...@googlegroups.com <cbiop...@googlegroups.com>; de Leeuw, Renee <rdel...@uic.edu>
Subject: Re: [cbioportal] Installation cBioPortalData error

 

[Levi Waldron]

I may have found a workaround for you though. Try this (note - Bioconductor users should use BiocManager::install instead of install.packages for all Bioconductor and CRAN packages):

BiocManager::install("rtracklayer", type="binary")

I noticed that rtracklayer (1.48.0) currently has a build error on OSX (http://bioconductor.org/checkResults/release/bioc-LATEST/rtracklayer/), so the release binary version is lagging at 1.47.0. If you chose "Yes" to this question when you installed ("do you want to install this from source? Yes/No/Cancel), your system would attempt to install from source, and likely fail for the same reason it is on the build system. Installing the binary rtracklayer (1.47.0) should solve the problem. 

It's very rare to have a package erroring in the release version of Bioconductor, especially for a package as widely used as rtracklayer, because they are tested at release and are not supposed to be fiddled with by the developer after release in ways that could cause errors.  I'll bring this up on the Bioconductor developer's mailing list and hopefully get rtracklayer back on "track" ASAP. 

Sorry for the trouble,

Levi

  

[de Leeuw, Renee]

That did the trick! Thank you, I really appreciate your help!

Take care,

Renée

---

From: Levi Waldron <lwaldron...@gmail.com>
Sent: Monday, June 1, 2020 3:00 PM
To: de Leeuw, Renee <rdel...@uic.edu>
Cc: mohammed imran Khan <imrankha...@gmail.com>; JJ Gao <jianji...@gmail.com>; Marcel Ramos <mram...@gmail.com>; cbiop...@googlegroups.com <cbiop...@googlegroups.com>

[de Leeuw, Renee]