cbio <- cBioPortal() does not work
ryao-mdanderson opened this issue · 10 comments
ryao-mdanderson commented
Greetings,
I installed cBioPortalData on R/4.0.0 on our institution HPC cluster. however I failed to use cBioPortal(),
$ module load R/4.0.0
$ R
$library(cBioPortalData)
cbio <- cBioPortal()
Error in Service(service = "cBioPortal", host = hostname, config = httr::config(ssl_verifypeer = 0L, :
unused arguments (api_reference_url = apiUrl, api_reference_md5sum = "b39b387c6fdd8b04badf38cb0777998f")
May you please advise what's the reason and how to fix?
Thanks,
Rong Yao
LiNk-NY commented
Hi Rong Yao, @ryao-mdanderson
Please make sure you have a valid Bioconductor installation by checking BiocManager::valid().
With R >= 4.0.0, you should have either Bioc 3.12 or 3.13 installed.
Can you provide more information on what sessionInfo() returns?
ryao-mdanderson commented
Hello,
Thanks for your quick response.
Our R 4.0.0 has Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Here is what the sessionInfo() returns
sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.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 stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] cBioPortalData_2.3.3 MultiAssayExperiment_1.14.0
[3] SummarizedExperiment_1.18.1 DelayedArray_0.14.0
[5] matrixStats_0.56.0 Biobase_2.48.0
[7] GenomicRanges_1.40.0 GenomeInfoDb_1.24.0
[9] IRanges_2.22.2 S4Vectors_0.26.1
[11] BiocGenerics_0.34.0 AnVIL_1.0.3
[13] dplyr_1.0.0
loaded via a namespace (and not attached):
[1] httr_1.4.1 bit64_0.9-7
[3] jsonlite_1.6.1 splines_4.0.0
[5] assertthat_0.2.1 askpass_1.1
[7] TCGAutils_1.10.0 BiocFileCache_1.12.0
[9] blob_1.2.1 Rsamtools_2.4.0
[11] GenomeInfoDbData_1.2.3 RTCGAToolbox_2.20.0
[13] yaml_2.2.1 progress_1.2.2
[15] pillar_1.4.4 RSQLite_2.2.0
[17] lattice_0.20-41 glue_1.4.1
[19] limma_3.44.1 digest_0.6.25
[21] XVector_0.28.0 rvest_0.3.6
[23] Matrix_1.2-18 XML_3.99-0.3
[25] pkgconfig_2.0.3 biomaRt_2.44.1
[27] zlibbioc_1.34.0 purrr_0.3.4
[29] RCircos_1.2.1 rapiclient_0.1.3
[31] BiocParallel_1.22.0 tibble_3.0.1
[33] openssl_1.4.1 generics_0.0.2
[35] ellipsis_0.3.1 GenomicFeatures_1.40.1
[37] survival_3.1-12 RJSONIO_1.3-1.4
[39] magrittr_1.5 crayon_1.3.4
[41] memoise_1.1.0 xml2_1.3.2
[43] tools_4.0.0 data.table_1.12.8
[45] prettyunits_1.1.1 hms_0.5.3
[47] formatR_1.7 lifecycle_0.2.0
[49] stringr_1.4.0 AnnotationDbi_1.50.0
[51] lambda.r_1.2.4 Biostrings_2.56.0
[53] compiler_4.0.0 rlang_0.4.6
[55] futile.logger_1.4.3 grid_4.0.0
[57] GenomicDataCommons_1.12.0 RCurl_1.98-1.2
[59] rappdirs_0.3.1 bitops_1.0-6
[61] DBI_1.1.0 curl_4.3
[63] R6_2.4.1 GenomicAlignments_1.24.0
[65] rtracklayer_1.48.0 bit_4.0.4
[67] futile.options_1.0.1 readr_1.3.1
[69] stringi_1.4.6 RaggedExperiment_1.12.0
[71] Rcpp_1.0.4.6 vctrs_0.3.0
[73] dbplyr_1.4.4 tidyselect_1.1.0
Thanks,
Rong
From: Marcel Ramos <notifications@github.com>
Reply-To: waldronlab/cBioPortalData <reply@reply.github.com>
Date: Wednesday, November 25, 2020 at 10:58 AM
To: waldronlab/cBioPortalData <cBioPortalData@noreply.github.com>
Cc: "Yao,Rong" <RYao@mdanderson.org>, Mention <mention@noreply.github.com>
Subject: [EXT] Re: [waldronlab/cBioPortalData] cbio <- cBioPortal() does not work (#35)
WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.
Hi Rong Yao, @ryao-mdanderson<https://urldefense.com/v3/__https:/github.com/ryao-mdanderson__;!!PfbeBCCAmug!1hV6O8fEs4MmehGNux-jgu1kG4qScwfcPGkx3MEVIs87AsAc_G6klWP08XF-2HA$>
Please make sure you have a valid Bioconductor installation by checking BiocManager::valid().
With R >= 4.0.0, you should have either Bioc 3.12 or 3.13 installed.
Can you provide more information on what sessionInfo() returns?
—
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LiNk-NY commented
Hi Rong Yao, @ryao-mdanderson
You're using the a 'too-new' version of cBioPortalData for the Bioconductor version that you have installed.
I would strongly recommend that you update your version of Bioconductor to 3.12 by using BiocManager::install(version = '3.12') but make sure that you have an appropriate location for the new package installations... See the BiocManager vignette for managing multiple Bioconductor versions.
Alternatively, the appropriate version of cBioPortalData for Bioconductor 3.11 is cBioPortalData_2.0.10. You
can re-install it using BiocManager::install("cBioPortalData").
Best,
Marcel
ryao-mdanderson commented
Thank you, Marcel. I will try.
Happy Thanksgiving!
Rong
From: Marcel Ramos <notifications@github.com>
Reply-To: waldronlab/cBioPortalData <reply@reply.github.com>
Date: Wednesday, November 25, 2020 at 4:07 PM
To: waldronlab/cBioPortalData <cBioPortalData@noreply.github.com>
Cc: "Yao,Rong" <RYao@mdanderson.org>, Mention <mention@noreply.github.com>
Subject: [EXT] Re: [waldronlab/cBioPortalData] cbio <- cBioPortal() does not work (#35)
WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.
Hi Rong Yao, @ryao-mdanderson<https://urldefense.com/v3/__https:/github.com/ryao-mdanderson__;!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4SL0mmSE$>
You're using the a 'too-new' version of cBioPortalData for the Bioconductor version that you have installed.
I would strongly recommend that you update your version of Bioconductor to 3.12 by using BiocManager::install(version = '3.12') but make sure that you have an appropriate location for the new package installations... See the BiocManager vignette<https://urldefense.com/v3/__https:/cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html__;!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4SkHRSdU$> for managing multiple Bioconductor versions.
Alternatively, the appropriate version of cBioPortalData for Bioconductor 3.11 is cBioPortalData_2.0.10. You
can re-install it using BiocManager::install("cBioPortalData").
Best,
Marcel
—
You are receiving this because you were mentioned.
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LiNk-NY commented
Feel free to re-open if you are having issues. AFAIK they should be resolved.
Best,
Marcel
ryao-mdanderson commented
Hello Marcel,
Thank you for your suggestion. Today, I followed your alternative suggestion: “Alternatively, the appropriate version of cBioPortalData for Bioconductor 3.11 is cBioPortalData_2.0.10. You can re-install it using BiocManager::install("cBioPortalData").
I reinstall cBioPortalData, the installation is successful. I am able to test :
$ module load R/4.0.0
$ R
packageVersion("cBioPortalData")
[1] ‘2.0.10’
cbio <- cBioPortal()
# this success!
laml <- cBioDataPack("laml_tcga")
Output as the following:
Study file in cache: laml_tcga
Working on: /tmp/RtmpCBSQek/136c70be6467_laml_tcga/data_cna_hg19.seg
Parsed with column specification:
cols(
ID = col_character(),
chrom = col_double(),
loc.start = col_double(),
loc.end = col_double(),
num.mark = col_double(),
seg.mean = col_double()
)
Working on: /tmp/RtmpCBSQek/136c70be6467_laml_tcga/data_CNA.txt
Parsed with column specification:
cols(
.default = col_double(),
Hugo_Symbol = col_character()
)
See spec(...) for full column specifications.
|=================================================================| 100% 9 MB
Parsed with column specification:
cols(
Hugo_Symbol = col_character()
)
Working on: /tmp/RtmpCBSQek/136c70be6467_laml_tcga/data_linear_CNA.txt
Parsed with column specification:
cols(
.default = col_double(),
Hugo_Symbol = col_character()
)
See spec(...) for full column specifications.
|=================================================================| 100% 29 MB
Parsed with column specification:
cols(
Hugo_Symbol = col_character()
)
Working on: /tmp/RtmpCBSQek/136c70be6467_laml_tcga/data_methylation_hm27.txt
Parsed with column specification:
cols(
.default = col_double(),
Hugo_Symbol = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
Hugo_Symbol = col_character()
)
Working on: /tmp/RtmpCBSQek/136c70be6467_laml_tcga/data_methylation_hm450.txt
Parsed with column specification:
cols(
.default = col_double(),
Hugo_Symbol = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
Hugo_Symbol = col_character()
)
Working on: /tmp/RtmpCBSQek/136c70be6467_laml_tcga/data_mutations_extended.txt
Parsed with column specification:
cols(
.default = col_character(),
Entrez_Gene_Id = col_double(),
Start_Position = col_double(),
End_Position = col_double(),
dbSNP_Val_Status = col_logical(),
Score = col_double(),
t_ref_count = col_double(),
t_alt_count = col_double(),
n_ref_count = col_double(),
n_alt_count = col_double(),
Protein_position = col_double(),
Hotspot = col_double(),
RNAVAF_WU = col_double(),
RNAVarReads_WU = col_double(),
stop = col_double(),
NormalVAF_WU = col_double(),
start = col_double(),
TumorVAF_WU = col_double(),
RNARefReads_WU = col_double()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
.default = col_character()
)
See spec(...) for full column specifications.
Error in .local(x, ...) : strand values must be in '+' '-' '*'
In addition: Warning messages:
1: In .find_seqnames_col(df_colnames0, seqnames.field0, xfix) :
cannnot determine seqnames column unambiguously
2: In .find_seqnames_col(df_colnames0, seqnames.field0, xfix) :
cannnot determine seqnames column unambiguously
3: In .find_seqnames_col(df_colnames0, seqnames.field0, xfix) :
cannnot determine seqnames column unambiguously
May you please advise what could be the cause of the error? How to fix?
Thank you very much for your help!
Rong
From: "Yao,Rong" <RYao@mdanderson.org>
Date: Wednesday, November 25, 2020 at 9:54 PM
To: waldronlab/cBioPortalData <reply@reply.github.com>, waldronlab/cBioPortalData <cBioPortalData@noreply.github.com>
Cc: Mention <mention@noreply.github.com>
Subject: Re: [EXT] Re: [waldronlab/cBioPortalData] cbio <- cBioPortal() does not work (#35)
Thank you, Marcel. I will try.
Happy Thanksgiving!
Rong
From: Marcel Ramos <notifications@github.com>
Reply-To: waldronlab/cBioPortalData <reply@reply.github.com>
Date: Wednesday, November 25, 2020 at 4:07 PM
To: waldronlab/cBioPortalData <cBioPortalData@noreply.github.com>
Cc: "Yao,Rong" <RYao@mdanderson.org>, Mention <mention@noreply.github.com>
Subject: [EXT] Re: [waldronlab/cBioPortalData] cbio <- cBioPortal() does not work (#35)
WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.
Hi Rong Yao, @ryao-mdanderson<https://urldefense.com/v3/__https:/github.com/ryao-mdanderson__;!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4SL0mmSE$>
You're using the a 'too-new' version of cBioPortalData for the Bioconductor version that you have installed.
I would strongly recommend that you update your version of Bioconductor to 3.12 by using BiocManager::install(version = '3.12') but make sure that you have an appropriate location for the new package installations... See the BiocManager vignette<https://urldefense.com/v3/__https:/cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html__;!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4SkHRSdU$> for managing multiple Bioconductor versions.
Alternatively, the appropriate version of cBioPortalData for Bioconductor 3.11 is cBioPortalData_2.0.10. You
can re-install it using BiocManager::install("cBioPortalData").
Best,
Marcel
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/waldronlab/cBioPortalData/issues/35*issuecomment-733966856__;Iw!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4sMyeacM$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AOGQX3CDXYWGTBTNK423KZDSRV5XJANCNFSM4UCUVPFA__;!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4X6I4koo$>.
The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.
LiNk-NY commented
Hi Rong Yao, @ryao-mdanderson
From the error, it looks like there is an issue with the dataset. Perhaps you may want to report it here: https://github.com/cBioPortal/datahub.
All datasets are not guaranteed to build as MultiAssayExperiment data objects with older versions of
cBioPortalData. We recommend using the latest version of R and cBioPortalData.
It is more likely that they build now since our success rate is around 83% for packaged studies.
We have also added functionality to only download the data in the case where the MultiAssayExperiment
build is not working. These are some of the features in the newest version of the package.
Best regards,
Marcel
ryao-mdanderson commented
Hello Marcel,
Thank you for your suggestion.
Just be curious, for cBioPortalData 2.0.10,
laml <- cBioDataPack("laml_tcga")
Access the website: https://cbioportal-datahub.s3.amazonaws.com to download data.
I also find dataset in
https://github.com/cBioPortal/datahub<https://urldefense.com/v3/__https:/github.com/cBioPortal/datahub__;!!PfbeBCCAmug!xbfMBQowNussIe5xTkKZq8hfZbC0xL418xjqEH-IzUExf9zEqLT1XlrlysPPXTI$>
e.g.
https://github.com/cBioPortal/datahub/tree/master/public/laml_tcga
In the new version of cBioPortalData, which is the above website that cBioDataPack() actually will access to download data? I am asking this, our HPC cluster has firewall restriction, it is better to know which url or both url(s) to for firewall open.
Thank you!
Rong
From: Marcel Ramos <notifications@github.com>
Reply-To: waldronlab/cBioPortalData <reply@reply.github.com>
Date: Wednesday, December 2, 2020 at 3:44 PM
To: waldronlab/cBioPortalData <cBioPortalData@noreply.github.com>
Cc: "Yao,Rong" <RYao@mdanderson.org>, Mention <mention@noreply.github.com>
Subject: [EXT] Re: [waldronlab/cBioPortalData] cbio <- cBioPortal() does not work (#35)
WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.
Hi Rong Yao, @ryao-mdanderson<https://urldefense.com/v3/__https:/github.com/ryao-mdanderson__;!!PfbeBCCAmug!xbfMBQowNussIe5xTkKZq8hfZbC0xL418xjqEH-IzUExf9zEqLT1XlrlLrv98u0$>
From the error, it looks like there is an issue with the dataset. Perhaps you may want to report it here: https://github.com/cBioPortal/datahub<https://urldefense.com/v3/__https:/github.com/cBioPortal/datahub__;!!PfbeBCCAmug!xbfMBQowNussIe5xTkKZq8hfZbC0xL418xjqEH-IzUExf9zEqLT1XlrlysPPXTI$>.
All datasets are not guaranteed to build as MultiAssayExperiment data objects with older versions of
cBioPortalData. We recommend using the latest version of R and cBioPortalData.
It is more likely that they build now since our success rate is around 83% for packaged studies.
We have also added functionality to only download the data in the case where the MultiAssayExperiment
build is not working. These are some of the features in the newest version of the package.
Best regards,
Marcel
—
You are receiving this because you were mentioned.
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LiNk-NY commented
Hi Rong, @ryao-mdanderson
cBioPortalData version 2.0.10 (and newer) uses the AWS URL https://cbioportal-datahub.s3.amazonaws.com.
You can see the code here: https://github.com/waldronlab/cBioPortalData/blob/RELEASE_3_11/R/cBioDataPack.R#L2
Best,
Marcel
ryao-mdanderson commented
Hi Marcel,
Thank you for your information.
Have a good night.
Rong
From: Marcel Ramos <notifications@github.com>
Reply-To: waldronlab/cBioPortalData <reply@reply.github.com>
Date: Wednesday, December 2, 2020 at 6:47 PM
To: waldronlab/cBioPortalData <cBioPortalData@noreply.github.com>
Cc: "Yao,Rong" <RYao@mdanderson.org>, Mention <mention@noreply.github.com>
Subject: [EXT] Re: [waldronlab/cBioPortalData] cbio <- cBioPortal() does not work (#35)
WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.
Hi Rong, @ryao-mdanderson<https://urldefense.com/v3/__https:/github.com/ryao-mdanderson__;!!PfbeBCCAmug!0sWqaxPF5fxYFWBUW2mCHxfmL3YkpsZZGbEB0bEMME9yPZtXGW9UkroRsnLCJhs$>
cBioPortalData version 2.0.10 (and newer) uses the AWS URL https://cbioportal-datahub.s3.amazonaws.com<https://urldefense.com/v3/__https:/cbioportal-datahub.s3.amazonaws.com__;!!PfbeBCCAmug!0sWqaxPF5fxYFWBUW2mCHxfmL3YkpsZZGbEB0bEMME9yPZtXGW9UkroRBU5raC4$>.
You can see the code here: https://github.com/waldronlab/cBioPortalData/blob/RELEASE_3_11/R/cBioDataPack.R#L2<https://urldefense.com/v3/__https:/github.com/waldronlab/cBioPortalData/blob/RELEASE_3_11/R/cBioDataPack.R*L2__;Iw!!PfbeBCCAmug!0sWqaxPF5fxYFWBUW2mCHxfmL3YkpsZZGbEB0bEMME9yPZtXGW9UkroRyuVyIwM$>
Best,
Marcel
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