[Bioc-devel] Fwd: [cbioportal] Installation cBioPortalData error
Levi Waldron
|w@|dron@re@e@rch @end|ng |rom gm@||@com
Mon Jun 1 22:04:31 CEST 2020
FYI, rtracklayer not installing on OSX (
http://bioconductor.org/checkResults/release/bioc-LATEST/rtracklayer/) may
be causing issues like the one below. (I've recommended to this user to
install the binary for the time being)
---------- Forwarded message ---------
From: de Leeuw, Renee <rdeleeuw using uic.edu>
Date: Mon, Jun 1, 2020 at 8:02 PM
Subject: Re: [cbioportal] Installation cBioPortalData error
To: mohammed imran Khan <imrankhanbioinfo using gmail.com>, Levi Waldron <
lwaldron.research using gmail.com>
Cc: JJ Gao <jianjiong.gao using gmail.com>, Marcel Ramos <mramos09 using gmail.com>,
cbioportal using googlegroups.com <cbioportal using googlegroups.com>
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 <imrankhanbioinfo using gmail.com>
*Sent:* Sunday, May 31, 2020 8:37 PM
*To:* Levi Waldron <lwaldron.research using gmail.com>
*Cc:* JJ Gao <jianjiong.gao using gmail.com>; Marcel Ramos <mramos09 using gmail.com>;
cbioportal using googlegroups.com <cbioportal using googlegroups.com>; de Leeuw, Renee <
rdeleeuw using uic.edu>
*Subject:* Re: [cbioportal] Installation cBioPortalData error
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
*imrankhanbioinfo using gmail.com <imrankhanbioinfo using gmail.com>*
*mkhan953 using uwo.ca <mkhan953 using uwo.ca>*
*Postdoctoral Associate (PDA)*
*Department of Otolaryngology-Head & Neck Surgery,*
*Western University, London, ON, Canada*
*https://www.researchgate.net/profile/Mohammed_Khan41
<https://www.researchgate.net/profile/Mohammed_Khan41>*
https://scholar.google.com/citations?hl=en&user=K3hnREYAAAAJ
On Sun, May 31, 2020 at 9:10 PM Levi Waldron <lwaldron.research using gmail.com>
wrote:
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?
On Sun, May 31, 2020 at 4:26 PM JJ Gao <jianjiong.gao using gmail.com> wrote:
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
On Sun, May 31, 2020 at 10:15 AM de Leeuw, Renee <rdeleeuw using uic.edu> wrote:
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
<https://www.google.com/maps/search/840+S+Wood+St,+Suite+130?entry=gmail&source=g>
CSN, (MC 847)
Chicago, IL, 60612-4325
Phone: (312) 355-4154
E-mail: rdeleeuw using uic.edu
Twitter: @deLeeuwRenee
Pronouns: she/her/hers
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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
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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
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