GenomicFeatures_1.31.3 imports RMySQL. I'm having great trouble installing RMySQL from source on a recent MacOS (10.13.3) with homebrew. The package's homepage says "The 'RMySQL' package contains an old implementation based on legacy code from S-PLUS which being phased out. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package" https://cran.r-project.org/web/packages/RMySQL/index.html So is it time to heed that advice and migrate GenomicFeatures to RMariaDB ? With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de http://www.huber.embl.de
[Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?
8 messages · Martin Morgan, Vincent Carey, Tim Triche, Jr. +3 more
1 day later
On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
GenomicFeatures_1.31.3 imports RMySQL. I'm having great trouble installing RMySQL from source on a recent MacOS (10.13.3) with homebrew. The package's homepage says "The 'RMySQL' package contains an old implementation based on legacy code from S-PLUS which being phased out. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package" https://cran.r-project.org/web/packages/RMySQL/index.html So is it time to heed that advice and migrate GenomicFeatures to RMariaDB ?
Out of curiosity, is MariaDB easier to install on your system? Its system dependencies are described at https://CRAN.R-project.org/package=RMariaDB FWIW MySQL is a relatively recent addition as a dependency to GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a much more stable solution than `makeTxDbFromBiomart()`. On the other had Johannes does an excellent job on the ensembldb packages, so perhaps this code could really be conditional with the RMySQL dependency moved to Suggests: Martin
With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de http://www.huber.embl.de
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On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:
On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
GenomicFeatures_1.31.3 imports RMySQL. I'm having great trouble installing RMySQL from source on a recent MacOS (10.13.3) with homebrew. The package's homepage says "The 'RMySQL' package contains an old implementation based on legacy code from S-PLUS which being phased out. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package" https://cran.r-project.org/web/packages/RMySQL/index.html So is it time to heed that advice and migrate GenomicFeatures to RMariaDB ?
Out of curiosity, is MariaDB easier to install on your system? Its system dependencies are described at https://CRAN.R-project.org/package=RMariaDB FWIW MySQL is a relatively recent addition as a dependency to GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a much more stable solution than `makeTxDbFromBiomart()`. On the other had Johannes does an excellent job on the ensembldb packages, so perhaps this code could really be conditional with the RMySQL dependency moved to Suggests:
I would vote for moving the relationship to Suggests.
Martin
With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de http://www.huber.embl.de
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Moving it to Suggests: would certainly ease installation on clusters and such. --t On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:
On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
GenomicFeatures_1.31.3 imports RMySQL. I'm having great trouble installing RMySQL from source on a recent MacOS (10.13.3) with homebrew. The package's homepage says "The 'RMySQL' package contains an old implementation based on legacy code from S-PLUS which being phased out. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package" https://cran.r-project.org/web/packages/RMySQL/index.html So is it time to heed that advice and migrate GenomicFeatures to RMariaDB ?
Out of curiosity, is MariaDB easier to install on your system? Its system dependencies are described at https://CRAN.R-project.org/package=RMariaDB FWIW MySQL is a relatively recent addition as a dependency to GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a much more stable solution than `makeTxDbFromBiomart()`. On the other had Johannes does an excellent job on the ensembldb packages, so perhaps this code could really be conditional with the RMySQL dependency moved to Suggests: Martin
With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de http://www.huber.embl.de
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Yep, moving RMySQL to Suggests makes sense. Will do. Also migrating to RMariaDB is on the TODO list. Note that the current problem of RMySQL being hard to install on Mac is only because CRAN doesn't provide an RMySQL binary for R 3.5 yet: https://cran.r-project.org/web/packages/RMySQL/index.html For the record, we had a similar situation one year ago when R 3.4 was in development: CRAN started to build package binaries for Mac a few weeks only before the release of R 3.4.0. Not ideal :-/ H.
On 01/26/2018 07:35 AM, Tim Triche, Jr. wrote:
Moving it to Suggests: would certainly ease installation on clusters and such. --t On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan < martin.morgan at roswellpark.org> wrote:
On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
GenomicFeatures_1.31.3 imports RMySQL. I'm having great trouble installing RMySQL from source on a recent MacOS (10.13.3) with homebrew. The package's homepage says "The 'RMySQL' package contains an old implementation based on legacy code from S-PLUS which being phased out. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package" https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_RMySQL_index.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fU7GJM0vRA454YjFLP8edDtDgyvICfjQmxPlT81V6vs&s=VnqaJPDwlPTUg8EwcI-uhm0UISQ6z5Cf7Ml5yb71KOI&e= So is it time to heed that advice and migrate GenomicFeatures to RMariaDB ?
Out of curiosity, is MariaDB easier to install on your system? Its system dependencies are described at https://urldefense.proofpoint.com/v2/url?u=https-3A__CRAN.R-2Dproject.org_package-3DRMariaDB&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fU7GJM0vRA454YjFLP8edDtDgyvICfjQmxPlT81V6vs&s=ENePjXHv_uoxwPiSLsoj0K0M4yAzHXPCDLsnTpoURJ8&e= FWIW MySQL is a relatively recent addition as a dependency to GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a much more stable solution than `makeTxDbFromBiomart()`. On the other had Johannes does an excellent job on the ensembldb packages, so perhaps this code could really be conditional with the RMySQL dependency moved to Suggests: Martin
With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de https://urldefense.proofpoint.com/v2/url?u=http-3A__www.huber.embl.de&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fU7GJM0vRA454YjFLP8edDtDgyvICfjQmxPlT81V6vs&s=vWnZbbUZzkP2WNC8YkvlMDP2U8YILpmkr0tD2i56_gs&e=
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Herv? Pag?s 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: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319
26.1.18 14:59, Martin Morgan scripsit:
On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
GenomicFeatures_1.31.3 imports RMySQL. I'm having great trouble installing RMySQL from source on a recent MacOS (10.13.3) with homebrew. The package's homepage says "The 'RMySQL' package contains an old implementation based on legacy code from S-PLUS which being phased out. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package" https://cran.r-project.org/web/packages/RMySQL/index.html So is it time to heed that advice and migrate GenomicFeatures to RMariaDB ?
Out of curiosity, is MariaDB easier to install on your system? Its system dependencies are described at https://CRAN.R-project.org/package=RMariaDB
I have no problems installing RMariaDB on MacOS (10.13.3) on an R-devel from source, after installing mariadb-connector-c with homebrew. OTOH, I have not figured out a way to install RMySQL neither on my R-devel from source (various complaints about missing .h files) nor on a binary R 3.4.2 with the binary package download (complaints about missing system libraries / wrong versions). Thanks and kind regards Wolfgang
FWIW MySQL is a relatively recent addition as a dependency to GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a much more stable solution than `makeTxDbFromBiomart()`. On the other had Johannes does an excellent job on the ensembldb packages, so perhaps this code could really be conditional with the RMySQL dependency moved to Suggests: Martin
With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de http://www.huber.embl.de
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With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de http://www.huber.embl.de
As an alternative to Suggests, perhaps make a GenomicFeaturesBuildTools. Not sure if it is better or worse, just different On Fri, Jan 26, 2018 at 2:39 PM, Wolfgang Huber <wolfgang.huber at embl.de> wrote:
26.1.18 14:59, Martin Morgan scripsit:
On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
GenomicFeatures_1.31.3 imports RMySQL. I'm having great trouble installing RMySQL from source on a recent MacOS (10.13.3) with homebrew. The package's homepage says "The 'RMySQL' package contains an old implementation based on legacy code from S-PLUS which being phased out. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package" https://cran.r-project.org/web/packages/RMySQL/index.html So is it time to heed that advice and migrate GenomicFeatures to RMariaDB ?
Out of curiosity, is MariaDB easier to install on your system? Its system dependencies are described at https://CRAN.R-project.org/package=RMariaDB
I have no problems installing RMariaDB on MacOS (10.13.3) on an R-devel
from source, after installing mariadb-connector-c with homebrew.
OTOH, I have not figured out a way to install RMySQL neither on my R-devel
from source (various complaints about missing .h files) nor on a binary R
3.4.2 with the binary package download (complaints about missing system
libraries / wrong versions).
Thanks and kind regards
Wolfgang
FWIW MySQL is a relatively recent addition as a dependency to
GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a much more stable solution than `makeTxDbFromBiomart()`. On the other had Johannes does an excellent job on the ensembldb packages, so perhaps this code could really be conditional with the RMySQL dependency moved to Suggests: Martin
With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de http://www.huber.embl.de
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-- With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de http://www.huber.embl.de
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3 days later
This is done in GenomicFeatures 1.31.6. Note that I also made a few changes to makeTxDbFromUCSC() to make it a little bit faster (about 2x). @Kasper: moving the makeTxDb* functions to a GenomicFeaturesBuildTools or GenomicFeaturesForge package is maybe an idea to explore... H.
On 01/26/2018 06:09 PM, Kasper Daniel Hansen wrote:
As an alternative to Suggests, perhaps make a GenomicFeaturesBuildTools. Not sure if it is better or worse, just different On Fri, Jan 26, 2018 at 2:39 PM, Wolfgang Huber <wolfgang.huber at embl.de> wrote:
26.1.18 14:59, Martin Morgan scripsit:
On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
GenomicFeatures_1.31.3 imports RMySQL. I'm having great trouble installing RMySQL from source on a recent MacOS (10.13.3) with homebrew. The package's homepage says "The 'RMySQL' package contains an old implementation based on legacy code from S-PLUS which being phased out. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package" https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_RMySQL_index.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jUD3XGyxapAK8nfWvxbR_9Rz7RBxP592NO0nWz_wyr0&s=0neTB2BJghm4wF-LnEZ9V9sV_AbF1botcOeTb_bWk-w&e= So is it time to heed that advice and migrate GenomicFeatures to RMariaDB ?
Out of curiosity, is MariaDB easier to install on your system? Its system dependencies are described at https://urldefense.proofpoint.com/v2/url?u=https-3A__CRAN.R-2Dproject.org_package-3DRMariaDB&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jUD3XGyxapAK8nfWvxbR_9Rz7RBxP592NO0nWz_wyr0&s=55tLfrRpaigMug-pW7L1AhpsD1A830xw1f9d1FZEANo&e=
I have no problems installing RMariaDB on MacOS (10.13.3) on an R-devel
from source, after installing mariadb-connector-c with homebrew.
OTOH, I have not figured out a way to install RMySQL neither on my R-devel
from source (various complaints about missing .h files) nor on a binary R
3.4.2 with the binary package download (complaints about missing system
libraries / wrong versions).
Thanks and kind regards
Wolfgang
FWIW MySQL is a relatively recent addition as a dependency to
GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a much more stable solution than `makeTxDbFromBiomart()`. On the other had Johannes does an excellent job on the ensembldb packages, so perhaps this code could really be conditional with the RMySQL dependency moved to Suggests: Martin
With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de https://urldefense.proofpoint.com/v2/url?u=http-3A__www.huber.embl.de&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jUD3XGyxapAK8nfWvxbR_9Rz7RBxP592NO0nWz_wyr0&s=Vp0j7sKJXiZSWHn3LVWSECRS-f-AFZZSSh0mq5rvJ-0&e=
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Herv? Pag?s 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: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319