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 <rdele...@uic.edu> Date: Mon, Jun 1, 2020 at 8:02 PM Subject: Re: [cbioportal] Installation cBioPortalData error To: mohammed imran Khan <imrankhanbioi...@gmail.com>, Levi Waldron < lwaldron.resea...@gmail.com> Cc: JJ Gao <jianjiong....@gmail.com>, Marcel Ramos <mramo...@gmail.com>, cbiopor...@googlegroups.com <cbiopor...@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 <imrankhanbioi...@gmail.com> *Sent:* Sunday, May 31, 2020 8:37 PM *To:* Levi Waldron <lwaldron.resea...@gmail.com> *Cc:* JJ Gao <jianjiong....@gmail.com>; Marcel Ramos <mramo...@gmail.com>; cbiopor...@googlegroups.com <cbiopor...@googlegroups.com>; de Leeuw, Renee < rdele...@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 *imrankhanbioi...@gmail.com <imrankhanbioi...@gmail.com>* *mkhan...@uwo.ca <mkhan...@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.resea...@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....@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 <rdele...@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: rdele...@uic.edu Twitter: @deLeeuwRenee Pronouns: she/her/hers -- You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/CY4PR13MB1190C41F09F130CD7E8EFE7AC28F0%40CY4PR13MB1190.namprd13.prod.outlook.com <https://groups.google.com/d/msgid/cbioportal/CY4PR13MB1190C41F09F130CD7E8EFE7AC28F0%40CY4PR13MB1190.namprd13.prod.outlook.com?utm_medium=email&utm_source=footer> . -- 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 -- You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/CAOUXvx5Gv9zEZsaSj80mRxHsf79AvsY2Px90WNKqTfpcHfcL6Q%40mail.gmail.com <https://groups.google.com/d/msgid/cbioportal/CAOUXvx5Gv9zEZsaSj80mRxHsf79AvsY2Px90WNKqTfpcHfcL6Q%40mail.gmail.com?utm_medium=email&utm_source=footer> . -- 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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel