Re: [Bioc-devel] List of Deprecated Packages for Bioc 3.12
The (very popular) safe package breaks due the quite disruptive class(matrix) update in R-4.0.0 which I could easily fix if given access. Marcel and I contacted the maintainer of the safe package (William T Barry), but received the following automatic notice. "AUTOMATIC NOTICE: Please note that as of March 17th, 2018, I am no longer employed at Dana-Farber Cancer Institute, nor affiliated with DF/HCC, HMS, B and the Alliance Statistics and Data Center. Please contact individuals in each organization with urgent or new matters. For ongoing activities, I will receive and respond to this message as I am able. Cheers," Could you please advise how to proceed as breaking of safe (and the package not being available for bioc-devel) currently prevents me from building my enrichOmics workshop for Bioc2020, and I would thus be interested in resolving this asap. Many thanks, Ludwig From: Bioc-devel on behalf of Shepherd, Lori Sent: Monday, June 8, 2020 11:50 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] List of Deprecated Packages for Bioc 3.12 ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. This is the current list of deprecated packages for Bioc 3.12 : Maintainer requested deprecation: Software: CGEN DESeq: please see DESeq2 chimera flowFit flowSpy netReg metaseqR: please see metaseqR2 MPFE OGSA prada PWMEnrich rTANDEM scsR shinyTANDEM spotSegmentation Unresponsive/not-maintained packages: Software: adaptest ArrayTV BioNet BioSeqClass CHARGE CNVtools CorMut flowType flowVS focalCall FourCSeq gage GeneOverlap GenRank GOFunction ImpulseDE ImpulseDE2 joda JunctionSeq LINC Logolas MAIT Mirsynergy MotIV NarrowPeaks netbenchmark NOISeq omicade4 omicRexposome OmicsMarkeR pathprint PathwaySplice PGSEA plrs Prize reb Roleswitch safe sampleClassifier sigaR signet Starr Experiment Data Package: FunciSNP.data mitoODEdata Mulder2012 PWMEnrich.Dmelanogaster.background PWMEnrich.Hsapiens.background PWMEnrich.Mmusculus.background RNAinteractMAPK RnaSeqSampleSizeData It should be noted, we did try to reach out to these package maintainers multiple times and they were either unresponsive or had emails bounce. We encourage anyone that is familiar with a package maintainer on this list to reach out to them and notify them directly. Packages can be un-deprecated if a maintainer fixes the package to build/check cleanly before the next release and requests un-deprecation on the bioc-devel@r-project.org mailing list. We will be sending emails out to packages that have been broken across all platforms for an extended period of time as those are packages that are up for immediate deprecation if not corrected in a timely fashion. Thank you Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] EXTERNAL: Re: List of Deprecated Packages Bioc 3.11
Great, thanks for the update! From: Interdonato, Kayla Sent: Thursday, February 27, 2020 2:40 PM To: Ludwig Geistlinger; bioc-devel@r-project.org Subject: Re: EXTERNAL: Re: [Bioc-devel] List of Deprecated Packages Bioc 3.11 When generating this annotation package, we believed the data we were downloading was stale which is why we chose to deprecate it. Upon seeing the deprecation list email, a user informed us of a different location where the data may be more up to date. We are currently working through our annotation pipeline with the new data to be sure we can generate all the information needed in the org.At.tair.db package. Once we have finished this pipeline and compared, we will determine if the package should in fact be deprecated and if so, what will the supplement be. Best, Kayla On 2/27/20, 1:24 PM, "Bioc-devel on behalf of Ludwig Geistlinger" wrote: Why will org.At.tair.db be deprecated and by what will it be replaced? It's the org package for Arabidopsis and thus central for gene ID mapping when working with Arabidopsis data ... Thanks, Ludwig -- Dr. Ludwig Geistlinger Department of Epidemiology and Biostatistics CUNY School of Public Health New York, NY 10027 From: Bioc-devel on behalf of Shepherd, Lori Sent: Thursday, February 27, 2020 12:32 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] List of Deprecated Packages Bioc 3.11 ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The current list of deprecated packages for Bioc 3.11 is as follows: Maintainer requested deprecation: Software: QUALIFIER motifRG triform CVE proteoQC affypdnn splicegear Genominator IdMappingAnalysis IdMappingRetrieval manta RefNet AnalysisPageServer scfind kimod plw Annotation: org.At.tair.db hom.At.inp.db hom.Ce.inp.db hom.Dm.inp.db hom.Dr.inp.db hom.Hs.inp.db hom.Mm.inp.db hom.Rn.inp.db hom.Sc.inp.db KEGG.db (use KEGGREST instead) Unresponsive/not-maintained packages: Software: SELEX CTDquerier MTseeker readat anamiR MEAL BiSeq CALIB cellGrowth chroGPS DEDS LVSmiRNA MANOR MCRestimate nem PAPi pcaGoPromoter pint RIPSeeker SANTA waveTiling BayesPeak RCAS bgafun lol M3D MergeMaid ExpermentData: MTseekerData RIPSeekerData The follow Annotation packages were deprecated in 3.10 and removed from 3.11 but not previously announced. MafDb.ESP6500SI.V2.SSA137.hs37d5 MafDb.EXP6500SI.V2.SSA137.GRCh38 It should be noted, we did try to reach out to these package maintainers multiple times and they were either unresponsive or had emails bounce. We encourage anyone that is familiar with a package maintainer on this list to reach out to them and notify them directly. Packages can be un-deprecated if a maintainer fixes the package to build/check cleanly before the next release and requests un-deprecation on the bioc-devel@r-project.org mailing list. We will be sending emails out to packages that have been broken across all platforms for an extended period of time as those are packages that are up for immediate deprecation if not corrected in a timely fashion. Thank you Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsibl
Re: [Bioc-devel] List of Deprecated Packages Bioc 3.11
Why will org.At.tair.db be deprecated and by what will it be replaced? It's the org package for Arabidopsis and thus central for gene ID mapping when working with Arabidopsis data ... Thanks, Ludwig -- Dr. Ludwig Geistlinger Department of Epidemiology and Biostatistics CUNY School of Public Health New York, NY 10027 From: Bioc-devel on behalf of Shepherd, Lori Sent: Thursday, February 27, 2020 12:32 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] List of Deprecated Packages Bioc 3.11 ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The current list of deprecated packages for Bioc 3.11 is as follows: Maintainer requested deprecation: Software: QUALIFIER motifRG triform CVE proteoQC affypdnn splicegear Genominator IdMappingAnalysis IdMappingRetrieval manta RefNet AnalysisPageServer scfind kimod plw Annotation: org.At.tair.db hom.At.inp.db hom.Ce.inp.db hom.Dm.inp.db hom.Dr.inp.db hom.Hs.inp.db hom.Mm.inp.db hom.Rn.inp.db hom.Sc.inp.db KEGG.db (use KEGGREST instead) Unresponsive/not-maintained packages: Software: SELEX CTDquerier MTseeker readat anamiR MEAL BiSeq CALIB cellGrowth chroGPS DEDS LVSmiRNA MANOR MCRestimate nem PAPi pcaGoPromoter pint RIPSeeker SANTA waveTiling BayesPeak RCAS bgafun lol M3D MergeMaid ExpermentData: MTseekerData RIPSeekerData The follow Annotation packages were deprecated in 3.10 and removed from 3.11 but not previously announced. MafDb.ESP6500SI.V2.SSA137.hs37d5 MafDb.EXP6500SI.V2.SSA137.GRCh38 It should be noted, we did try to reach out to these package maintainers multiple times and they were either unresponsive or had emails bounce. We encourage anyone that is familiar with a package maintainer on this list to reach out to them and notify them directly. Packages can be un-deprecated if a maintainer fixes the package to build/check cleanly before the next release and requests un-deprecation on the bioc-devel@r-project.org mailing list. We will be sending emails out to packages that have been broken across all platforms for an extended period of time as those are packages that are up for immediate deprecation if not corrected in a timely fashion. Thank you Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10
Thanks Nitesh. I ported the fix and the package builds fine - besides the deprecation warning: http://bioconductor.org/checkResults/devel/bioc-LATEST/PathNet Best, Ludwig From: Turaga, Nitesh Sent: Thursday, December 19, 2019 2:12 PM To: Shepherd, Lori Cc: Ludwig Geistlinger; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10 Hi Ludwig, Thank you for volunteering to take over as maintainer for PathNet and PathNetData. You should now have access to both packages as the maintainer. They should show up on the build machine tomorrow. You should port your fix(s) to the build machine for the PathNet package when you can and see if it is fixed on the devel builder. Best regards, Nitesh > On Dec 4, 2019, at 1:54 PM, Shepherd, Lori > wrote: > > We will start the process and be in touch off the bioc mailing list. > > We would require you officially take over as maintainer as all bioconductor > packages require an active maintainer. PathNet was failing and we reached > out (several times) and deemed the package orphaned as we never heard back > from the currently listed maintainer. > > Cheers, > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > From: Ludwig Geistlinger > Sent: Wednesday, December 4, 2019 1:32 PM > To: Shepherd, Lori ; bioc-devel@r-project.org > > Subject: Re: Final List of Deprecated Packages for Bioc3.10 > > > Yes, I could do that if needed. > > ____ > From: Shepherd, Lori > Sent: Wednesday, December 4, 2019 1:28 PM > To: Ludwig Geistlinger; bioc-devel@r-project.org > Subject: Re: Final List of Deprecated Packages for Bioc3.10 > > ***ATTENTION: This email came from an external source. Do not open > attachments or click on links from unknown senders or unexpected emails.*** > > Are you volunteering to permanently take over as maintainer of this package? > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > From: Ludwig Geistlinger > Sent: Wednesday, December 4, 2019 1:22 PM > To: Shepherd, Lori ; bioc-devel@r-project.org > > Subject: Re: Final List of Deprecated Packages for Bioc3.10 > > Hi Lori, > > Is it possible to undeprecate the "PathNet" package? > I just checked, the problem is a failing unit test, causing the otherwise > well working package to fail R CMD check. > > I fixed this here on a local clone of > https://git.bioconductor.org/packages/PathNet<https://urldefense.proofpoint.com/v2/url?u=https-3A__git.bioconductor.org_packages_PathNet=DwMFAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE=hXVVPnvQ8N1q2LgQkQOS5W7zBluTCo4kY2Gmj4i4RXY=q1rBhXn6bs7NDTSKvbP9xKPMjQ4tUSuSwBvC-YYzWSI=> > and could push these minor changes if granted access. > > The PathNet package implements a solid network-based enrichment method and > the corresponding paper has some 50 citations - it would thus be unfortunate > to see it gone. > > Thanks, > Ludwig > > > > From: Bioc-devel on behalf of Shepherd, > Lori > Sent: Monday, October 7, 2019 9:41 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10 > > The Bioconductor Team is continuing to identify packages that will be > deprecated in the next release to allow for the Bioconductor community to > respond accordingly. > > The final list for the 3.10 release is as follows: > > Maintainer requested deprecation: > > Software: > > SNPchip > GenomeGraphs > HTSanalyzeR > Rchemcpp > charm > Pbase > > > Experiment Data Package: > > charmData > > > > Unresponsive/not-maintained packages: > > Software: > > dSimer > flipflop > exomePeak > CNPBayes > brainImageR > plateCore > rHVDM > SEPA > condcomp > PathNet > scone > birte > mlm4omics > RnaSeqSampleSize > > > Experiment Data Package: > > facopy.annot > allenpvc > > > Renaming The package CAMTHC is marked for deprecation. This package has been > renamed to debCAM > > > > The following Annotation Packages have been user requested deprecated: > > MafDb.gnomADex.r2.0.1.GRCh38 > MafDb.gnomAD.r2.0.1.GRCh38 > Maf
Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10
Yes, I could do that if needed. From: Shepherd, Lori Sent: Wednesday, December 4, 2019 1:28 PM To: Ludwig Geistlinger; bioc-devel@r-project.org Subject: Re: Final List of Deprecated Packages for Bioc3.10 ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Are you volunteering to permanently take over as maintainer of this package? Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ____ From: Ludwig Geistlinger Sent: Wednesday, December 4, 2019 1:22 PM To: Shepherd, Lori ; bioc-devel@r-project.org Subject: Re: Final List of Deprecated Packages for Bioc3.10 Hi Lori, Is it possible to undeprecate the "PathNet" package? I just checked, the problem is a failing unit test, causing the otherwise well working package to fail R CMD check. I fixed this here on a local clone of https://git.bioconductor.org/packages/PathNet<https://urldefense.proofpoint.com/v2/url?u=https-3A__git.bioconductor.org_packages_PathNet=DwMFAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE=hXVVPnvQ8N1q2LgQkQOS5W7zBluTCo4kY2Gmj4i4RXY=q1rBhXn6bs7NDTSKvbP9xKPMjQ4tUSuSwBvC-YYzWSI=> and could push these minor changes if granted access. The PathNet package implements a solid network-based enrichment method and the corresponding paper has some 50 citations - it would thus be unfortunate to see it gone. Thanks, Ludwig From: Bioc-devel on behalf of Shepherd, Lori Sent: Monday, October 7, 2019 9:41 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10 The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The final list for the 3.10 release is as follows: Maintainer requested deprecation: Software: SNPchip GenomeGraphs HTSanalyzeR Rchemcpp charm Pbase Experiment Data Package: charmData Unresponsive/not-maintained packages: Software: dSimer flipflop exomePeak CNPBayes brainImageR plateCore rHVDM SEPA condcomp PathNet scone birte mlm4omics RnaSeqSampleSize Experiment Data Package: facopy.annot allenpvc Renaming The package CAMTHC is marked for deprecation. This package has been renamed to debCAM The following Annotation Packages have been user requested deprecated: MafDb.gnomADex.r2.0.1.GRCh38 MafDb.gnomAD.r2.0.1.GRCh38 MafDb.gnomADex.r2.0.1.hs37d5 MafDb.gnomAD.r2.0.1.hs37d5 They are replaced with MafDb.gnomADex.r2.1.GRCh38 MafDb.gnomAD.r2.1.GRCh38 MafDb.gnomADex.r2.1.hs37d5 MafDb.gnomAD.r2.1.hs37d5 The Bioconductor team will continue to send emails out to packages that have been broken across all platforms for an extended period of time as those are packages that are up for immediate deprecation if not corrected in a timely fashion. Packages that are ERRORing and not fixed before the October 30th 3.10 release will immediately be marked as deprecated in devel 3.11. Thank you Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwMFAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE=hXVVPnvQ8N1q2LgQkQOS5W7zBluTCo4kY2Gmj4i4RXY=npv0ZxWtaD0vGTxwpMw-hYI6BMzlx-YhCp1dtAugg6U=> This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] __
Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10
Hi Lori, Is it possible to undeprecate the "PathNet" package? I just checked, the problem is a failing unit test, causing the otherwise well working package to fail R CMD check. I fixed this here on a local clone of https://git.bioconductor.org/packages/PathNet and could push these minor changes if granted access. The PathNet package implements a solid network-based enrichment method and the corresponding paper has some 50 citations - it would thus be unfortunate to see it gone. Thanks, Ludwig From: Bioc-devel on behalf of Shepherd, Lori Sent: Monday, October 7, 2019 9:41 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10 The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The final list for the 3.10 release is as follows: Maintainer requested deprecation: Software: SNPchip GenomeGraphs HTSanalyzeR Rchemcpp charm Pbase Experiment Data Package: charmData Unresponsive/not-maintained packages: Software: dSimer flipflop exomePeak CNPBayes brainImageR plateCore rHVDM SEPA condcomp PathNet scone birte mlm4omics RnaSeqSampleSize Experiment Data Package: facopy.annot allenpvc Renaming The package CAMTHC is marked for deprecation. This package has been renamed to debCAM The following Annotation Packages have been user requested deprecated: MafDb.gnomADex.r2.0.1.GRCh38 MafDb.gnomAD.r2.0.1.GRCh38 MafDb.gnomADex.r2.0.1.hs37d5 MafDb.gnomAD.r2.0.1.hs37d5 They are replaced with MafDb.gnomADex.r2.1.GRCh38 MafDb.gnomAD.r2.1.GRCh38 MafDb.gnomADex.r2.1.hs37d5 MafDb.gnomAD.r2.1.hs37d5 The Bioconductor team will continue to send emails out to packages that have been broken across all platforms for an extended period of time as those are packages that are up for immediate deprecation if not corrected in a timely fashion. Packages that are ERRORing and not fixed before the October 30th 3.10 release will immediately be marked as deprecated in devel 3.11. Thank you Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Reference manual as HTML
ffWkIbqQKnBCRhuovHpI4lI-2526e-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-257C0-257C637051329265489883-26amp-3Bsdata-3Dh43tcLTXczYDUsZRCDZgrAxxgjqacXbRhp-252FOmIULkag-253D-26amp-3Breserved-3D0-3D=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ=whVthWQxSLPHIXmYqhg3Vx1wd2RLsroluMCrLbrloAA=
>>
>> it should not be hard to have it do the same for all other
>> packages in principle.
>>
>> "The other R Core" Martin
>>
>> Martin Maechler
>> ETH Zurich
>>
>>
>> > What is your experience with pkgdown?
>>
>> > Martin
>>
>> > On 9/25/19, 9:44 AM, "Bioc-devel on behalf of Laurent Gatto"
>>
>> wrote:
>>
>> > I think this would be very useful. This is one of the reasons I
>> create pkgdown sites for my packages: manual pages, news and html vignettes
>> are readily available for all (including me) to browse.
>>
>> > Best wishes,
>>
>> > Laurent
>>
>> >
>> > From: Bioc-devel on behalf of
>> Ludwig Geistlinger
>> > Sent: 25 September 2019 13:31
>> > To: bioc-devel@r-project.org
>> > Subject: [Bioc-devel] Reference manual as HTML
>>
>> > Dear Bioc-Team,
>>
>>
>> > I repeatedly wondered whether it would be possible to display the
>> reference manual
>> > as HTML instead of PDF on a package's landing page. This is already
>> possible for vignettes.
>>
>> > HTML reference manuals have at least two advantages:
>>
>> > 1. links to functions of other package in the man pages of my
>> package would
>> > actually work. Links to functions / classes of other packages of the
>> form
>>
>> > \code{\link{p.adjust}}
>>
>> > or
>>
>> > \code{\linkS4class{SummarizedExperiment}}
>>
>> > within the pdf reference manual currently point nowhere (bring me
>> back to the
>> > first page of the pdf). Within the html reference manual
>>
>> > help(package="myPackage", help_type="html")
>>
>> > these links work as expected, ie bring me to the help pages of
>> functions / classes
>> > of other packages.
>>
>> > 2. I could easily refer users to the documentation link of a
>> specific function
>> > (without them having to search through the pdf) such as "check the
>> documentation of
>> > the DESeq function here:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Frdrr.io-5Fbioc-5FDESeq2-5Fman-5FDESeq.html-2526d-253DDwIDaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253Dc4VdSQh-5FZ9zl5XbA2uoUx-2DcLMNMKpPP7NOvfAEo82ms-2526s-253DsHA2r6mT4RdU-2D4xFyz7-2DaE0PH2f-5FrygY4C5S3QToH-5FE-2526e-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-257C0-257C637051329265489883-26amp-3Bsdata-3Dm2tonNHuf9DWKWclzPxfLs5hZSOWBnvW5wHGH3Yu1lY-253D-26amp-3Breserved-3D0-3D=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ=UVpKGa8NF8NIdjl1LUsn3aVICpK42SdrSQuT6UgcjjI=
>> ".
>>
>> > (where the link would be preferably:
>> bioconductor.org/packages/DESeq2/man/DESeq.html).
>>
>>
>> > Thank you,
>>
>> > Ludwig
>>
>> > [[alternative HTML version deleted]]
>>
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fstat.ethz.ch-5Fmailman-5Flistinfo-5Fbioc-2D2Ddevel-2526d-253DDwIDaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253Dc4VdSQh-5FZ9zl5XbA2uoUx-2DcLMNMKpPP7NOvfAEo82ms-2526s-253D1vQt-5F1VkcxKSPxoc2fKM0H9PT8bo0ZmM-5Fb5QfLvzUP0-2526e-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-2
[Bioc-devel] Reference manual as HTML
Dear Bioc-Team,
I repeatedly wondered whether it would be possible to display the reference
manual
as HTML instead of PDF on a package's landing page. This is already possible
for vignettes.
HTML reference manuals have at least two advantages:
1. links to functions of other package in the man pages of my package would
actually work. Links to functions / classes of other packages of the form
\code{\link{p.adjust}}
or
\code{\linkS4class{SummarizedExperiment}}
within the pdf reference manual currently point nowhere (bring me back to the
first page of the pdf). Within the html reference manual
help(package="myPackage", help_type="html")
these links work as expected, ie bring me to the help pages of functions /
classes
of other packages.
2. I could easily refer users to the documentation link of a specific function
(without them having to search through the pdf) such as "check the
documentation of
the DESeq function here: https://rdrr.io/bioc/DESeq2/man/DESeq.html;.
(where the link would be preferably:
bioconductor.org/packages/DESeq2/man/DESeq.html).
Thank you,
Ludwig
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] SPB inconsistencies
Hi, According to http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html all SPB machines run different snapshots of R-devel with the most recent one (2019-01-22 r76000, already >1 month outdated) installed on celaya2. I observe two things: 1. My package builds on celaya2, but fails to build on the other SPB machines running older R-devel snapshots. http://bioconductor.org/checkResults/devel/bioc-LATEST/CNVRanger/ 2. Further, I can't reproduce the SPB built error using a recent R-devel snapshot (2019-02-24 r76155) through the bioconductor/devel_base2 docker container. Can you please advise on how to best proceed from my side? Just wait for the SPB R-devel being updated? > sessionInfo() R Under development (unstable) (2019-02-24 r76155) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 9 (stretch) Matrix products: default BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=C [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] stats4parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] TCGAutils_1.3.19 [2] BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99 [3] BSgenome.Btaurus.UCSC.bosTau6_1.4.0 [4] BSgenome_1.51.0 [5] rtracklayer_1.43.1 [6] Biostrings_2.51.2 [7] XVector_0.23.0 [8] regioneR_1.15.2 [9] BiocStyle_2.11.0 [10] CNVRanger_0.99.7 [11] curatedTCGAData_1.5.8 [12] edgeR_3.25.3 [13] limma_3.39.12 [14] RaggedExperiment_1.7.4 [15] MultiAssayExperiment_1.9.15 [16] SummarizedExperiment_1.13.0 [17] DelayedArray_0.9.8 [18] BiocParallel_1.17.16 [19] matrixStats_0.54.0 [20] ensembldb_2.7.9 [21] AnnotationFilter_1.7.0 [22] GenomicFeatures_1.35.7 [23] AnnotationDbi_1.45.0 [24] Biobase_2.43.1 [25] GenomicRanges_1.35.1 [26] GenomeInfoDb_1.19.2 [27] IRanges_2.17.4 [28] S4Vectors_0.21.10 [29] AnnotationHub_2.15.7 [30] BiocGenerics_0.29.1 loaded via a namespace (and not attached): [1] ProtGenerics_1.15.0 bitops_1.0-6 [3] bit64_0.9-7 progress_1.2.0 [5] httr_1.4.0GenomicDataCommons_1.7.3 [7] tools_3.6.0 R6_2.4.0 [9] DBI_1.0.0 lazyeval_0.2.1 [11] tidyselect_0.2.5 prettyunits_1.0.2 [13] bit_1.1-14curl_3.3 [15] compiler_3.6.0rvest_0.3.2 [17] xml2_1.2.0readr_1.3.1 [19] rappdirs_0.3.1stringr_1.4.0 [21] digest_0.6.18 Rsamtools_1.99.2 [23] rmarkdown_1.11pkgconfig_2.0.2 [25] htmltools_0.3.6 rlang_0.3.1 [27] rstudioapi_0.9.0 RSQLite_2.1.1 [29] shiny_1.2.0 jsonlite_1.6 [31] dplyr_0.8.0.1 RCurl_1.95-4.11 [33] magrittr_1.5 GenomeInfoDbData_1.2.0 [35] Matrix_1.2-15 Rcpp_1.0.0 [37] stringi_1.3.1 yaml_2.2.0 [39] zlibbioc_1.29.0 grid_3.6.0 [41] blob_1.1.1promises_1.0.1 [43] ExperimentHub_1.9.1 crayon_1.3.4 [45] lattice_0.20-38 hms_0.4.2 [47] locfit_1.5-9.1knitr_1.21 [49] pillar_1.3.1 biomaRt_2.39.2 [51] XML_3.98-1.17 glue_1.3.0 [53] evaluate_0.13 BiocManager_1.30.4 [55] httpuv_1.4.5.1purrr_0.3.0 [57] assertthat_0.2.0 xfun_0.5 [59] mime_0.6 xtable_1.8-3 [61] later_0.8.0 tibble_2.0.1 [63] GenomicAlignments_1.19.1 memoise_1.1.0 [65] interactiveDisplayBase_1.21.0 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Single Package Builder for New Submissions
Dear Lori, Is the update of the MAC SPB still ongoing? Today, I managed to produce three different build reports - from "all-ok" to "timeout" and "errors" just by documentation enhancements and version number bumps, ie no changes on the actual R stuff (code, vignette chunks, examples, etc): http://bioconductor.org/spb_reports/CNVRanger_buildreport_20190128130552.html http://bioconductor.org/spb_reports/CNVRanger_buildreport_20190128145534.html http://bioconductor.org/spb_reports/CNVRanger_buildreport_20190128160110.html Particularly, the mac builder doesn't seem to have an internet connection? Thank you, Ludwig -- Dr. Ludwig Geistlinger CUNY School of Public Health From: Bioc-devel on behalf of Shepherd, Lori Sent: Tuesday, January 22, 2019 9:26 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Single Package Builder for New Submissions During this week we will be updating the Single Package Builder to use a new MAC builder. During this updating and testing, the Single Package Builder may produce some sporadic ERRORs or experience intermittent periods of downtime. We will be as quick as possible and hope to keep the interruptions to a minimum. We appreciate your understanding. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] support the stable version of R
> Having said that, I'll note that specifying R as a dependency, and a version
> of R as a criterion for your package, is really a mis-nomer for a
> Bioconductor package -- of course it uses R, and the version of R in use
> determines the Bioconductor version(s) that can be used! So a rational change
> is to remove R and its version requirement from the DESCRIPTION file
> entirely, a strategy taken by I think about 400 of our 1650+ packages.
Maybe worth including under
https://bioconductor.org/developers/package-guidelines/#description
-> 8. “Depends/Imports/Suggests/Enhances:” fields: --> Depends
From: Bioc-devel on behalf of Martin Morgan
Sent: Monday, January 14, 2019 6:52 PM
To: Lulu Chen; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] support the stable version of R
Remember that Bioconductor packages are tested nightly on our build system, and
this nightly testing is an important component of offering your users a stable
environment, not just for your package but the other packages they use.
Recreating this standard environment is facilitated by the standard
Bioconductor package installation instruction
BiocManager::install("YourPackage")
The nightly builds are done on a platform where all packages are from the same
Bioconductor release, built on the same version of R. Your newly accepted
package is in the '3.9' version of Bioconductor, which uses the 3.6 version of
R. It follows that the best user experience is provided to those using R 3.6.
By 'allowing' R 3.5 and non-standard installation (e.g., from github) you are
ultimately compromising the quality standards of Bioconductor and the
experience of the users of your package. The support site has many questions
from people who install packages from different Bioconductor versions, so it is
clearly not in your interest, or the Bioconductor project interest, or your
user's interest, to enable this kind of usage.
It is hard to see into the future, so saying something like R >= 3.5 is really
quite bold! Conversely, packages with out-of-date promises like R >= 2.1 are
not tested on the systems they claim compatibility with, and can be easily
broken on old versions of R where their dependencies are no longer available.
From some scraping of the file summarizing the current devel repository
https://bioconductor.org/packages/devel/bioc/VIEWS I see
> as_tibble(tbl) %>% arrange(desc(n))
# A tibble: 84 x 2
Var1 n
1 R (>= 3.5) 130
2 R (>= 2.10) 125
3 R (>= 3.4) 117
4 R (>= 3.5.0) 83
5 R (>= 3.4.0) 64
6 R (>= 3.3) 58
7 R (>= 2.10.0)41
8 R (>= 3.0.0) 41
9 R (>= 3.2.0) 41
10 R (>= 3.3.0) 41
# ... with 74 more rows
> as_tibble(tbl) %>% filter(grepl("3.6", Var1)) %>% arrange(desc(n))
# A tibble: 2 x 2
Var1 n
1 R (>= 3.6) 17
2 R (>= 3.6.0) 6
> as_tibble(tbl) %>% filter(grepl("<", Var1)) %>% arrange(desc(n))
# A tibble: 1 x 2
Var1n
1 R (< 3.7.0) 1
so there are many very optimistic assertions about suitability, only a few
current versions, and a single package that is not clairvoyant!
Having said that, I'll note that specifying R as a dependency, and a version of
R as a criterion for your package, is really a mis-nomer for a Bioconductor
package -- of course it uses R, and the version of R in use determines the
Bioconductor version(s) that can be used! So a rational change is to remove R
and its version requirement from the DESCRIPTION file entirely, a strategy
taken by I think about 400 of our 1650+ packages.
Martin
On 1/14/19, 5:40 PM, "Bioc-devel on behalf of Lulu Chen"
wrote:
Dear all,
When submitting package to bioconductor, it is required to change R version
in "Depends" to be >= the develop version (3.6) . As my package is also
available in GitHub, someone asks if it be possible to make it available
with the stable version of R (R3.5). In fact, my package can work well with
R3.5 if I change "Depends" back to R(>=3.5) .
So I hope to support R3.5 for the moment before next release. Should I
create another repository? Can I use a branch to support R3.5?
Thanks,
Lulu
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Why bioconductor?
While this might be obvious to most of us, it seems to be less clear to others. In particular, those who worked out their first package and wonder what's the difference between having a package available on Github, CRAN, or Bioconductor. I wonder whether it would be helpful for the Bioc webpage to pick up on the benefits of submitting to CRAN by Hadley http://r-pkgs.had.co.nz/release.html and several considerations with respect to Bioconductor https://bioinformatics.stackexchange.com/questions/639/why-bioconductor (Maybe FAQ?) Just a thought. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] build machines
Hi Hervé, > Some packages are good citizens and limit the number of > cores to 1 or 2 only during 'R CMD check' but some packages > try to use all the cores that are available That seems to be an important note for developers using parallel computation. What's best practice to realize this within my code, i.e. checking whether the code is currently subject to R CMD check (and accordingly reducing the number of cores used)? Thanks, Ludwig -- Dr. Ludwig Geistlinger CUNY School of Public Health From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Kasper Daniel Hansen <kasperdanielhan...@gmail.com> Sent: Friday, April 27, 2018 10:29 AM To: Hervé Pagès Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] build machines Thanks. I used /usr/bin/time -v R CMD check ... to record the max memory usage of the check, which for minfi suggests around 5Gb. That's a lot. Best, Kasper On Thu, Apr 26, 2018 at 3:02 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi, > > The Linux and Windows builders have 32 GB of RAM, the Mac > builders 64 Gb. > > We also run concurrent R CMD check's. > > Here is a summary: > > platform RAM nb of nb of concurrent > (Gb) coresR CMD check's > --- > Linux (malbecs) 32 20 10 > Windows (tokays)32 40 24 > Mac (meridas) 64 24 18 > > That's a lot of concurrency. And there is actually more > concurrency than that if you consider the fact that many > packages run things in parallel during 'R CMD check'. > Some packages are good citizens and limit the number of > cores to 1 or 2 only during 'R CMD check' but some packages > try to use all the cores that are available. This will have > a strong impact on the overall progress of the builds. We > don't have an easy way to identify those packages right now. > > In average, based on our monitoring of the build machines > things seem to work ok i.e. the concurrent R CMD check's > don't seem to be competing too much to access resources. > > But occasionally there could be too much competition. The > crazy big elapsed time compared to the relatively short user > and system times that you observed Kasper are likely to reflect > that. They could be the sign that the machine ran out of memory > and started swapping. Not because it happens to your package > means that your package uses too much memory. The swapping is > the result of the **cumulated** memory usage of all the > R CMD check's running at that moment. It could be worth checking > how much memory R CMD check'ing your package uses though. > > The exact set of packages that are being R CMD check'ed at any > given time is in constant fluctuation and will also vary from > one day to the other. This would explain why some days you see > timeouts on some platforms and some days not. We don't have > an easy way to know which packages were competing with yours > during the 40 min window that 'R CMD check' was running on your > package until the build system declared a timeout. It's possible > (by looking at the BBS logs) but is time consuming. > > We should probably add some memory at some point to the Windows > builders. 32 Gb is not enough to smoothly run 24 R CMD check's > concurrently. > > H. > > > On 04/26/2018 08:48 AM, Diogo FT Veiga wrote: > >> Hi Daniel, >> >> I have the same issue with my package (new contribution). I just finish >> reviewing the package with the modifications requested. >> >> I am having a warning because R CMD check is exceeding 5 min, but this is >> happening only in the Windows machine. >> >> In Linux and OSX the check finishes in <= 4min, while in Windows takes >> ~6min. >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__biocondu >> ctor.org_spb-5Freports_maser-5Fbuildreport-5F20180425114748 >> .html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY >> _wJYbW0WYiZvSXAJJKaaPhzWA=JwiMI-3BEUJlonlihLD_mDkPuEIalQbk >> rQPSGahzfsg=1aMitB3PnVLoojx1lnj_UT_ZeKlJ_OcJDFT4D6BPXow= >> >> >> Not sure how to proceed from here. >> >> Thanks, >> Diogo >> >> >> On Thu, Apr 26, 2018 at 9:52 AM, Kasper Daniel Hansen < >> kasperdanielhan...@gmail.com> wrote: >> >> We have been working on the minfi package lately, with a move to a >>> DelayedArray backend. >>> >>> Right now there are some weird issues regarding timings in R CMD check. >>> Leaving aside the issue that the tests (now disabled) and examples are >>> too &g
Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7
Hi Lori, I have worked through the ToPASeq package. 1. The package implements an extended range of operations for the 'Pathway' class (defined in the graphite package). I am currently in contact with the author of the graphite package, Gabriele Sales, whether these operations are generally useful for the class and could be accordingly moved to the graphite package. 2. The implementations of the pathway enrichment methods SPIA, DEGraph, and TopologyGSA are redundant with existing functionality in Bioconductor and will be accordingly delegated to corresponding implementations in the graphite and EnrichmentBrowser package. The core of the package that I will maintain further are the implementations of the pathway enrichment methods PRS, PWEA and TAPPA, which seem to be unique to the package. 3. Parallel computation will be reworked to be based on BiocParallel, thereby resolving the package's current platform dependence (linux-only). I have required access rights, have set up a github repo under lgeistlinger/ToPASeq, and I am optimistic to have a working version ready in devel in agreement with the respective deadline of the release schedule (Wed, April 25, Deadline for packages passing ��R CMD build�� and ��R CMD check�� without errors or warnings). Best, Ludwig -- Dr. Ludwig Geistlinger CUNY School of Public Health From: Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Monday, March 26, 2018 8:07 AM To: Ludwig Geistlinger Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7 Hi Ludwig, I just wanted to touch base and make sure you had the access rights to ToPASeq. The release is scheduled for next month http://bioconductor.org/developers/release-schedule/<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_release-2Dschedule_=DwMFAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE=A6USjX0wMQjoU6_viKxatj3j6gq2X7SCNrkkK-6gGRA=aaqpSz33LI5XkpuV6t-9hktb7ikL64-9vt9lybZgr60=> and I was curious as to your estimated time frame for looking at fixing the ERRORs in the package? Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________ From: Ludwig Geistlinger <ludwig.geistlin...@sph.cuny.edu> Sent: Saturday, March 3, 2018 5:51:10 PM To: Shepherd, Lori; Martin Morgan Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7 Hi Lori, Yes I would take over maintenance. Anything particular that I need to take care of? Otherwise I would just follow: https://bioconductor.org/developers/how-to/git/maintain-github-bioc/<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_how-2Dto_git_maintain-2Dgithub-2Dbioc_=DwMFAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE=A6USjX0wMQjoU6_viKxatj3j6gq2X7SCNrkkK-6gGRA=5Fgho__A-8_HMECEdkVGInWgNTMX6sweJl1aUrtpPGo=> to accordingly set this up. Thanks, Ludwig -- Dr. Ludwig Geistlinger CUNY School of Public Health From: Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Saturday, March 3, 2018 5:14 PM To: Ludwig Geistlinger; Martin Morgan Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7 Hi Ludwig, Were you still interested in taking over maintainership of ToPaSeq? We have switched permission and you should have access now. If you are no longer interested please let us know. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ____ From: Ludwig Geistlinger <ludwig.geistlin...@sph.cuny.edu> Sent: Friday, December 15, 2017 1:05:16 PM To: Shepherd, Lori; Martin Morgan Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7 Hi Lori, I would be willing to take over maintenance of ToPASeq in case maintainers remain unresponsive. Best, Ludwig -- Dr. Ludwig Geistlinger CUNY School of Public Health From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Friday, December 15, 2017 9:29 AM To: Martin Morgan Subject: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7 The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The current list of deprecated packages is as follows: Maintainer requested deprecation: Software Package: ontoCAT Experiment Data Package: RnaSeqTutorial cheung2010 Unresponsive/not-maintained packages: Software: GMRP MBttest OperaMa
Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7
Hi Lori, Yes I would take over maintenance. Anything particular that I need to take care of? Otherwise I would just follow: https://bioconductor.org/developers/how-to/git/maintain-github-bioc/ to accordingly set this up. Thanks, Ludwig -- Dr. Ludwig Geistlinger CUNY School of Public Health From: Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Saturday, March 3, 2018 5:14 PM To: Ludwig Geistlinger; Martin Morgan Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7 Hi Ludwig, Were you still interested in taking over maintainership of ToPaSeq? We have switched permission and you should have access now. If you are no longer interested please let us know. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ____ From: Ludwig Geistlinger <ludwig.geistlin...@sph.cuny.edu> Sent: Friday, December 15, 2017 1:05:16 PM To: Shepherd, Lori; Martin Morgan Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7 Hi Lori, I would be willing to take over maintenance of ToPASeq in case maintainers remain unresponsive. Best, Ludwig -- Dr. Ludwig Geistlinger CUNY School of Public Health From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Friday, December 15, 2017 9:29 AM To: Martin Morgan Subject: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7 The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The current list of deprecated packages is as follows: Maintainer requested deprecation: Software Package: ontoCAT Experiment Data Package: RnaSeqTutorial cheung2010 Unresponsive/not-maintained packages: Software: GMRP MBttest OperaMate ToPASeq Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwMFAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE=U_m_leinYsy4QmdwhzgtnqkLI0Nyqx3hADyGLrc9Qs0=MI8Wx4E5bER4kpsrf72qXRTElrE8aW8eFJl5WkhqkxY=> This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] BiocParallel: windows vs. mac/linux behavior
Hi,
I am currently considering the following snippet:
> data.ids <- paste0("d", 1:5)
> f <- function(x) paste("dataset", x, sep=" = ")
> res <- BiocParallel::bplapply(data.ids, function(d) f(d))
Using a recent R-devel on both a Linux machine and a Mac machine, this works
fine.
However, on a Windows R-devel this throws:
Error: BiocParallel errors
element index: 1, 2, 3, 4, 5
first error: could not find function "f"
Is this a bug or is this related to the different ways in which parallel (for
windows here serial) computation is carried out?
Thanks,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocParallel and AnnotationDbi: database disk image is malformed
Thanks for these explanations, Martin.
What I actually want to do is sending each expression dataset on probe level to
a worker, where probe level expression is summarized to gene level expression
according to a chosen summarization function (such as 'mean').
The worker should then return the expression dataset on gene level back to the
manager.
Taking also Vince' suggestion and your considerations on work load into
account, it seems best if I first collect the probe2gene mappings for the
unique set of annotation packages (which would only be 2 in the example) in
serial mode on the manager.
Then, I can send the datasets together with the respective mapping as a simple
table to the workers, which carry out the actual computational part, ie. the
summarization.
This would avoid parallel access on the database and would also spare
retrieving the mappings on each worker over in over again, as it is likely that
some datasets of the compendium share the corresponding annotation db.
Thanks,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
From: Martin Morgan <martin.mor...@roswellpark.org>
Sent: Friday, January 19, 2018 4:10 PM
To: Ludwig Geistlinger; Gabe Becker; Vincent Carey
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocParallel and AnnotationDbi: database disk image
is malformed
On 01/19/2018 02:24 PM, Ludwig Geistlinger wrote:
> I apologize if I haven't been specific enough - however, I am also having
> trouble to reliably reproduce the error.
> It does not seem to be exclusively related to the combination of
> AnnotationDbi and parallel computation, but also with some other packages I
> load.
>
> While still trying to produce a minimal reproducible example, here is what
> returns the error quite reliably on an 8-core Linux machine:
>
> # loading some dependencies of my package
> library(org.Hs.eg.db)
> library(pathview)
> library(graph)
> library(BiocParallel)
>
> # annotation packages for the datasets in the compendium
> pkgs <- rep(c("hgu133plus2.db","hgu133a.db"), 42)
>
> #
> getSymbols <- function ( anno.pkg )
> {
> require(anno.pkg, character.only=TRUE)
> anno.pkg <- get(anno.pkg)
> syms <- AnnotationDbi::mapIds(anno.pkg, keys=keys(anno.pkg),
> keytype="PROBEID", column="ENTREZID")
> return(syms)
> }
>
>> x <- bplapply( pkgs , getSymbols ) ### sometimes I have to run this 2
>> or 3 times in a row to produce this error
> Loading required package: hgu133plus2.db
>
> Error: BiocParallel errors
>element index: 29, 30, 31, 32, 33, 34, ...
>first error: database disk image is malformed
My guess is that the database is being accessed by multiple processes
simultaneously and, even though the data bases are opened read-only,
this causes a corruption in the access of some sort. You can avoid
multiple processes accessing the database at the same time by using a 'lock'
getSymbols <- function ( anno.pkg, id )
{
nmspc <- loadNamespace(anno.pkg)
anno.pkg <- get(anno.pkg, nmspc)
BiocParallel::ipclock(id)
syms <- suppressMessages({
AnnotationDbi::mapIds(
anno.pkg, keys=keys(anno.pkg), keytype="PROBEID",
column="ENTREZID"
)
})
BiocParallel::ipcunlock(id)
length(syms)
}
x <- bplapply(pkgs , getSymbols, ipcid())
There are two additional considerations here.
The first is that one wants to worry about the amount of data transfered
between worker and manager compared to the amount of time spent in
computation. So in your previous formulation you sent back all the
symbols -- this will be relatively expensive compared to the amount of
work done in the function (reading the ids from the database), and you
would rather do more work and transmit less (both to and from the
worker) in each call to getSymbol().
The second is similar, but from the lock perspective -- since the lock
imposes essential serial evaluation through that portion of the code,
you'd like the locked portion of the worker's task to be just a small
portion of the total work done by the worker.
I guess a more clever use of locks would be one per data base (generate
two ipcid()'s in the manager, and pass these to the worker in such a way
that the worker uses the same lock for each database.
Martin
>
>
>> sessionInfo()
> R version 3.4.1 (2017-06-30)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: SUSE Linux Enterprise Desktop 12 SP3
>
> Matrix products: default
> BLAS: /mnt/raidbio/biosoft/software/R/R-3.4.1/lib/libRblas.so
> LAPACK: /mnt/raidbio/biosoft/software/R/R-3.4.1/lib/libRlapack.so
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERI
Re: [Bioc-devel] BiocParallel and AnnotationDbi: database disk image is malformed
I apologize if I haven't been specific enough - however, I am also having
trouble to reliably reproduce the error.
It does not seem to be exclusively related to the combination of AnnotationDbi
and parallel computation, but also with some other packages I load.
While still trying to produce a minimal reproducible example, here is what
returns the error quite reliably on an 8-core Linux machine:
# loading some dependencies of my package
library(org.Hs.eg.db)
library(pathview)
library(graph)
library(BiocParallel)
# annotation packages for the datasets in the compendium
pkgs <- rep(c("hgu133plus2.db","hgu133a.db"), 42)
#
getSymbols <- function ( anno.pkg )
{
require(anno.pkg, character.only=TRUE)
anno.pkg <- get(anno.pkg)
syms <- AnnotationDbi::mapIds(anno.pkg, keys=keys(anno.pkg),
keytype="PROBEID", column="ENTREZID")
return(syms)
}
> x <- bplapply( pkgs , getSymbols ) ### sometimes I have to run this 2
> or 3 times in a row to produce this error
Loading required package: hgu133plus2.db
Error: BiocParallel errors
element index: 29, 30, 31, 32, 33, 34, ...
first error: database disk image is malformed
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: SUSE Linux Enterprise Desktop 12 SP3
Matrix products: default
BLAS: /mnt/raidbio/biosoft/software/R/R-3.4.1/lib/libRblas.so
LAPACK: /mnt/raidbio/biosoft/software/R/R-3.4.1/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_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 stats4stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BiocParallel_1.12.0 graph_1.56.0 pathview_1.18.0
[4] org.Hs.eg.db_3.5.0 AnnotationDbi_1.40.0 IRanges_2.12.0
[7] S4Vectors_0.16.0 Biobase_2.38.0 BiocGenerics_0.24.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.14 KEGGgraph_1.38.1 XVector_0.18.0zlibbioc_1.24.0
[5] bit_1.1-12R6_2.2.2 rlang_0.1.6 blob_1.1.0
[9] httr_1.3.1tools_3.4.1 grid_3.4.1png_0.1-7
[13] DBI_0.7 bit64_0.9-7 digest_0.6.13 tibble_1.4.1
[17] Rgraphviz_2.22.0 KEGGREST_1.18.0 memoise_1.1.0 RSQLite_2.0
[21] compiler_3.4.1pillar_1.1.0 Biostrings_2.46.0 XML_3.98-1.9
[25] pkgconfig_2.0.1
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Martin Morgan
<martin.mor...@roswellpark.org>
Sent: Friday, January 19, 2018 1:54 PM
To: Gabe Becker; Vincent Carey
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocParallel and AnnotationDbi: database disk image
is malformed
On 01/19/2018 12:37 PM, Gabe Becker wrote:
> IT seems like you could also force a copy of the reference object via
> $copy() and then force a refresh of the conn slot by assigning a
> new db connection into it.
>
> I'm having trouble confirming that this would work, however, because I
> actually can't reproduce the error. The naive way works for me on my mac
> laptop (which is running an old R and Bioconductor) and on the linux
> cluster I have access to (running Bioc 3.6):
>
>
> (cluster)
>
>> getSymbol <- function ( x ) {
>
> + return( AnnotationDbi::mget( x , hgu95av2SYMBOL ) )
>
> + }
pass the data base connection to the function
getSymbol <- function ( x, db )
## olde schoole
AnnotationDbi::mget(x, db)
## AnnotationDbi::mapIds(db, x, "SYMBOL", "PROBEID")
and arrange for the general case, i.e., distinct processes with data
serialized between them
> cl = parallel::makePSOCKcluster(2)
> parLapply(cl, x, getSymbol, hgu95av2SYMBOL)
Error in checkForRemoteErrors(val) :
2 nodes produced errors; first error: external pointer is not valid
(getSymbol would fail as originally written in the serial case, since
the workers would not have access to hgu95av2SYMBOL
The workaround is to open the connection on the node, e.g.,
getSymbol <- function ( x, dbname ) {
nmspc <- loadNamespace(dbname)
db <- get(dbname, nmspc)
AnnotationDbi::mapIds(db, x, "SYMBOL", "PROBEID")
}
lapply(x, getSymbol, "hgu95av2.db")
bplapply(x, getSymbol, "hgu95av2.db")
bplapply(x, getSymbol, "hgu95av2.db", BPPARAM = SnowParam())
Martin
>>
>
>> x <- list( "36090_at" , "38785_at&qu
[Bioc-devel] BiocParallel and AnnotationDbi: database disk image is malformed
Hi, Within a package I am developing, I would like to enable parallel probe to gene mapping for a compendium of microarray datasets. This accordingly makes use of annotation packages such as hgu133a.db, which in turn connect to the SQLite database via AnnotationDbi. When running in multi-core mode (i.e. using a MulticoreParam with BiocParallel) using more than 2 cores, this causes the error: database disk image is malformed In a very similar problem: https://support.bioconductor.org/p/38541/ Adi Tarca and Dan Tenenbaum identified and resolved this problem by ensuring that each process has its own unique database connection, i.e. AnnotationDbi is not loaded before sending the job to the workers. This solution was easily realized as this analysis was carried out within a script and not a package. However, within my package, AnnotationDbi is loaded as a dependency of my package's imports. How to resolve this here? I am not sure whether I perfectly understand the underlying mechanisms, but is there a way to make my workers load their own version of AnnotationDbi instead of using the one of the parent process? Or am I supposed to unload all packages depending on AnnotationDbi, and AnnotationDbi itself, before sending the job to the workers (and reload all of them after the job has finished?) Thanks a lot, Ludwig -- Dr. Ludwig Geistlinger CUNY School of Public Health [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] BiocParallel: fine-grained progress bar
Hi,
I'm currently playing around with progress bars in BiocParallel - which is a
great package! ;-)
For demonstration, I'm using the example code from DESeq2::DESeq.
library(DESeq2)
library(BiocParallel)
f <- function(mu)
{
cnts <- matrix(rnbinom(n=1000, mu=mu, size=1/0.5), ncol=10)
cond <- factor(rep(1:2, each=5))
# object construction
suppressMessages({
dds <- DESeqDataSetFromMatrix(cnts, DataFrame(cond), ~ cond)
dds <- DESeq(dds)
})
res <- results(dds)
return(res)
}
and apply 'f' to a range of 'mu' values using 'bplapply'.
mu.grid <- 90:120
x <- bplapply(mu.grid, f)
Now, switching to serial execution and verbosing progress
bp <- registered()$SerialParam
bpprogressbar(bp) <- TRUE
register(bp)
x <- bplapply(mu.grid, f)
gives me somehow no progress bar at all.
Furthermore, switching to multi-core execution (2 cores) and verbosing progress
bp <- registered()$MulticoreParam
bpprogressbar(bp) <- TRUE
register(bp)
x <- bplapply(mu.grid, f)
|
|
|=== |
|==| 100%
gives me only a very coarse-grained progress bar (updates when 50% of the job
is done, and when the complete job = 100% is done).
What I actually want to have is a fine-grained progress bar that updates
whenever f finishes execution on an element of the vector I am applying over.
In "normal" serial R execution, the desired behavior can be illustrated via
pb <- txtProgressBar(90, 120, style=3, width=length(mu.grid))
r <- vector(mode="list", length=length(mu.grid))
for(i in mu.grid)
{
setTxtProgressBar(pb, i)
r[[i-89]] <- f(i)
}
close(pb)
Is there a way to obtain something similar using BiocParallel?
Thanks,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.1
Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.4/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 stats4stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BiocParallel_1.12.0DESeq2_1.18.1
[3] SummarizedExperiment_1.8.0 DelayedArray_0.4.1
[5] matrixStats_0.52.2 Biobase_2.38.0
[7] GenomicRanges_1.30.0 GenomeInfoDb_1.14.0
[9] IRanges_2.12.0 S4Vectors_0.16.0
[11] BiocGenerics_0.24.0
loaded via a namespace (and not attached):
[1] genefilter_1.60.0 locfit_1.5-9.1 splines_3.4.2
[4] lattice_0.20-35 colorspace_1.3-2htmltools_0.3.6
[7] base64enc_0.1-3 blob_1.1.0 survival_2.41-3
[10] XML_3.98-1.9rlang_0.1.4 DBI_0.7
[13] foreign_0.8-69 bit64_0.9-7 RColorBrewer_1.1-2
[16] GenomeInfoDbData_0.99.1 plyr_1.8.4 stringr_1.2.0
[19] zlibbioc_1.24.0 munsell_0.4.3 gtable_0.2.0
[22] htmlwidgets_0.9 memoise_1.1.0 latticeExtra_0.6-28
[25] knitr_1.17 geneplotter_1.56.0 AnnotationDbi_1.40.0
[28] htmlTable_1.9 Rcpp_0.12.14acepack_1.4.1
[31] xtable_1.8-2scales_0.5.0backports_1.1.1
[34] checkmate_1.8.5 Hmisc_4.0-3 annotate_1.56.1
[37] XVector_0.18.0 bit_1.1-12 gridExtra_2.3
[40] ggplot2_2.2.1 digest_0.6.12 stringi_1.1.6
[43] grid_3.4.2 tools_3.4.2 bitops_1.0-6
[46] magrittr_1.5RSQLite_2.0 lazyeval_0.2.1
[49] RCurl_1.95-4.8 tibble_1.3.4Formula_1.2-2
[52] cluster_2.0.6 Matrix_1.2-12 data.table_1.10.4-3
[55] rpart_4.1-11nnet_7.3-12 compiler_3.4.2
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] GSE62944, empty EH164 and EH165
Great! Thanks for resolving this so fast. Ludwig From: Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Friday, December 15, 2017 1:48 PM To: Ludwig Geistlinger; bioc-devel@r-project.org Subject: Re: GSE62944, empty EH164 and EH165 Thank you for bringing this to our attention. The resources were created with a previous version of SummarizedExperiment that were not compatible with the current version. New resources have been added and are visible in both release 3.6 and devel 3.7. Please note the new EH_id's: > library(ExperimentHub) > hub <- ExperimentHub() snapshotDate(): 2017-10-30 > gse <- AnnotationHub::query(hub, "GSE62944") > gse ExperimentHub with 3 records # snapshotDate(): 2017-10-30 # $dataprovider: GEO # $species: Homo sapiens # $rdataclass: SummarizedExperiment, ExpressionSet # additional mcols(): taxonomyid, genome, description, # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["EH1"]]' title EH1| RNA-Sequencing and clinical data for 7706 tumor samples from The... EH1043 | RNA-Sequencing and clinical data for 9246 tumor samples from The... EH1044 | RNA-Sequencing and clinical data for 741 normal samples from The... > x = gse[["EH1043"]] > x class: SummarizedExperiment dim: 23368 9264 metadata(0): assays(1): CancerRaw rownames(23368): 1/2-SBSRNA4 A1BG ... ZZZ3 tAKR rowData names(0): colnames(9264): TCGA-G9-A9S0-01A-11R-A41O-07 TCGA-E1-5318-01A-01R-1470-07 ... TCGA-A7-A0DC-01A-11R-A00Z-07 TCGA-A5-A0VQ-01A-11R-A104-07 colData names(549): bcr_patient_uuid bcr_patient_barcode ... lymph_nodes_aortic_pos_total CancerType > dim(x) [1] 23368 9264 > x = gse[["EH1044"]] > x class: SummarizedExperiment dim: 23368 741 metadata(0): assays(1): NormalRaw rownames(23368): 1/2-SBSRNA4 A1BG ... ZZZ3 tAKR rowData names(0): colnames(741): TCGA-K4-A3WV-11A-21R-A22U-07 TCGA-49-6742-11A-01R-1858-07 ... TCGA-BH-A0H5-11A-62R-A115-07 TCGA-22-5489-11A-01R-1635-07 colData names(2): sample type > dim(x) [1] 23368 741 Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Ludwig Geistlinger <ludwig.geistlin...@sph.cuny.edu> Sent: Thursday, December 14, 2017 3:01:56 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] GSE62944, empty EH164 and EH165 Hi, I'm trying to obtain the most recent version of GSE62944 from ExperimentHub via > library(ExperimentHub) > hub <- ExperimentHub() > gse <- AnnotationHub::query(hub, "GSE62944") > gse ExperimentHub with 3 records # snapshotDate(): 2017-10-30 # $dataprovider: GEO # $species: Homo sapiens # $rdataclass: SummarizedExperiment, ExpressionSet # additional mcols(): taxonomyid, genome, description, # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["EH1"]]' title EH1 | RNA-Sequencing and clinical data for 7706 tumor samples from The... EH164 | RNA-Sequencing and clinical data for 9246 tumor samples from The... EH165 | RNA-Sequencing and clinical data for 741 normal samples from The... Retrieving the original (outdated) dataset works fine: > x <- gse[["EH1"]] > dim(x) Features Samples 23368 7706 However, obtaining the most recent version of the data via > x <- gse[["EH164"]] gives me: > dim(x) NULL > class(x) [1] "SummarizedExperiment0" attr(,"package") [1] "SummarizedExperiment" > str(x) Formal class 'SummarizedExperiment0' [package "SummarizedExperiment"] with 0 slots Named list() It would be great if this could be updated. Thanks a lot, Ludwig -- Dr. Ludwig Geistlinger CUNY School of Public Health > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.1 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] stats4parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] SummarizedExperiment_1.8.0 DelayedArray_0.4.1 [3] matrixStats_0.52.2 GenomicRanges_1.30.0 [5] GenomeInfoDb_1.14.0IRanges_2.12.0 [7] S4Vectors_0.16.0 GSE62944_1.6.0 [9] GEOquery_2.46.8Biobase_2.38.0 [11] Expe
Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7
Hi Lori, I would be willing to take over maintenance of ToPASeq in case maintainers remain unresponsive. Best, Ludwig -- Dr. Ludwig Geistlinger CUNY School of Public Health From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Friday, December 15, 2017 9:29 AM To: Martin Morgan Subject: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7 The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The current list of deprecated packages is as follows: Maintainer requested deprecation: Software Package: ontoCAT Experiment Data Package: RnaSeqTutorial cheung2010 Unresponsive/not-maintained packages: Software: GMRP MBttest OperaMate ToPASeq Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] GSE62944, empty EH164 and EH165
Hi, I'm trying to obtain the most recent version of GSE62944 from ExperimentHub via > library(ExperimentHub) > hub <- ExperimentHub() > gse <- AnnotationHub::query(hub, "GSE62944") > gse ExperimentHub with 3 records # snapshotDate(): 2017-10-30 # $dataprovider: GEO # $species: Homo sapiens # $rdataclass: SummarizedExperiment, ExpressionSet # additional mcols(): taxonomyid, genome, description, # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["EH1"]]' title EH1 | RNA-Sequencing and clinical data for 7706 tumor samples from The... EH164 | RNA-Sequencing and clinical data for 9246 tumor samples from The... EH165 | RNA-Sequencing and clinical data for 741 normal samples from The... Retrieving the original (outdated) dataset works fine: > x <- gse[["EH1"]] > dim(x) Features Samples 23368 7706 However, obtaining the most recent version of the data via > x <- gse[["EH164"]] gives me: > dim(x) NULL > class(x) [1] "SummarizedExperiment0" attr(,"package") [1] "SummarizedExperiment" > str(x) Formal class 'SummarizedExperiment0' [package "SummarizedExperiment"] with 0 slots Named list() It would be great if this could be updated. Thanks a lot, Ludwig -- Dr. Ludwig Geistlinger CUNY School of Public Health > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.1 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] stats4parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] SummarizedExperiment_1.8.0 DelayedArray_0.4.1 [3] matrixStats_0.52.2 GenomicRanges_1.30.0 [5] GenomeInfoDb_1.14.0IRanges_2.12.0 [7] S4Vectors_0.16.0 GSE62944_1.6.0 [9] GEOquery_2.46.8Biobase_2.38.0 [11] ExperimentHub_1.4.0AnnotationHub_2.10.1 [13] BiocGenerics_0.24.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.14 XVector_0.18.0 [3] BiocInstaller_1.28.0 compiler_3.4.2 [5] bindr_0.1 zlibbioc_1.24.0 [7] bitops_1.0-6 tools_3.4.2 [9] digest_0.6.12 bit_1.1-12 [11] lattice_0.20-35 RSQLite_2.0 [13] memoise_1.1.0 tibble_1.3.4 [15] pkgconfig_2.0.1 rlang_0.1.4 [17] Matrix_1.2-12 shiny_1.0.5 [19] DBI_0.7 curl_3.0 [21] yaml_2.1.14 bindrcpp_0.2 [23] GenomeInfoDbData_0.99.1 xml2_1.1.1 [25] httr_1.3.1dplyr_0.7.4 [27] hms_0.3 grid_3.4.2 [29] bit64_0.9-7 glue_1.2.0 [31] R6_2.2.2 AnnotationDbi_1.40.0 [33] limma_3.34.3 purrr_0.2.4 [35] tidyr_0.7.2 readr_1.1.1 [37] blob_1.1.0magrittr_1.5 [39] htmltools_0.3.6 assertthat_0.2.0 [41] mime_0.5 interactiveDisplayBase_1.16.0 [43] xtable_1.8-2 httpuv_1.3.5 [45] RCurl_1.95-4.8 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Vignette rebuild for MutationalPatterns
Yes, I am experiencing the same problem for the EnrichmentBrowser package.
The release package landing page holds all the new stuff, but the vignette
is still the one of the old release.
Best,
Ludwig
--
Dr. Ludwig Geistlinger
eMail: ludwig.geistlin...@bio.ifi.lmu.de
> Dear,
>
> It seems that the 3.6 release contains an old version of the vignette of
> MutationalPatterns.
> In commit d1c4e14 I pushed updates of the corresponding bioRxiv paper, but
> the changes in the vignette haven't made it in.
>
> Should I now bump the release number without making any further changes?
>
> Kind regards,
> Roel Janssen
> --
>
> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender
> direct
> te informeren door het bericht te retourneren. Het Universitair Medisch
> Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de
> W.H.W.
> (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd
> bij
> de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
>
> Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
>
> --
>
> This message may contain confidential information and ...{{dropped:10}}
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Organism.dplyr::supportedFilters warning
Hi, R CMD check of the devel version of my package lately started to trigger a warning: http://bioconductor.org/checkResults/devel/bioc-LATEST/EnrichmentBrowser/malbec1-checksrc.html * checking whether package EnrichmentBrowser can be installed ... WARNING Found the following significant warnings: Warning: no function found corresponding to methods exports from Organism.dplyr for: supportedFilters See /home/biocbuild/bbs-3.6-bioc/meat/EnrichmentBrowser.Rcheck/00install.out for details. I am not quite sure how to deal with that. Any advice? Thanks, Ludwig -- Dr. Ludwig Geistlinger eMail: ludwig.geistlin...@bio.ifi.lmu.de > Hi, > > This Friday, October 6, is the last day to submit new packages for > inclusion in BioC 3.6. Packages submitted by Friday still need to complete > the review process before the release but we'll do our best to get them > in. Packages submitted after the deadline will be included in the new > devel, BioC 3.7. > > http://www.bioconductor.org/developers/release-schedule/ > > Valerie > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocStyle2: issue with wide figure command
Yes, I was indeed sitting on an old Tex version.
Upgrading to Tex Live 2017 fixed that.
Thanks,
Ludwig
> Hi Ludwig,
>
> thank you! This sounds like an issue with your LaTeX distribution, in
> particular the package 'marginfix'. Please make sure that all the packages
> listed in the BiocStyle vignette under Appendix B "Attached LATEX
> packages"
> are installed, and possibly the up-to-date.
>
> Best,
> Andrzej
>
> On Tue, Sep 12, 2017 at 11:03 PM, Ludwig Geistlinger <
> ludwig.geistlin...@bio.ifi.lmu.de> wrote:
>
>> Dear Andrzej,
>>
>> BiocStyle2 is a great piece of work and the new vignettes look really
>> nice!
>> Thank you!
>>
>> However, I am having a problem with the widefigure (figure*)
>> environment,
>> which apparently only holds for my local installation, as the same
>> vignette builds fine here:
>>
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/EnrichmentBrowser/
>>
>>
>>
>> However, on my machine (- do I need to update any external
>> dependencies?):
>>
>> Rdev CMD build EnrichmentBrowser
>> * checking for file âEnrichmentBrowser/DESCRIPTIONâ ... OK
>> * preparing âEnrichmentBrowserâ:
>> * checking DESCRIPTION meta-information ... OK
>> * installing the package to build vignettes
>> * creating vignettes ... ERROR
>> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,
>> :
>> Execution of 'texi2dvi' for 'EnrichmentBrowser.tex' failed.
>> LaTeX errors:
>> ! Undefined control sequence.
>> \\figure* [#1]->\blockmargin
>> \@biocfloat@wide {figure}{#1}
>> l.761 \centering
>>
>> ! Undefined control sequence.
>> \endfigure* ->\endfigure \unblockmargin
>> [1em]
>> l.768 \end{figure*}
>>
>> ! Undefined control sequence.
>> \\figure* [#1]->\blockmargin
>> \@biocfloat@wide {figure}{#1}
>> l.1002 \begin{figure*}[!h]
>>
>> ! Undefined control sequence.
>> \endfigure* ->\endfigure \unblockmargin
>> [1em]
>> l.1008 \end{figure*}
>>
>> Call: -> texi2pdf -> texi2dvi
>> Exectuion halted.
>>
>>
>>
>> Here is some information on the build environment, please let me know if
>> I
>> should provide additional information:
>>
>> > sessionInfo()
>> R version 3.4.1 (2017-06-30)
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> Running under: macOS Sierra 10.12.6
>>
>> Matrix products: default
>> BLAS:
>> /Library/Frameworks/R.framework/Versions/3.4/
>> Resources/lib/libRblas.0.dylib
>> LAPACK:
>> /Library/Frameworks/R.framework/Versions/3.4/
>> Resources/lib/libRlapack.dylib
>>
>> locale:
>> [1] C/UTF-8/C/C/C/C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] BiocStyle_2.5.37
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.4.1 backports_1.1.0 magrittr_1.5rprojroot_1.2
>> [5] htmltools_0.3.6 tools_3.4.1 yaml_2.1.14 Rcpp_0.12.12
>> [9] stringi_1.1.5 rmarkdown_1.6 knitr_1.16 stringr_1.2.0
>> [13] digest_0.6.12 evaluate_0.10.1
>>
>>
>> Thanks,
>> Ludwig
>>
>>
>> > Dear Bioconductor Developers,
>> >
>> > overall the transition to the updated formatting went smooth
>> considering
>> > the number of packages using BiocStyle, and the different possible
>> input
>> > (.Rnw/.Rmd) and output formats (PDF/HTML).
>> >
>> > However, we have identified some common issues with specifying author
>> > information in Sweave/knitr (.Rnw) vignettes which lead to package
>> build
>> > errors or timeouts. The updated style loads the 'authblk' LaTeX
>> package
>> to
>> > standardize the way of specifying author affiliations, but
>> unfortunately
>> > this approach is also more fragile than the default LaTeX macros. In
>> > particular, the usual author separator ' \and' is not compatible with
>> the
>> > authblk's footnote mode used by BiocStyle.
>> >
>> > The maintainers of the following packages are encouraged to review
>> their
>> > vignettes and ensure that '\author{}' does not contain any custom
>> > formatting and meets the guidelines outlined in Section 2.1.2 "Authors
>> and
>> > affiliation
[Bioc-devel] BiocStyle2: issue with wide figure command
Dear Andrzej,
BiocStyle2 is a great piece of work and the new vignettes look really nice!
Thank you!
However, I am having a problem with the widefigure (figure*) environment,
which apparently only holds for my local installation, as the same
vignette builds fine here:
http://bioconductor.org/checkResults/devel/bioc-LATEST/EnrichmentBrowser/
However, on my machine (- do I need to update any external dependencies?):
Rdev CMD build EnrichmentBrowser
* checking for file EnrichmentBrowser/DESCRIPTION ... OK
* preparing EnrichmentBrowser:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Execution of 'texi2dvi' for 'EnrichmentBrowser.tex' failed.
LaTeX errors:
! Undefined control sequence.
\\figure* [#1]->\blockmargin
\@biocfloat@wide {figure}{#1}
l.761 \centering
! Undefined control sequence.
\endfigure* ->\endfigure \unblockmargin
[1em]
l.768 \end{figure*}
! Undefined control sequence.
\\figure* [#1]->\blockmargin
\@biocfloat@wide {figure}{#1}
l.1002 \begin{figure*}[!h]
! Undefined control sequence.
\endfigure* ->\endfigure \unblockmargin
[1em]
l.1008 \end{figure*}
Call: -> texi2pdf -> texi2dvi
Exectuion halted.
Here is some information on the build environment, please let me know if I
should provide additional information:
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] C/UTF-8/C/C/C/C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocStyle_2.5.37
loaded via a namespace (and not attached):
[1] compiler_3.4.1 backports_1.1.0 magrittr_1.5rprojroot_1.2
[5] htmltools_0.3.6 tools_3.4.1 yaml_2.1.14 Rcpp_0.12.12
[9] stringi_1.1.5 rmarkdown_1.6 knitr_1.16 stringr_1.2.0
[13] digest_0.6.12 evaluate_0.10.1
Thanks,
Ludwig
> Dear Bioconductor Developers,
>
> overall the transition to the updated formatting went smooth considering
> the number of packages using BiocStyle, and the different possible input
> (.Rnw/.Rmd) and output formats (PDF/HTML).
>
> However, we have identified some common issues with specifying author
> information in Sweave/knitr (.Rnw) vignettes which lead to package build
> errors or timeouts. The updated style loads the 'authblk' LaTeX package to
> standardize the way of specifying author affiliations, but unfortunately
> this approach is also more fragile than the default LaTeX macros. In
> particular, the usual author separator ' \and' is not compatible with the
> authblk's footnote mode used by BiocStyle.
>
> The maintainers of the following packages are encouraged to review their
> vignettes and ensure that '\author{}' does not contain any custom
> formatting and meets the guidelines outlined in Section 2.1.2 "Authors and
> affiliations" of the "Bioconductor LaTeX Style 2.0" vignette [1].
>
> DiffBind
> GMRP
> groHMM
> MBttest
> MutationalPatterns
> OncoScore
> OperaMate
> quantro
> rCGH
> RiboProfiling
> sampleClassifier
> TRONCO
>
>
> Additionally, the following packages fail to build because their vignettes
> contain some LaTeX customizations incompatible with the current version of
> BiocStyle.
>
> funtooNorm
> Linnorm
> NanoStringQCPro
>
>
> Thank you for your understanding and cooperation.
>
> Kind regards,
> Andrzej OleÅ
>
> [1]
> http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle2.pdf
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Dr. Ludwig Geistlinger
eMail: ludwig.geistlin...@bio.ifi.lmu.de
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] clarifying initialization for BiocCheck
Let's consider loading the `bods` object via `data` from the pathview
package.
I guess you can either use
> bods <- get(data("bods", package="pathview"))
or
> bods <- NULL
> data("bods", package="pathview")
to make this note go away.
> "Consider clarifying how 6 object(s) are initialized"
>
> Suppose an object is initialized via data() ... how can I make
>
> this note go away? I don't understand how to clarify the situation.
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Dr. Ludwig Geistlinger
eMail: ludwig.geistlin...@bio.ifi.lmu.de
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment
Concerning 1) Why have some developers chosen to extend eSet instead of ExpressionSet: As far as I understand it, ExpressionSet was thought to exclusively represent a microarray experiment (MIAME = Minimum Information About a Microarray Experiment). Thus, back in the days when more and more people started using RNA-seq and there was no SummarizedExperiment, developers extended eSet with e.g. assayData slots called `counts` instead of `exprs` to represent RNA-seq data. > On Mon, Sep 11, 2017 at 2:02 PM, Hervé Pagès <hpa...@fredhutch.org> > wrote: > >> Hi, >> >> I added coercion from ExpressionSet to SummarizedExperiment in >> SummarizedExperiment 1.7.6. >> > > Thank you Hervé! > > >> The current behavior of the SummarizedExperiment() constructor >> when called on a ExpressionSet object doesn't make much sense to >> me. I'd rather have it consistent with what the coercion does. >> Will fix it. >> > > Thank you, again. > > A couple more questions while I'm at it, that may expose the limitations > in > my understanding of inheritance and project history... 1) Why have some > developers chosen to extend eSet instead of ExpressionSet (definition > <https://github.com/Bioconductor/Biobase/blob/536f137165ca08b3be22819e51e055b3e7afe86d/R/DataClasses.R#L166>), > and 2) why are these coercion methods developed for ExpressionSet rather > than eSet? Wouldn't an eSet coercion method be preferable because it would > cover ExpressionSet as well as all the classes that extend eSet? > > [[alternative HTML version deleted]] > > ___________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Dr. Ludwig Geistlinger eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment
ht want something like this in
>>>>>>> GenomicRanges
>>>>>>> (that's where SummarizedExperiment is managed, right?) and I will
>>>>>>> add
>>>>>>> it
>>>>>>> if there are no objections
>>>>>>>
>>>>>>> the arguments are currently
>>>>>>>
>>>>>>>assayname = "exprs",# for naming SimpleList element
>>>>>>>fngetter =
>>>>>>> function(z) rownames(exprs(z)), # extract usable
>>>>>>> feature names
>>>>>>>annDbGetter =
>>>>>>> function(z) {
>>>>>>> clnanno = sub(".db", "", annotation(z))
>>>>>>> stopifnot(require(paste0(annotation(z), ".db"),
>>>>>>> character.only=TRUE) )
>>>>>>> get(paste0(annotation(z), ".db")) # obtain
>>>>>>> resource
>>>>>>> for
>>>>>>> mapping feature names to coordinates
>>>>>>> },
>>>>>>>probekeytype = "PROBEID", # chipDb field to use
>>>>>>>duphandler = function(z) {# action to take to process
>>>>>>> duplicated
>>>>>>> features
>>>>>>> if (any(isd <- duplicated(z[,"PROBEID"])))
>>>>>>> return(z[!isd,,drop=FALSE])
>>>>>>> z
>>>>>>> },
>>>>>>>signIsStrand = TRUE, # verify that signs of addresses
>>>>>>> define
>>>>>>> strand
>>>>>>>ucsdChrnames = TRUE# prefix 'chr' to chromosome token
>>>>>>>
>>>>>>> [[alternative HTML version deleted]]
>>>>>>>
>>>>>>> ___
>>>>>>> Bioc-devel@r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>
>>>>>>>
>>>>>>> [[alternative HTML version deleted]]
>>>>>>
>>>>>> ___
>>>>>> Bioc-devel@r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>> 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...@fhcrc.org
>>>> Phone: (206) 667-5791
>>>> Fax:(206) 667-1319
>>>>
>>>>
>>>> ___
>>>> Bioc-devel@r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>>
>>>
>>>
>>>
>>
>> This email message may contain legally privileged and/or confidential
>> information. If you are not the intended recipient(s), or the employee
>> or
>> agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
>> distribution, or use of this email message is prohibited. If you have
>> received this message in error, please notify the sender immediately by
>> e-mail and delete this email message from your computer. Thank you.
>>
>
>
>
> --
> Levi Waldron
> http://www.waldronlab.org
> Assistant Professor of Biostatistics CUNY School of Public Health
> US: +1 646-364-9616 Skype:
> levi.waldron
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Dr. Ludwig Geistlinger
eMail: ludwig.geistlin...@bio.ifi.lmu.de
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] failing to build on moscato2
Hi, according to http://bioconductor.org/checkResults/release/bioc-LATEST/EnrichmentBrowser/moscato2-buildsrc.html my package is failing to build due to ERROR: dependencies 'Biobase', 'S4Vectors', 'graph', 'limma' are not available for package 'EnrichmentBrowser' However, these dependencies seems to have built without problems. What is the problem here? Thanks, Ludwig -- Dr. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] package devel page not available
Thx Martin, I've missed that. BTW: Is there a best practice for incorporating packages that are not maintained anymore? Am I supposed to copy the part of the discontinued package I am building on and include that in my package? Or am I able to somehow import from an archived version of the package? Thx, Ludwig > On 07/18/2016 04:27 AM, Ludwig Geistlinger wrote: >> Hi, >> >> I am trying to access the devel page of my package >> >> https://www.bioconductor.org/packages/devel/bioc/html/EnrichmentBrowser.html >> >> but I am obtaining >> >> Page Not Found >> The page you were looking for was not found. >> >> What is the reason for that? > > it (has always?) failed to build in devel > > http://bioconductor.org/checkResults/3.4/bioc-LATEST/EnrichmentBrowser/ > > because neaGUI is one of the 17 packages marked as deprecated (the > package was not building and the author did not respond to email) in > release 3.3 for removal in 3.4. > > Martin > >> >> Thx, >> Ludwig >> >> > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > -- Dr. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] package devel page not available
Hi, I am trying to access the devel page of my package https://www.bioconductor.org/packages/devel/bioc/html/EnrichmentBrowser.html but I am obtaining Page Not Found The page you were looking for was not found. What is the reason for that? Thx, Ludwig -- Dr. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] ExperimentHub::GSE62944 outdated
FYI
That works for me, but maybe this is also of interest for others, so I
wonder if somebody of the Bioc annotation/experiment team (Sonali,
Valerie, Martin?) could update this accordingly for ExperimentHub?
Best,
Ludwig
--
Dr. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München
Tel.: 089-2180-4067
eMail: ludwig.geistlin...@bio.ifi.lmu.de
> Hi Ludwig,
>
> In november I sent the updated recipe to Martin, but I think it was not
> updated yet.
>
> Anyway, you can do it yourself with the code here below:
>
> library("GEOquery")
> library("Biobase")
>
> suppl <- GEOquery::getGEOSuppFiles("GSE62944")
>
> setwd("GSE62944")
>
> clinvar <-
>
> read.delim("GSE62944_06_01_15_TCGA_24_548_Clinical_Variables_9264_Samples.txt.gz")
> clinvar2 <- t(clinvar)
>
> # add variable names
> colnames(clinvar2) <- clinvar2[1,]
> # and remove the 2nd abbreviation, with the CDE_ID too
> clinvar3 <- clinvar2[-c(1:3),]
>
> # substitute dots with dashes in the ids, to be consistent with
> previous object
> clinvar4 <- clinvar3
> rownames(clinvar4) <- gsub("\\.","-",rownames(clinvar3))
> clinvar4 <- as.data.frame(clinvar4)
>
> CancerType <-
> read.delim("GSE62944_06_01_15_TCGA_24_CancerType_Samples.txt.gz",
> header=FALSE, colClasses=c("character", "factor"),
> col.names=c("sample", "type"))
> idx <- match(rownames(clinvar4), CancerType$sample)
> # these are already nicely sorted
> clinvar4$CancerType <- CancerType$type[idx]
>
>
> countFile <-
> "GSM1536837_06_01_15_TCGA_24.tumor_Rsubread_FeatureCounts.txt.gz"
> untar("GSE62944_RAW.tar", countFile)
>
> counts <- local({
>data <- scan(countFile, what=character(), sep="\t", quote="")
>m <- matrix(data, 9265)
>dimnames(m) <- list(m[,1], m[1,])
>m <- t(m[-1, -1])
>mode(m) <- "integer"
>m
> })
>
> # just to be sure
> gplots::venn(list(colnames(counts),rownames(cl4))) # they are all
> there, but not correctly sorted
> head(colnames(counts))
> head(rownames(clinvar4))
>
> # re-sorting according to the counts object
> cl5 <-
> clinvar4[rownames(clinvar4)[match(colnames(counts),rownames(clinvar4))],]
> head(rownames(cl5),20)
> head(colnames(counts),20)
>
> # as in your example
> eset_new <- Biobase::ExpressionSet(counts, AnnotatedDataFrame(cl5))
>
> # or as SummarizedExperiment
> library("GenomicRanges")
> se <- SummarizedExperiment(assays=list(counts))
> colData(se) <- S4Vectors::DataFrame(cl5)
>
> # data exploration to see how samples are related to each other
> library("DESeq2")
> ddsTCGA <- DESeqDataSet(se,design=~CancerType)
>
> ddsTCGA <- estimateSizeFactors(ddsTCGA)
> log2tcga <- log2(1+counts(ddsTCGA,normalized=TRUE))
> se_log2tcga <- SummarizedExperiment(assays=list(log2tcga))
> colData(se_log2tcga) <- colData(ddsTCGA) # the rlog transform takes
> very long time, so just a quick and dirty check
>
> pca_d4 <- function (x, intgroup = "condition", ntop = 500,
> returnData = FALSE,title=NULL,
> pcX = 1, pcY = 2,text_labels=TRUE,point_size=3)
> # customized principal components
> {
>library("DESeq2")
>library("genefilter")
>library("ggplot2")
>rv <- rowVars(assay(x))
>select <- order(rv, decreasing =
> TRUE)[seq_len(min(ntop,length(rv)))]
>pca <- prcomp(t(assay(x)[select, ]))
>percentVar <- pca$sdev^2/sum(pca$sdev^2)
>
>intgroup.df <- as.data.frame(colData(x)[, intgroup, drop = FALSE])
>group <- factor(apply(intgroup.df, 1, paste, collapse = " : "))
>d <- data.frame(PC1 = pca$x[, pcX], PC2 = pca$x[, pcY], group =
> group,
>intgroup.df, names = colnames(x))
>colnames(d)[1] <- paste0("PC",pcX)
>colnames(d)[2] <- paste0("PC",pcY)
>if (returnData) {
> attr(d, "percentVar") <- percentVar[1:2]
> return(d)
>}
># clever way of positioning the labels
>d$hjust = ifelse((sig
[Bioc-devel] ExperimentHub::GSE62944 outdated
Hi, I would like to do some analysis on the TCGA data as provided in ExperimentHub's GSE62944 ExpressionSet. The Description of the dataset reads: "TCGA re-processed RNA-Seq data from 9264 Tumor Samples and 741 normal samples across 24 cancer types" However, when loading the dataset via > eh <- ExperimentHub() > query(eh , "GSE62944") > tcga_data <- eh[["EH1"]] and counting the samples > dim(tcga_data) Features Samples 23368 7706 as well as the cancer types > length(table(pData(tcga_data)[,"CancerType"])) results in the observed discrepancies with the above description, indicating that this is an outdated version of the dataset. Is it possible to (1) update it accordingly (2) include a varLabel, i.e. pData column indicating whether this is a tumor or an adjacent normal sample for the respective cancer type. That would be great! Thx & Best, Ludwig -- Dr. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] graph: maximum acyclic subgraph / minimum feedback edge set
Hi, I would like to transform a directed graph with cycles, e.g. a gene regulatory network, into a DAG. In particular, I would like to do that by removing a minimal set of edges. This problem is known to be NP-hard https://en.wikipedia.org/wiki/Feedback_arc_set but, apparently, several approximation algorithms for the problem have been developed. However, when screening e.g. through the manuals of the graph, igraph, and ggm packages, I do not find functionality for that. I wonder, whether developers on the mailing list, dealing with graphs and networks, can point me to an R implementation of the desired functionality? Thx & Best, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] some new warnings in a package
> So yes, you should update the NAMESPACE file following the warning
> message you see in your build report.
Hi Martin, I did not encounter such a note on importing from base packages
ever before - but ok, I followed your suggestion and added the imports.
However all remaining NOTEs and WARNINGs that appeared in the latest build
persist, for example
* checking for code/documentation mismatches ... WARNING
just issues a warning with any further details.
Thx,
Ludwig
>
>
> On 05/02/2016 11:11 AM, Ludwig Geistlinger wrote:
>> I encounter the same issue with EnrichmentBrowser - and apparently,
>> several other packages too, e.g. ensembldb, erma, ExiMiR ...
>>
>> The warnings seem to be, at first glance, linked to messages e.g. for
>> masking:
>>
>> ---
>>
>> * checking S3 generic/method consistency ... WARNING
>>
>>
>> Attaching package: 'EnrichmentBrowser'
>>
>> The following object is masked from 'package:BiocGenerics':
>>
>> normalize
>>
>> See section 'Generic functions and methods' in the 'Writing R
>> Extensions' manual.
>>
>>
>>
>> However, even when renaming the function, so that masking is not
>> necessary
>> (and the message is thus not given anymore), the issue persists.
>>
>> There seems to be something weird with the current R-devel (2016-04-29
>> r70565), as R CMD check as prompts me to import from base packages:
>>
>> -
>> Undefined global functions or variables:
>>available.packages browseURL capture.output col2rgb data dev.off
>>formula head mad median memory.limit model.matrix p.adjust par pchisq
>>phyper png pnorm qnorm quantile read.delim rgb rnorm runif sd
>>segments symbols text unzip write.table
>> Consider adding
>>importFrom("grDevices", "col2rgb", "dev.off", "png", "rgb")
>>importFrom("graphics", "par", "segments", "symbols", "text")
>>importFrom("stats", "formula", "mad", "median", "model.matrix",
>> "p.adjust", "pchisq", "phyper", "pnorm", "qnorm",
>> "quantile", "rnorm", "runif", "sd")
>>importFrom("utils", "available.packages", "browseURL",
>> "capture.output", "data", "head", "memory.limit",
>> "read.delim", "unzip", "write.table")
>> to your NAMESPACE file.
>> ---
>
> the advice here -- to import from base packages -- is correct. This
> ensures that a user cannot define a function, e.g., col2rgb, that masks
> the one in grDevices. It is appropriate because these base packages are
> not by default imported into your package namespace, so symbols are
> resolved by looking on the search() path. The only exception to this is
> the actual 'base' package, which _is_ imported by default.
>
> The advice is conservative, in that it does not say that you should add
> Imports: grDevices etc to your NAMESPACE file. This is also correct, in
> that the grDevices package is always installed.
>
>
> Martin
>
>>
>> Somebody an idea? Or just waiting for the next R-devel snapshot?
>>
>> Thx,
>> Ludwig
>>
>>
>>>
>>>
>>>
>>> On Fri, 29-04-2016, at 23:49, Martin Morgan
>>> <martin.mor...@roswellpark.org> wrote:
>>>> On 04/29/2016 05:23 PM, Ramon Diaz-Uriarte wrote:
>>>>> Dear All,
>>>>>
>>>>> In case it matters, and since we are past the 22, I just noticed that
>>>>> a
>>>>> package I maintain (ADaCGH2) is giving warnings in Linux and Mac
>>>>> (e.g.,
>>>>> https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/zin2-checksrc.html)
>>>>> that, if I recall correctly, were not being given around the 22nd. I
>>>>> think
>>>>> these warnings have started appearing with the latest Rs in BioC
>>>>> (around
>>>>> r70549?). I haven't been able to understand the ultimate cause of the
>>>>> warnings (as they seem to refer to issues
Re: [Bioc-devel] some new warnings in a package
I encounter the same issue with EnrichmentBrowser - and apparently,
several other packages too, e.g. ensembldb, erma, ExiMiR ...
The warnings seem to be, at first glance, linked to messages e.g. for
masking:
---
* checking S3 generic/method consistency ... WARNING
Attaching package: 'EnrichmentBrowser'
The following object is masked from 'package:BiocGenerics':
normalize
See section Generic functions and methods in the Writing R
Extensions manual.
However, even when renaming the function, so that masking is not necessary
(and the message is thus not given anymore), the issue persists.
There seems to be something weird with the current R-devel (2016-04-29
r70565), as R CMD check as prompts me to import from base packages:
-
Undefined global functions or variables:
available.packages browseURL capture.output col2rgb data dev.off
formula head mad median memory.limit model.matrix p.adjust par pchisq
phyper png pnorm qnorm quantile read.delim rgb rnorm runif sd
segments symbols text unzip write.table
Consider adding
importFrom("grDevices", "col2rgb", "dev.off", "png", "rgb")
importFrom("graphics", "par", "segments", "symbols", "text")
importFrom("stats", "formula", "mad", "median", "model.matrix",
"p.adjust", "pchisq", "phyper", "pnorm", "qnorm",
"quantile", "rnorm", "runif", "sd")
importFrom("utils", "available.packages", "browseURL",
"capture.output", "data", "head", "memory.limit",
"read.delim", "unzip", "write.table")
to your NAMESPACE file.
---
Somebody an idea? Or just waiting for the next R-devel snapshot?
Thx,
Ludwig
>
>
>
> On Fri, 29-04-2016, at 23:49, Martin Morgan
> <martin.mor...@roswellpark.org> wrote:
>> On 04/29/2016 05:23 PM, Ramon Diaz-Uriarte wrote:
>>> Dear All,
>>>
>>> In case it matters, and since we are past the 22, I just noticed that a
>>> package I maintain (ADaCGH2) is giving warnings in Linux and Mac (e.g.,
>>> https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/zin2-checksrc.html)
>>> that, if I recall correctly, were not being given around the 22nd. I
>>> think
>>> these warnings have started appearing with the latest Rs in BioC
>>> (around
>>> r70549?). I haven't been able to understand the ultimate cause of the
>>> warnings (as they seem to refer to issues that are not in the code of
>>> my
>>> package), but they disappear when I move a package from Imports to
>>> Depends.
>>
>> They seem to come from GLAD's use of packageStartupMessage() in .onLoad
>> (e.g., when the package is imported) rather than the recommended
>> .onAttach (when the package is attached to the search() path, e.g., via
>> library() or Depends: in the DESCRIPTION file).
>>
>> I updated GLAD to use packageStartuupMessage() in .onAttach; I think the
>> warnings will go away.
>
> Martin, thanks for the reply and details. And sorry for my
> not-particularly-explicit message; yes, GLAD is the package that I moved
> to
> Depends. And I did not say (though I had intended too ---time to go to
> bed)
> that I had committed my changes to svn.
>
> Anyway, should I revert my changes to keep GLAD in Imports?
>
> Best,
>
> R.
>
>
>>
>> Martin
>>
>>>
>>>
>>> Best,
>>>
>>> R.
>>>
>>>
>>>
>>>
>>
>>
>> This email message may contain legally privileged and/or confidential
>> information. If you are not the intended recipient(s), or the employee
>> or agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
>> distribution, or use of this email message is prohibited. If you have
>> received this message in error, please notify the sender immediately by
>> e-mail and delete this email message from your computer. Thank you.
>
>
> --
> Ramon Diaz-Uriarte
> Department of Biochemistry, Lab B-25
> Facultad de Medicina
> Universidad Autónoma de Madrid
> Arzobispo Morcillo, 4
> 28029 Madrid
> Spain
>
> Phone: +34-91-497-2412
>
> Email: rdia...@gmail.com
>ramon.d...@iib.uam.es
>
> http://ligarto.org/rdiaz
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Dipl.-Bioinf. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München
Tel.: 089-2180-4067
eMail: ludwig.geistlin...@bio.ifi.lmu.de
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] build reports are not updated
Dear Dan, For some reason, the build reports are still showing the snapshot of Saturday: http://bioconductor.org/checkResults/release/bioc-LATEST/EnrichmentBrowser/ As there is an error, I would like to know whether this is something persistent or only something temporary. Thanks, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Feedback on OrganismDb development
Dear Valerie, Thank you for the update. 1) Class name: I'd definitely prefer the exisiting naming over the three other suggestions you gave. 2) Pre-made packages: Yes, I think it would be great to have such packages available for well-established Bioc model organisms, i.e. as returned by AnnotationForge::available.db0pkgs(), or at the very least for ecoli (Escherichia.coli) yeast (Saccharomyces.cerevisiae) arabidopsis (Arabidopsis.thaliana) fly (Drosophila.melanogaster) zebrafish (Danio.rerio) worm (Caenorhabditis.elegans) (in addition to the exisiting 3 for human, mouse and rat) Thx & Best, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de > BioC developers, > > After the release we plan to continue development the OrganismDb class and packages. This email outlines some ideas for future direction. We're interested in feedback on these points as well as other thoughts people might have. > > ## Background > > The OrganismDb class is defined in the OrganismDbi package and consists of a TxDb object and the combined mappings from GO.db and an OrgDb. It supports the select() interface as well as several range-based > extractors such as exons(), transcripts(), etc. The idea was that given a particular organism, a user would only need a single package to access both system biology and transcripts-centric annotations. > > We currently have 3 OrganismDb packages > (http://www.bioconductor.org/packages/release/BiocViews.html#___OrganismDb). These are light weight and don't contain any data themselves but instead point to the GO.db, OrgDb and TxDb packages. > > ## Current issues > > - Support for sequence representation > > We've discussed incorporating an optional sequence component, maybe BSgenome or 2bit or ... ? > > > - Class name > > OrganismDb is similar to OrgDb which could cause some confusion. We are considering renaming ... here are a few ideas. Let us know what you think or add your suggestion. > > OrganismDb (fine as is, leave it) > FullOrgDb > CrossDb > MultipleDb > > > - Package name > > The current names are not very descriptive: Homo.sapiens, Mus.musculus and Rattus.norvegicus. We'd like to follow the naming convention used in our BSgenome and TxDb packages which means including the source, build and track from the TxDb as well as preceding with the class type. > > For example, the current 'Homo.sapiens' package would be renamed 'OrganismDb.Hsapiens.UCSC.hg19.knownGene'. > > > - Pre-made packages > > Is it useful to supply pre-made packages or just increase awareness of the helpers so users can make their own? Current helpers: > >> ?makeOrganism > ?makeOrganismDbFromBiomart ?makeOrganismDbFromTxDb > ?makeOrganismDbFromUCSC ?makeOrganismPackage > > NOTE: makeOrgansimPackage() will be renamed to makeOrganismDbPackage(). > > > Thanks. > Valerie > > > This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] ggbio error
Hi, I am wondering whether this is only something temporary, but given that the new Bioc release is upcoming and packages should pass R CMD build/check by now, I am reporting that a ggbio R CMD check error http://bioconductor.org/checkResults/devel/bioc-LATEST/ggbio/zin2-checksrc.html causes ReportingTools to fail: > ERROR: dependency ggbio is not available for package ReportingTools and, eventually, EnrichmentBrowser to fail: > ERROR: dependency ReportingTools is not available for package EnrichmentBrowser Which steps need to be undertaken here? Thx, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] package citation and version is not updated
Dear Dan, For some reason the citation on my package's landing page http://bioconductor.org/packages/EnrichmentBrowser.html is not displayed in agreement with my inst/CITATION file. Furthermore, the version number is also not up to date here, although displayed correctly at the bottom of the page (--> Package Archives). How to resolve this? Thx, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Announcing the EnrichmentBrowser 2.0
Dear Bioconductors, I am delighted to announce a major re-release of the EnrichmentBrowser package in line with its recent publication: Geistlinger L, Csaba G, Zimmer R. Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. BMC Bioinformatics, 17:45, Jan 2016. http://doi.org/10.1186/s12859-016-0884-1 The EnrichmentBrowser is a meta-package implementing an analysis pipeline for high-throughput gene expression data as measured with microarrays and RNA-seq. Functionality includes data preparation, preprocessing, differential expression analysis, set- and network-based enrichment analysis, combination as well as visualization and exploration of results. In a workflow-like manner, the package brings together a selection of finest Bioc packages which have shown to work distinghuishably well in practice for the respective purposes. Additional features of the package are the adaption of enrichment methods using sample permutation for RNA-seq read count data, an improved implementation of the network-based enrichment method GGEA (Geistlinger et al., Bioinformatics, ISMB/ECCB 2011), and novel ways of combining and exploring results across methods. Comments and suggestions to further improve the EnrichmentBrowser are highly appreciated. In addition, I would be glad if a short announcement of the paper could also be posted on the Bioc Twitter channel in order to make users aware. Thx & Best, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment
Dear Martin, I finally found the time to make the code available via GitHub: https://github.com/lgeistlinger/MapIds and added you as a collaborator. This is currently just a quick put-together for you to get an impression. NA and duplicated mappings currently need to be removed to ensure uniqueness of featureNames and rownames, respectively (via na.rm=TRUE and dupl.rm=TRUE). But there are, of course, other/better ways to summarize over NA's/Duplicates, e.g. by appropriately passing that on to the 'multiVals' Argument of AnnotationDbi::mapIds(). Just let me know in case you find that of any use or you find things that could be improved/extended. Best, Ludwig --- Dear Martin, Ok, I am tyding that up and provide that via GitHub for you. BTW, these ranges to Ids and vice versa sounds very cool! > The original intention of the annotation() slot in ExpressionSet was to > include the microarray chip identifier, so that one references this when > translating from probeset to gene identifiers. One question to that, as I often find my functions to ask for the organism uder study (which I believe is actually most typically known when investigating an expression dataset). While there are convenient ways to ask microarray annotation packages for the organism under study (and thus infer it from annotation(eset)), I wonder whether there is a similar slot for SummarizedExperiment, eg an 'organism' slot? Or are there specific reasons arguing against that? Best, Ludwig > Hi Ludwig -- > > It would be really great to see what you've put together; can you make > your code available somewhere, maybe via github? > > I think the facilities already in Bioconductor include: > > - select() and the OrganismDb (e.g., Homo.sapiens) packages > > - (Recently introduced, in bioc-devel) GenomicFeatures::mapIds() > > - GSEABase mapIdentifiers() > > - The AnnotationFuncs package (some of this functionality might be > redundant with select() / mapIds(); maybe your idea is a more refined > version of this? > > - biomaRt, including the relatively under-known use of select() with mart > objects. > > I think a particularly valuable development (initial implementation in > GenomicFeatures::mapIds()) is transparent mapping to / from genomic > ranges. > > The original intention of the annotation() slot in ExpressionSet was to > include the microarray chip identifier, so that one references this when > translating from probeset to gene identifiers. > > Martin > ____________ > From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig > Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] > Sent: Thursday, December 17, 2015 5:05 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] mapIds methods for ExpressionSet and > SummarizedExperiment > > Dear Bioc Team, > > I have implemented mapIds methods mapping featureNames (ExpressionSet) and > rownames (SummarizedExperiment) between major gene ID types such as > ENSEMBL and ENTREZ by passing that on AnnotationDbi::mapIds. > > Given an ExpressionSet/SummarizedExperiment and an organism under > investigation such as 'Homo sapiens', the methods are checking whether the > corresponding org.db package is available, otherwise the package is > automatically installed and loaded. > Subsequently, the featureNames/rownames are mapped from the specified > from.id.type to the desired to.id.type, corresponding to keytypes of the > org.db package. > Options to deal with NA and duplicate mappings are also provided in order > to ensure that featureNames/rownames are unique after the mapping. > > Advantage is that end users do not require knowledge of the Bioc > annotation infrastructure, but rather just need to provide the organism > under investigation in a convenient format also for non-Biocs. > > I have not found something similar in existing packages and I am wondering > whether this could be something of general interest. > > Best, > Ludwig > > -- > Dipl.-Bioinf. Ludwig Geistlinger > > Lehr- und Forschungseinheit für Bioinformatik > Institut für Informatik > Ludwig-Maximilians-Universität München > Amalienstrasse 17, 2. Stock, Büro A201 > 80333 München > > Tel.: 089-2180-4067 > eMail: ludwig.geistlin...@bio.ifi.lmu.de > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is
Re: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment
Dear Martin, Ok, I am tyding that up and provide that via GitHub for you. BTW, these ranges to Ids and vice versa sounds very cool! > The original intention of the annotation() slot in ExpressionSet was to > include the microarray chip identifier, so that one references this when > translating from probeset to gene identifiers. One question to that, as I often find my functions to ask for the organism uder study (which I believe is actually most typically known when investigating an expression dataset). While there are convenient ways to ask microarray annotation packages for the organism under study (and thus infer it from annotation(eset)), I wonder whether there is a similar slot for SummarizedExperiment, eg an 'organism' slot? Or are there specific reasons arguing against that? Best, Ludwig > Hi Ludwig -- > > It would be really great to see what you've put together; can you make > your code available somewhere, maybe via github? > > I think the facilities already in Bioconductor include: > > - select() and the OrganismDb (e.g., Homo.sapiens) packages > > - (Recently introduced, in bioc-devel) GenomicFeatures::mapIds() > > - GSEABase mapIdentifiers() > > - The AnnotationFuncs package (some of this functionality might be > redundant with select() / mapIds(); maybe your idea is a more refined > version of this? > > - biomaRt, including the relatively under-known use of select() with mart > objects. > > I think a particularly valuable development (initial implementation in > GenomicFeatures::mapIds()) is transparent mapping to / from genomic > ranges. > > The original intention of the annotation() slot in ExpressionSet was to > include the microarray chip identifier, so that one references this when > translating from probeset to gene identifiers. > > Martin > ____________ > From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig > Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] > Sent: Thursday, December 17, 2015 5:05 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] mapIds methods for ExpressionSet and > SummarizedExperiment > > Dear Bioc Team, > > I have implemented mapIds methods mapping featureNames (ExpressionSet) and > rownames (SummarizedExperiment) between major gene ID types such as > ENSEMBL and ENTREZ by passing that on AnnotationDbi::mapIds. > > Given an ExpressionSet/SummarizedExperiment and an organism under > investigation such as 'Homo sapiens', the methods are checking whether the > corresponding org.db package is available, otherwise the package is > automatically installed and loaded. > Subsequently, the featureNames/rownames are mapped from the specified > from.id.type to the desired to.id.type, corresponding to keytypes of the > org.db package. > Options to deal with NA and duplicate mappings are also provided in order > to ensure that featureNames/rownames are unique after the mapping. > > Advantage is that end users do not require knowledge of the Bioc > annotation infrastructure, but rather just need to provide the organism > under investigation in a convenient format also for non-Biocs. > > I have not found something similar in existing packages and I am wondering > whether this could be something of general interest. > > Best, > Ludwig > > -- > Dipl.-Bioinf. Ludwig Geistlinger > > Lehr- und Forschungseinheit für Bioinformatik > Institut für Informatik > Ludwig-Maximilians-Universität München > Amalienstrasse 17, 2. Stock, Büro A201 > 80333 München > > Tel.: 089-2180-4067 > eMail: ludwig.geistlin...@bio.ifi.lmu.de > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment
Dear Bioc Team, I have implemented mapIds methods mapping featureNames (ExpressionSet) and rownames (SummarizedExperiment) between major gene ID types such as ENSEMBL and ENTREZ by passing that on AnnotationDbi::mapIds. Given an ExpressionSet/SummarizedExperiment and an organism under investigation such as 'Homo sapiens', the methods are checking whether the corresponding org.db package is available, otherwise the package is automatically installed and loaded. Subsequently, the featureNames/rownames are mapped from the specified from.id.type to the desired to.id.type, corresponding to keytypes of the org.db package. Options to deal with NA and duplicate mappings are also provided in order to ensure that featureNames/rownames are unique after the mapping. Advantage is that end users do not require knowledge of the Bioc annotation infrastructure, but rather just need to provide the organism under investigation in a convenient format also for non-Biocs. I have not found something similar in existing packages and I am wondering whether this could be something of general interest. Best, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
Hi,
I am experiencing troubles installing "Hmisc", especially its dependency
"acepack", via
> biocLite("acepack")
in R-devel installed from the "R-devel-mavericks-signed.pkg" downloaded
from https://r.research.att.com/.
The error reads:
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development (unstable)
(2015-11-16 r69640).
Installing package(s) acepack
Paket, das nur als Quelltext vorliegt und eventuell Übersetzung von
C/C++/Fortran benötigt.: acepack
Do you want to attempt to install these from sources?
y/n: y
installing the source package acepack
versuche URL 'https://cran.rstudio.com/src/contrib/acepack_1.3-3.3.tar.gz'
Content type 'application/x-gzip' length 33590 bytes (32 KB)
==
downloaded 32 KB
* installing *source* package acepack ...
** Paket acepack erfolgreich entpackt und MD5 Summen überprüft
** libs
gfortran-4.8 -fPIC -g -O2 -c ace.f -o ace.o
make: gfortran-4.8: No such file or directory
make: *** [ace.o] Error 1
ERROR: compilation failed for package acepack
* removing
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/acepack
which indicates that "gfortran-4.8" is missing.
I have however installed the recommended "gfortran-5.2" for El Capitan
from here:
https://gcc.gnu.org/wiki/GFortranBinaries#MacOS
Yesterday, I tried quite some time to install 4.8-versions of gfortran
available from the website above, however they are not compatible with El
Capitan (Error reads: kern.osversion not recognized: »15.0.0) and searched
through several newsgroups reporting on that issue, I was however not able
to fix that.
Did anyone of the community here experienced similar issues and have some
suggestions for me!?
Thank you very much!
Best,
Ludwig
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
ages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocInstaller_1.21.1
>
> loaded via a namespace (and not attached):
> [1] tools_3.3.0
>
>
> Im installing the fortran through homebrew, actually, fortran is part of
> the gcc bottle there, thus I installed
> brew install gcc
>
> and Im building and compiling R always from source with:
>
> /configure SHELL='/bin/bash' \
> --prefix=$PREFIX \
> r_arch=x86_64 \
> --x-includes=/usr/X11/include/ \
> --x-libraries=/usr/X11/lib/ \
> CC="clang" \
> CXX="clang++" \
> OBJC="clang" \
> F77="gfortran -arch x86_64" \
> FC="gfortran -arch x86_64" \
> --with-system-zlib \
> --with-blas='-framework Accelerate' \
> --with-lapack \
> CPPFLAGS="-D__ACCELERATE__ \
> --enable-R-framework=no \
> --enable-memory-profiling \
> --enable-R-shlib
>
>
> I never had any problems anymore with missing fortran compilers on OS X
>
> Hope that helps,
>
> cheers, jo
>
>> On 18 Nov 2015, at 12:12, Morgan, Martin <martin.mor...@roswellpark.org>
>> wrote:
>>
>> Probably the definitive answer will be the R-SIG-Mac mailing list
>>
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>> perhaps specifically this thread
>>
>> https://stat.ethz.ch/pipermail/r-sig-mac/2015-October/011641.html
>>
>> which points to the R-admin manual and especially
>>
>> https://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X
>>
>> From the discussion (especially the posts by Brian Ripley) it seems like
>> it should be possible to use gfortran-5.2 via editing the
>> R_HOME/etc/Makeconf or ~/.R/Makevars.
>>
>> Martin
>>
>>
>>
>> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig
>> Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de]
>> Sent: Wednesday, November 18, 2015 5:53 AM
>> To: bioc-devel@r-project.org
>> Subject: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El
>> Capitan 10.11.1
>>
>> Hi,
>>
>> I am experiencing troubles installing "Hmisc", especially its dependency
>> "acepack", via
>>
>>> biocLite("acepack")
>>
>> in R-devel installed from the "R-devel-mavericks-signed.pkg" downloaded
>> from https://r.research.att.com/.
>>
>> The error reads:
>>
>>
>> BioC_mirror: https://bioconductor.org
>> Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development
>> (unstable)
>> (2015-11-16 r69640).
>> Installing package(s) acepack
>> Paket, das nur als Quelltext vorliegt und eventuell Übersetzung von
>> C/C++/Fortran benötigt.: acepack
>> Do you want to attempt to install these from sources?
>> y/n: y
>> installing the source package acepack
>>
>> versuche URL
>> 'https://cran.rstudio.com/src/contrib/acepack_1.3-3.3.tar.gz'
>> Content type 'application/x-gzip' length 33590 bytes (32 KB)
>> ==
>> downloaded 32 KB
>>
>> * installing *source* package acepack ...
>> ** Paket acepack erfolgreich entpackt und MD5 Summen überprüft
>> ** libs
>> gfortran-4.8 -fPIC -g -O2 -c ace.f -o ace.o
>> make: gfortran-4.8: No such file or directory
>> make: *** [ace.o] Error 1
>> ERROR: compilation failed for package acepack
>> * removing
>> /Library/Frameworks/R.framework/Versions/3.3/Resources/library/acepack
>>
>>
>> which indicates that "gfortran-4.8" is missing.
>> I have however installed the recommended "gfortran-5.2" for El Capitan
>> from here:
>>
>> https://gcc.gnu.org/wiki/GFortranBinaries#MacOS
>>
>> Yesterday, I tried quite some time to install 4.8-versions of gfortran
>> available from the website above, however they are not compatible with
>> El
>> Capitan (Error reads: kern.osversion not recognized: »15.0.0) and
>> searched
>> through several newsgroups reporting on that issue, I was however not
>> able
>> to fix that.
>>
>> Did anyone of the community here experienced similar issues and have
>> some
>> suggestions for me!?
>>
>> Thank you very much!
>>
>> Best,
>> Ludwig
>>
>> ___
>> Bioc-de
Re: [Bioc-devel] Base class for interaction data - expressions of interest
I agree with Martin, I would love to see something like that. Especially if this would not be restricted to chromatin interactions, but also allows to represent protein-protein, transcriptionFactor-targetGene, miRNA-mRNA etc (e.g. via suitably tailored subclasses). This might nicely work together with bringing in existing regulatory networks via AnnotationHub ... If help is needed, I'm happy to contribute ... Best, Ludwig > Just to say that this is a great idea. If this starts as a github package > (or in svn, we can create a location for you if you'd like) I and others > would I am sure be happy to try to provide any guidance / insight. The > main design principles are probably to reuse as much as possible from > existing classes, especially the S4Vectors / GRanges world, and to > integrate metadata as appropriate (like SummarizedExepriment, for > instance). > > Martin > > From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Aaron Lun > [a...@wehi.edu.au] > Sent: Thursday, November 05, 2015 12:27 PM > To: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] Base class for interaction data - expressions of > interest > > There's a growing number of Bioconductor packages dealing with > interaction data; diffHic, GenomicInteractions, HiTC, to name a few (and > probably more in the future). Each of these packages defines its own > class to store interaction data - DIList for diffHic, > GenomicInteractions for GenomicInteractions, and HTClist for HiTC. > > These classes seem to share a lot of features, which suggests that they > can be (easily?) replaced with a common class. This would have two > advantages - one, developers of new and existing packages don't have to > continually write and maintain new classes; and two, it provides users > with a consistent user experience across the relevant packages. > > My question is, does anybody have anything in the pipeline with respect > to a base package for an interaction class? If not, I'm planning to put > something together for the next BioC release. To this end, I'd welcome > any ideas/input/code; the aim is to make a drop-in replacement (insofar > as that's possible) for the existing classes in each package. > > Cheers, > > Aaron > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] best practice: dependencies of dependencies / no visible global function definition
I'm surely not the first asking this question. But as I did not find a clear answer to that (e.g. in the 'Writing R extensions' manual or in the diverse posts on this), I risk asking it again. As an example: I'm dealing a lot with ExpressionSets (from Biobase) and GeneSet[Collection]s (from GSEABase) in my package and they are in- outputs of my exported functions, so I want them to be available when my package is loaded. Thus, I would tend to put both, 'Biobase' and 'GSEABase', in the 'Depends' field of my DESCRIPTION file and a corresponding 'import' directive in my NAMESPACE file. However, I do know that 'GSEABase' depends on 'Biobase' - so in order to be not redundant and keeping the 'Depends' field as small as possible, I could also remove 'Biobase' from my 'Depends'. Now, everything still works fine (building, installing, and I still got the ExpressionSets when loading my package), however R CMD CHECK now *notes* on many occasions: no visible global function definition for pData no visible global function definition for exprs no visible global function definition for fData ... Ok, these are NOTES, but I assume they are there for a reason. So, I wonder what a developer's best practice is on that - ignoring the notes, adding all Biobase/ExpressionSet functionality via imports, or indeed depending on both packages. Best, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency
Dear Johannes, one follow-up question/comment on the EnsDb packages: The reason they escaped my notice (and thus potentially will also others) is that I expected such packages to be named ^TxDb What actually argues against sticking to existing Bioc vocabulary and naming eg EnsDb.Hsapiens.v79 TxDb.Hsapiens.Ensembl.hg38.ensGene (or alternatively, if packages like BSgenome.Hsapiens.NCBI.GRCh38 will indeed make it in the long run: TxDb.Hsapiens.Ensembl.GRCh38.ensGene) This would also have the advantage that genome build and idType could be inferred right from the package name. Best, Ludwig dear Robert and Ludwig, the EnsDb packages provide all the gene/transcript etc annotations for all genes defined in the Ensembl database (for a given species and Ensembl release). Except the column/attribute entrezid that is stored in the internal database there is however no link to NCBI or UCSC annotations. So, basically, if you want to use pure Ensembl based annotations: use EnsDb, if you want to have the UCSC annotations: use the TxDb packages. In case you need EnsDbs of other species or Ensembl versions, the ensembldb package provides functionality to generate such packages either using the Ensembl Perl API or using GTF files provided by Ensembl. If you have problems building the packages, just drop me a line and I'll do that. cheers, jo On 03 Jun 2015, at 15:56, Robert M. Flight rfligh...@gmail.com wrote: Ludwig, If you do this search on the UCSC genome browser (which this annotation package is built from), you will see that the longest variant is what is shown http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammalorg=Humandb=hg38position=brca1hgt.positionInput=brca1hgt.suggestTrack=knownGeneSubmit=submithgsid=429339723_8sd4QD2jSAnAsa6cVCevtoOy4GAzpix=1885 If instead of genes you do transcripts, you will see 20 different transcripts for this gene, including the one listed by NCBI. I havent tried it yet (haven't upgraded R or bioconductor to latest version), but there is now an Ensembl based annotation package as well, that may work better?? http://bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v79.html -Robert On Wed, Jun 3, 2015 at 7:04 AM Ludwig Geistlinger ludwig.geistlin...@bio.ifi.lmu.de wrote: Dear Bioc annotation team, Querying TxDb.Hsapiens.UCSC.hg38.knownGene for gene coordinates, e.g. for BRCA1; ENSG0012048; entrez:672 via genes(TxDb.Hsapiens.UCSC.hg38.knownGene, vals=list(gene_id=672)) gives me: GRanges object with 1 range and 1 metadata column: seqnames ranges strand | gene_id RleIRanges Rle | character 672chr17 [43044295, 43170403] - | 672 --- seqinfo: 455 sequences (1 circular) from hg38 genome However, querying Ensembl and NCBI Gene http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG0012048 http://www.ncbi.nlm.nih.gov/gene/672 the gene is located at (note the difference in the end position) Chromosome 17: 43,044,295-43,125,483 reverse strand How is the inconsistency explained and how to extract an ENSEMBL/NCBI conform annotation from the TxDb object? (I am aware of biomaRt, but I want to explicitely use the Bioc annotation functionality). Thanks! Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency
Dear Johannes, Thx for providing the great EnsDb packages! One question: As of now, I am able to choose between TxDb and EnsDb for genomic coordinates of genomic features such as genes, transcripts, and exons. For the sequences themselves I need the corresponding BSgenome package. While it is easy to automatically map from a specific TxDb package (eg TxDb.Hsapiens.UCSC.hg38.knownGene) to the corresponding BSgenome package (here: BSgenome.Hsapiens.UCSC.hg38), I wonder how to do that for an EnsDb package as the package name (eg EnsDb.Hsapiens.v79) contains no information about the genome build. A cumbersome option would be to extract the genome_build from the metadata of the EnsDb package (which would give me for EnsDb.Hsapiens.v79: 'GRCh38') and then ask all existing BSgenome.Hsapiens packages for their metadata release name (eg 'GRCh38' for BSgenome.Hsapiens.UCSC.hg38). This however needs all BSgenome.Hsapiens packages installed and takes thus too much time and space for a programmatic access. Can you suggest a better way to map from coordinates to sequence (within the BioC annotation functionality)? Thanks Best, Ludwig dear Robert and Ludwig, the EnsDb packages provide all the gene/transcript etc annotations for all genes defined in the Ensembl database (for a given species and Ensembl release). Except the column/attribute entrezid that is stored in the internal database there is however no link to NCBI or UCSC annotations. So, basically, if you want to use pure Ensembl based annotations: use EnsDb, if you want to have the UCSC annotations: use the TxDb packages. In case you need EnsDbs of other species or Ensembl versions, the ensembldb package provides functionality to generate such packages either using the Ensembl Perl API or using GTF files provided by Ensembl. If you have problems building the packages, just drop me a line and I'll do that. cheers, jo On 03 Jun 2015, at 15:56, Robert M. Flight rfligh...@gmail.com wrote: Ludwig, If you do this search on the UCSC genome browser (which this annotation package is built from), you will see that the longest variant is what is shown http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammalorg=Humandb=hg38position=brca1hgt.positionInput=brca1hgt.suggestTrack=knownGeneSubmit=submithgsid=429339723_8sd4QD2jSAnAsa6cVCevtoOy4GAzpix=1885 If instead of genes you do transcripts, you will see 20 different transcripts for this gene, including the one listed by NCBI. I havent tried it yet (haven't upgraded R or bioconductor to latest version), but there is now an Ensembl based annotation package as well, that may work better?? http://bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v79.html -Robert On Wed, Jun 3, 2015 at 7:04 AM Ludwig Geistlinger ludwig.geistlin...@bio.ifi.lmu.de wrote: Dear Bioc annotation team, Querying TxDb.Hsapiens.UCSC.hg38.knownGene for gene coordinates, e.g. for BRCA1; ENSG0012048; entrez:672 via genes(TxDb.Hsapiens.UCSC.hg38.knownGene, vals=list(gene_id=672)) gives me: GRanges object with 1 range and 1 metadata column: seqnames ranges strand | gene_id RleIRanges Rle | character 672chr17 [43044295, 43170403] - | 672 --- seqinfo: 455 sequences (1 circular) from hg38 genome However, querying Ensembl and NCBI Gene http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG0012048 http://www.ncbi.nlm.nih.gov/gene/672 the gene is located at (note the difference in the end position) Chromosome 17: 43,044,295-43,125,483 reverse strand How is the inconsistency explained and how to extract an ENSEMBL/NCBI conform annotation from the TxDb object? (I am aware of biomaRt, but I want to explicitely use the Bioc annotation functionality). Thanks! Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency
Dear Bioc annotation team, Querying TxDb.Hsapiens.UCSC.hg38.knownGene for gene coordinates, e.g. for BRCA1; ENSG0012048; entrez:672 via genes(TxDb.Hsapiens.UCSC.hg38.knownGene, vals=list(gene_id=672)) gives me: GRanges object with 1 range and 1 metadata column: seqnames ranges strand | gene_id RleIRanges Rle | character 672chr17 [43044295, 43170403] - | 672 --- seqinfo: 455 sequences (1 circular) from hg38 genome However, querying Ensembl and NCBI Gene http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG0012048 http://www.ncbi.nlm.nih.gov/gene/672 the gene is located at (note the difference in the end position) Chromosome 17: 43,044,295-43,125,483 reverse strand How is the inconsistency explained and how to extract an ENSEMBL/NCBI conform annotation from the TxDb object? (I am aware of biomaRt, but I want to explicitely use the Bioc annotation functionality). Thanks! Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] AnnotationHub: Error in Docker release_core
Dear Elena, thank you for your quick response. Seems as I have make this up to early - it works now for me as well, must have been a pure connection issue. Thx for pointing me to the docker scripts (I must have overread it, is ac tually also stated under http://bioconductor.org/help/docker/). Sorry for the inconvenience!! Best, Ludiwg Hi, On Thu, Apr 9, 2015 at 10:27 AM, Ludwig Geistlinger ludwig.geistlin...@bio.ifi.lmu.de wrote: Error in file(con, r) : cannot open the connection In addition: Warning message: In file(con, r) : unable to resolve 'annotationhub.bioconductor.org' That's strange, on linux it's working. Seems related to network unavailability inside Docker with Mac OS X (I know, not a very insightful suggestion...). BTW: are the docker scripts that were used to create the bioc dockers under http://www.bioconductor.org/help/docker/ somewhere available? https://github.com/Bioconductor/bioc_docker E. -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core
Here you go ... sessionInfo() R Under development (unstable) (2015-03-09 r67969) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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] stats graphics grDevices utils datasets methods base other attached packages: [1] AnnotationHub_1.99.72 BiocInstaller_1.17.5 loaded via a namespace (and not attached): [1] Rcpp_0.11.5 IRanges_2.1.43 [3] digest_0.6.8 bitops_1.0-6 [5] mime_0.2 GenomeInfoDb_1.3.13 [7] R6_2.0.1 xtable_1.7-4 [9] DBI_0.3.1stats4_3.2.0 [11] RSQLite_1.0.0httr_0.6.1 [13] S4Vectors_0.5.22 RJSONIO_1.3-0 [15] stringr_0.6.2Biobase_2.27.2 [17] RCurl_1.95-4.5 shiny_0.11.1 [19] httpuv_1.3.2 parallel_3.2.0 [21] BiocGenerics_0.13.6 AnnotationDbi_1.29.17 [23] htmltools_0.2.6 interactiveDisplayBase_1.5.1 Please provide sessionInfo() The class is defined in AnnotationHub in devel. Perhaps it is not suitably exported. On Thu, Apr 9, 2015 at 5:33 AM, Ludwig Geistlinger ludwig.geistlin...@bio.ifi.lmu.de wrote: Hi, As I pulled down the devel_core image (running boot2docker under OS X Yosemite) docker run -ti bioconductor/release_core R and then executed library(AnnotationHub) hub - AnnotationHub() and selected the recently integrated GSE62944 TCGA dataset (announced in the latest BioC newsletter, April 2015) h - hub[hub$rdataclass == ExpressionSet] h AnnotationHub with 1 record # snapshotDate(): 2015-03-26 # names(): AH28855 # $dataprovider: GEO # $species: Homo sapiens # $rdataclass: ExpressionSet # $title: RNA-Sequencing and clinical data for 7706 tumor samples from The C... # $description: TCGA RNA-seq Rsubread-summarized raw count data for 7706 tum... # $taxonomyid: 9606 # $genome: hg19 # $sourcetype: tar.gz # $sourceurl: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944 # $sourcelastmodifieddate: NA # $sourcesize: NA # $tags: TCGA, RNA-seq, Expression, Count # retrieve record with 'object[[AH28855]]' and then tried to retrieve the record with either h[[AH28855]] or h[[1]] I received the following error: Error in value[[3L]](cond) : failed to create a 'AnnotationHubResource' instance for hub resource âRNA-Sequencing and clinical data for 7706 tumor samples from The Cancer Genome Atlasâ of class ExpressionSet; reason: âExpressionSetResourceâ is not a defined class Did I do something wrong? Thank you for your help, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core
Hi, As I pulled down the devel_core image (running boot2docker under OS X Yosemite) docker run -ti bioconductor/release_core R and then executed library(AnnotationHub) hub - AnnotationHub() and selected the recently integrated GSE62944 TCGA dataset (announced in the latest BioC newsletter, April 2015) h - hub[hub$rdataclass == ExpressionSet] h AnnotationHub with 1 record # snapshotDate(): 2015-03-26 # names(): AH28855 # $dataprovider: GEO # $species: Homo sapiens # $rdataclass: ExpressionSet # $title: RNA-Sequencing and clinical data for 7706 tumor samples from The C... # $description: TCGA RNA-seq Rsubread-summarized raw count data for 7706 tum... # $taxonomyid: 9606 # $genome: hg19 # $sourcetype: tar.gz # $sourceurl: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944 # $sourcelastmodifieddate: NA # $sourcesize: NA # $tags: TCGA, RNA-seq, Expression, Count # retrieve record with 'object[[AH28855]]' and then tried to retrieve the record with either h[[AH28855]] or h[[1]] I received the following error: Error in value[[3L]](cond) : failed to create a 'AnnotationHubResource' instance for hub resource RNA-Sequencing and clinical data for 7706 tumor samples from The Cancer Genome Atlas of class ExpressionSet; reason: ExpressionSetResource is not a defined class Did I do something wrong? Thank you for your help, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] supported organisms
Dear BioC Team, The annotation utilities of BioC are great and enable very comfortable mapping! I am currently wondering whether I am able to programmatically access which BioC currently supports. I am aware of the available.db0pkgs() from AnnotationForge, however what I am actually interested in are the corresponding org.Species.IDType.db packages. As far as I can currently tell, there is no easy map between the .db0 and the org.db packages, is it? In part, this is possible by mapping human.db0 - human - Homo sapiens - Hs - org.Hs.eg.db; but there are exceptions to the 1. org.Xx format for species (e.g. org.Mmu, org.Sco, org.Tgondii) and 2. the default usage of entrez gene ids (.eg) even for popular model organisms such as yeast (org.Sc.sgd.db) and arabidopsis (org.At.tair.db) - for which there are surely good reasons, e.g. historical, however impairing programmatic + unified access. Now there are two options to resolve this: 1. passing this on to the user assuring the organism package is there and requiring him to provide his data based on corresponding IDs - which is not a good idea for end users not familiar with the BioC anno structure 2. giving end users a convenient unified way of inputting data such as: give me your expression values for Entrez gene IDs and I will do what needs to be done. This would hoever require me to hardcode such exceptions to a generic mapping, and this is apparently a bad idea as these mapping might change and new organisms are expected to come into the game. So how to resolve this - am I overseeing something? Thanks Best, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
