Re: [Bioc-devel] [ext] Re: RCAS build error on Nebbiolo2 - Missing BiocManager
Dear Herve & Kasper,
Thank you very much for your responses.
The checkSeqDb(‘hg19’) function calls the BSgenome::available.genomes function
which in turn calls
“get_data_annotation_contrib_url<https://rdrr.io/bioc/BSgenome/src/R/utils.R>“.
The method tries to access `BiocManager::repositories` function to find a
certain url. So, it basically fails because BiocManager is not seen, not
because it is used to install a dependency here.
In this case, it would be okay add BiocManager to the suggests field of my
package, is that right?
Best,
Bora
From: Hervé Pagès
Date: Friday, 27. October 2023 at 17:57
To: "Uyar, Bora" , "bioc-devel@r-project.org"
Subject: [ext] Re: [Bioc-devel] RCAS build error on Nebbiolo2 - Missing
BiocManager
Hi Bora,
BiocManager is installed on the machine but 'R CMD check' does not "see" it
because you don't have it listed in Suggests. This 'R CMD check' behavior is
controlled by the _R_CHECK_SUGGESTS_ONLY_ behavior and is only enabled on our
Linux builders for now.
However, please note that the code in your examples, vignettes or unit tests
should NOT install packages. I don't know what package exactly
checkSeqDb('hg19') is trying to install but that is what should be listed in
Suggests instead of BiocManager. That way it won't be reinstalled over and over
again by 'R CMD check'.
Best,
H.
On 10/27/23 05:56, bora.u...@mdc-berlin.de<mailto:bora.u...@mdc-berlin.de>
wrote:
Hi Bioc-Devel Team,
My package RCAS has been getting build errors on Nebbiolo2. It fails to run the
tests/examples/vignettes all due to a missing dependency, which can’t be
installed because BiocManager is not available.
Here is the build report:
https://bioconductor.org/checkResults/release/bioc-LATEST/RCAS/nebbiolo2-checksrc.html
The relevant error is :
Error in get_data_annotation_contrib_url(type) :
Install 'BiocManager' from CRAN to get 'BioCann' contrib.url
Error: processing vignette 'RCAS.vignette.Rmd' failed with diagnostics:
Install 'BiocManager' from CRAN to get 'BioCann' contrib.url
The other machines all build it properly.
Best,
Bora
---
Dr. Bora Uyar
Bioinformatics Scientist
Bioinformatics and Omics Data Science Platform
Max Delbrueck Center (MDC) for Molecular Medicine
The Berlin Institute for Medical Systems Biology
Hannoversche Str. 28, 10115 Berlin
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Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com<mailto:hpages.on.git...@gmail.com>
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[Bioc-devel] RCAS build error on Nebbiolo2 - Missing BiocManager
Hi Bioc-Devel Team, My package RCAS has been getting build errors on Nebbiolo2. It fails to run the tests/examples/vignettes all due to a missing dependency, which can’t be installed because BiocManager is not available. Here is the build report: https://bioconductor.org/checkResults/release/bioc-LATEST/RCAS/nebbiolo2-checksrc.html The relevant error is : Error in get_data_annotation_contrib_url(type) : Install 'BiocManager' from CRAN to get 'BioCann' contrib.url Error: processing vignette 'RCAS.vignette.Rmd' failed with diagnostics: Install 'BiocManager' from CRAN to get 'BioCann' contrib.url The other machines all build it properly. Best, Bora --- Dr. Bora Uyar Bioinformatics Scientist Bioinformatics and Omics Data Science Platform Max Delbrueck Center (MDC) for Molecular Medicine The Berlin Institute for Medical Systems Biology Hannoversche Str. 28, 10115 Berlin [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Package failure due to GenomicFeatures update
Thank you Herve! Then, I will pull the code from github to update my code, too. Hopefully my package will also go through by 24th :) Best, Bora From: Hervé Pagès [hpa...@fredhutch.org] Sent: Monday, October 23, 2017 6:17 AM To: Uyar, Bora; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Package failure due to GenomicFeatures update Hi Bora, I just fixed this in GenomicFeatures 1.29.15. The error on the build report won't clear until Tuesday Oct 24 though. Cheers, H. On 10/22/2017 02:59 PM, bora.u...@mdc-berlin.de wrote: > Hi, > > I am the maintainer of the RCAS package. Currently, my package build report > shows errors related to the latest commit to GenomicFeatures package (See > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_GenomicFeatures_commit_22b2ea0a81bc064b8554400ce8f7e13e2c833d38&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e8T4CsJ2raHfOGvsnVFQx06c-caNBkRlC-Wgnb6hL7Q&s=bz4mjLoa7FjycKUx_wCB7Ic1b2nOpTJt0J69fXSaasQ&e=). > GenomicFeatures is showing errors because of the same reason. > > This is an excerpt from the GenomicFeatures build report: > "# Creation time: 2017-10-22 00:29:43 -0400 (Sun, 22 Oct 2017) > > # GenomicFeatures version at creation time: 1.29.14 > # RSQLite version at creation time: 2.0 > # DBSCHEMAVERSION: 1.2 >> >> ## Reverse operation: >> gr2 <- asGFF(txdb) >> >> ## Sanity check: >> stopifnot(identical(as.list(txdb), as.list(makeTxDbFromGRanges(gr2 > Error in .get_cds_IDX(type, phase) : >when 'gr' contains CDS features, it must have a "phase" metadata column >and the phase must be 0, 1, or 2, for all the CDS features > Calls: stopifnot ... identical -> as.list -> makeTxDbFromGRanges -> > .get_cds_IDX > Execution halted” > > The build report for RCAS shows the same error. However, I cannot fix this > problem because I can only install GenomicFeatures version 1.29.13, but the > bioc-build system is using GenomicFeatures v1.29.14. > > Do you know when this will be solved? > > Best, > Bora > > _ > > Dr. Bora Uyar > > Bioinformatics Scientist > Scientific Bioinformatics Platform > The Berlin Institute for Medical Systems Biology (BIMSB) > Max Delbrueck Center (MDC) for Molecular Medicine > > Robert-Rössle-Str. 10, 13125, Berlin, Germany > Building 89, Room 1.08 > > web: > https://urldefense.proofpoint.com/v2/url?u=http-3A__bioinformatics.mdc-2Dberlin.de_team.html-23bora-2Duyar-2Dphd&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e8T4CsJ2raHfOGvsnVFQx06c-caNBkRlC-Wgnb6hL7Q&s=9gkC_jhjUe4nWpERCOvchonLiz90IwwrayNY4zEsYSE&e= > email: bora.u...@mdc-berlin.de<mailto:bora.u...@mdc-berlin.de> > office tel: +49 30 9406 1802 > > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e8T4CsJ2raHfOGvsnVFQx06c-caNBkRlC-Wgnb6hL7Q&s=goCJ-xKRJaiSn68lr8aP4w7yW1ZQMc9lFunuDYuSSIY&e= > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Package failure due to GenomicFeatures update
Hi, I am the maintainer of the RCAS package. Currently, my package build report shows errors related to the latest commit to GenomicFeatures package (See https://github.com/Bioconductor/GenomicFeatures/commit/22b2ea0a81bc064b8554400ce8f7e13e2c833d38). GenomicFeatures is showing errors because of the same reason. This is an excerpt from the GenomicFeatures build report: "# Creation time: 2017-10-22 00:29:43 -0400 (Sun, 22 Oct 2017) # GenomicFeatures version at creation time: 1.29.14 # RSQLite version at creation time: 2.0 # DBSCHEMAVERSION: 1.2 > > ## Reverse operation: > gr2 <- asGFF(txdb) > > ## Sanity check: > stopifnot(identical(as.list(txdb), as.list(makeTxDbFromGRanges(gr2 Error in .get_cds_IDX(type, phase) : when 'gr' contains CDS features, it must have a "phase" metadata column and the phase must be 0, 1, or 2, for all the CDS features Calls: stopifnot ... identical -> as.list -> makeTxDbFromGRanges -> .get_cds_IDX Execution halted” The build report for RCAS shows the same error. However, I cannot fix this problem because I can only install GenomicFeatures version 1.29.13, but the bioc-build system is using GenomicFeatures v1.29.14. Do you know when this will be solved? Best, Bora _ Dr. Bora Uyar Bioinformatics Scientist Scientific Bioinformatics Platform The Berlin Institute for Medical Systems Biology (BIMSB) Max Delbrueck Center (MDC) for Molecular Medicine Robert-Rössle-Str. 10, 13125, Berlin, Germany Building 89, Room 1.08 web: http://bioinformatics.mdc-berlin.de/team.html#bora-uyar-phd email: bora.u...@mdc-berlin.de<mailto:bora.u...@mdc-berlin.de> office tel: +49 30 9406 1802 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
