Question: [Rd] enabling reproducible research & R package management & install.package.version & BiocLite
0
gravatar for Malcolm Cook
6.5 years ago by
Malcolm Cook1.5k
United States
Malcolm Cook1.5k wrote:
All, What got me started on this line of inquiry was my attempt at balancing the advantages of performing a periodic (daily or weekly) update to the 'release' version of locally installed R/Bioconductor packages on our institute-wide installation of R with the disadvantages of potentially changing the result of an analyst's workflow in mid-project. I just got the "green light" to institute such periodic updates that I have been arguing is in our collective best interest. In return, I promised my best effort to provide a means for preserving or reverting to a working R library configuration. Please note that the reproducibility I am most eager to provide is limited to reproducibility within the computing environment of our institute, which perhaps takes away some of the dragon's nests, though certainly not all. There are technical issues of updating package installations on an NFS mount that might have files/libraries open on it from running R sessions. I am interested in learning of approaches for minimizing/eliminating exposure to these issue as well. The first/best approach seems to be to institute a 'black out' period when users should expect the installed library to change. Perhaps there are improvements to this???? Best, Malcolm .-----Original Message----- .From: Mike Marchywka [mailto:marchywka at hotmail.com] .Sent: Tuesday, March 05, 2013 5:24 AM .To: amackey at virginia.edu; Cook, Malcolm .Cc: r-devel at r-project.org; bioconductor at r-project.org; r-discussion at listserv.stowers.org .Subject: RE: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite . . .I hate to ask what go this thread started but it sounds like someone was counting on .exact numeric reproducibility or was there a bug in a specific release? In actual .fact, the best way to determine reproducibility is run the code in a variety of .packages. Alternatively, you can do everything in java and not assume .that calculations commute or associate as the code is modified but it seems .pointless. Sensitivity determination would seem to lead to more reprodicible results .than trying to keep a specific set of code quirks. . .I also seem to recall that FPU may have random lower order bits in some cases, .same code/data give different results. Alsways assume FP is stochastic and plan .on anlayzing the "noise." . . .---------------------------------------- .> From: amackey at virginia.edu .> Date: Mon, 4 Mar 2013 16:28:48 -0500 .> To: MEC at stowers.org .> CC: r-devel at r-project.org; bioconductor at r-project.org; r-discussion at listserv.stowers.org .> Subject: Re: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite .> .> On Mon, Mar 4, 2013 at 4:13 PM, Cook, Malcolm <mec at="" stowers.org=""> wrote: .> .> > * where do the dragons lurk .> > .> .> webs of interconnected dynamically loaded libraries, identical versions of .> R compiled with different BLAS/LAPACK options, etc. Go with the VM if you .> really, truly, want this level of exact reproducibility. .> .> An alternative (and arguably more useful) strategy would be to cache .> results of each computational step, and report when results differ upon .> re-execution with identical inputs; if you cache sessionInfo along with .> each result, you can identify which package(s) changed, and begin to hunt .> down why the change occurred (possibly for the better); couple this with .> the concept of keeping both code *and* results in version control, then you .> can move forward with a (re)analysis without being crippled by out-of-date .> software. .> .> -Aaron .> .> -- .> Aaron J. Mackey, PhD .> Assistant Professor .> Center for Public Health Genomics .> University of Virginia .> amackey at virginia.edu .> http://www.cphg.virginia.edu/mackey .> .> [[alternative HTML version deleted]] .> .> ______________________________________________ .> R-devel at r-project.org mailing list .> https://stat.ethz.ch/mailman/listinfo/r-devel .
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ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by Malcolm Cook1.5k
Answer: [Rd] enabling reproducible research & R package management & install.package.ver
0
gravatar for Steve Lianoglou
6.5 years ago by
Denali
Steve Lianoglou12k wrote:
Hi Paul, You outline some great suggestions! I just wanted to point that in this case: On Tue, Mar 5, 2013 at 5:34 PM, Paul Gilbert <pgilbert902 at="" gmail.com=""> wrote: [snip] > Regarding NFS mounts, it is relatively robust. There can be occasional > problems, especially for users that have a habit of keeping an R session > open for days at a time and using site-library-fresh packages. In my > experience this did not happen often enough to worry about a "blackout > period". if users have a habit of working like this, they could also create an R-library directory under their home directory, and put this library path at the front of their .libPaths() so the continually updated "fresh" stuff won't affect them. Just wanted to point that out as I really like your general approach you've outlined, and just wanted to point out that there's an easy work around in case someone else tries to institute such a regime but is getting friction due to that point in particular. Good stuff, though .. thanks for sharing that! -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD COMMENTlink written 6.5 years ago by Steve Lianoglou12k
Answer: [Rd] enabling reproducible research & R package management & install.package.ver
0
gravatar for Malcolm Cook
6.5 years ago by
Malcolm Cook1.5k
United States
Malcolm Cook1.5k wrote:
Paul, I think your balanced and reasoned approach addresses all my current concerns. Nice! I will likely adopt your methods. Let me ruminate. Thanks for this. ~ Malcolm .-----Original Message----- .From: Paul Gilbert [mailto:pgilbert902 at gmail.com] .Sent: Tuesday, March 05, 2013 4:34 PM .To: Cook, Malcolm .Cc: 'r-devel at r-project.org'; 'bioconductor at r-project.org'; 'r-discussion at listserv.stowers.org' .Subject: Re: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite . .(More on the original question further below.) . .On 13-03-05 09:48 AM, Cook, Malcolm wrote: .> All, .> .> What got me started on this line of inquiry was my attempt at .> balancing the advantages of performing a periodic (daily or weekly) .> update to the 'release' version of locally installed R/Bioconductor .> packages on our institute-wide installation of R with the .> disadvantages of potentially changing the result of an analyst's .> workflow in mid-project. . .I have implemented a strategy to try to address this as follows: . .1/ Install a new version of R when it is released, and packages in the R .version's site-library with package versions as available at the time .the R version is installed. Only upgrade these package versions in the .case they are severely broken. . .2/ Install the same packages in site-library-fresh and upgrade these .package versions on a regular basis (e.g. daily). . .3/ When a new version of R is released, freeze but do not remove the old .R version, at least not for a fairly long time, and freeze .site-library-fresh for the old version. Begin with the new version as in .1/ and 2/. The old version remains available, so "reverting" is trivial. . . .The analysts are then responsible for choosing the R version they use, .and the library they use. This means they do not have to change R and .package version mid-project, but they can if they wish. I think the .above two libraries will cover most cases, but it is possible that a few .projects will need their own special library with a combination of .package versions. In this case the user could create their own library, .or you might prefer some more official mechanism. . .The idea of the above strategy is to provide the stability one might .want for an ongoing project, and the possibility of an upgraded package .if necessary, but not encourage analysts to remain indefinitely with old .versions (by say, putting new packages in an old R version library). . .This strategy has been implemented in a set of make files in the project .RoboAdmin available at http://automater.r-forge.r-project.org/. It can .be done entirely automatically with a cron job. Constructive comments .are always appreciated. . .(IT departments sometimes think that there should be only one version of .everything available, which they test and approve. So the initial .reaction to this approach could be negative. I think they have not .really thought about the advantages. They usually cannot test/approve an .upgrade without user input, and timing is often extremely complicate .because of ongoing user needs. This strategy is simply shifting .responsibility and timing to the users, or user departments, that can .actually do the testing and approving.) . .Regarding NFS mounts, it is relatively robust. There can be occasional .problems, especially for users that have a habit of keeping an R session .open for days at a time and using site-library-fresh packages. In my .experience this did not happen often enough to worry about a "blackout .period". . .Regarding the original question, I would like to think it could be .possible to keep enough information to reproduce the exact environment, .but I think for potentially sensitive numerical problems that is .optimistic. As others have pointed out, results can depend not only on R .and package versions, configuration, OS versions, and library and .compiler versions, but also on the underlying hardware. You might have .some hope using something like an Amazon core instance. (BTW, this .problem is not specific to R.) . .It is true that restricting to a fixed computing environment at your .institution may ease things somewhat, but if you occasionally upgrade .hardware or the OS then you will probably lose reproducibility. . .An alternative that I recommend is that you produce a set of tests that .confirm the results of any important project. These can be conveniently .put in the tests/ directory of an R package, which is then maintained .local, not on CRAN, and built/tested whenever a new R and packages are .installed. (Tools for this are also available at the above indicated web .site.) This approach means that you continue to reproduce the old .results, or if not, discover differences/problems in the old or new .version of R and/or packages that may be important to you. I have been .successfully using a variant of this since about 1993, using R and .package tests/ since they became available. . .Paul . .> .> I just got the "green light" to institute such periodic updates that .> I have been arguing is in our collective best interest. In return, .> I promised my best effort to provide a means for preserving or .> reverting to a working R library configuration. .> .> Please note that the reproducibility I am most eager to provide is .> limited to reproducibility within the computing environment of our .> institute, which perhaps takes away some of the dragon's nests, .> though certainly not all. .> .> There are technical issues of updating package installations on an .> NFS mount that might have files/libraries open on it from running R .> sessions. I am interested in learning of approaches for .> minimizing/eliminating exposure to these issue as well. The .> first/best approach seems to be to institute a 'black out' period .> when users should expect the installed library to change. Perhaps .> there are improvements to this???? .> .> Best, .> .> Malcolm .> .> .> .-----Original Message----- .From: Mike Marchywka .> [mailto:marchywka at hotmail.com] .Sent: Tuesday, March 05, 2013 5:24 .> AM .To: amackey at virginia.edu; Cook, Malcolm .Cc: .> r-devel at r-project.org; bioconductor at r-project.org; .> r-discussion at listserv.stowers.org .Subject: RE: [Rd] [BioC] enabling .> reproducible research & R package management & .> install.package.version & BiocLite . . .I hate to ask what go this .> thread started but it sounds like someone was counting on .exact .> numeric reproducibility or was there a bug in a specific release? In .> actual .fact, the best way to determine reproducibility is run the .> code in a variety of .packages. Alternatively, you can do everything .> in java and not assume .that calculations commute or associate as the .> code is modified but it seems .pointless. Sensitivity determination .> would seem to lead to more reprodicible results .than trying to keep .> a specific set of code quirks. . .I also seem to recall that FPU may .> have random lower order bits in some cases, .same code/data give .> different results. Alsways assume FP is stochastic and plan .on .> anlayzing the "noise." . . .---------------------------------------- .> .> From: amackey at virginia.edu .> Date: Mon, 4 Mar 2013 16:28:48 .> -0500 .> To: MEC at stowers.org .> CC: r-devel at r-project.org; .> bioconductor at r-project.org; r-discussion at listserv.stowers.org .> .> Subject: Re: [Rd] [BioC] enabling reproducible research & R package .> management & install.package.version & BiocLite .> .> On Mon, Mar 4, .> 2013 at 4:13 PM, Cook, Malcolm <mec at="" stowers.org=""> wrote: .> .> > * .> where do the dragons lurk .> > .> .> webs of interconnected .> dynamically loaded libraries, identical versions of .> R compiled .> with different BLAS/LAPACK options, etc. Go with the VM if you .> .> really, truly, want this level of exact reproducibility. .> .> An .> alternative (and arguably more useful) strategy would be to cache .> .> results of each computational step, and report when results differ .> upon .> re-execution with identical inputs; if you cache sessionInfo .> along with .> each result, you can identify which package(s) changed, .> and begin to hunt .> down why the change occurred (possibly for the .> better); couple this with .> the concept of keeping both code *and* .> results in version control, then you .> can move forward with a .> (re)analysis without being crippled by out-of-date .> software. .> .> .> -Aaron .> .> -- .> Aaron J. Mackey, PhD .> Assistant Professor .> .> Center for Public Health Genomics .> University of Virginia .> .> amackey at virginia.edu .> http://www.cphg.virginia.edu/mackey .> .> .> [[alternative HTML version deleted]] .> .> .> ______________________________________________ .> .> R-devel at r-project.org mailing list .> .> https://stat.ethz.ch/mailman/listinfo/r-devel . .> .> ______________________________________________ R-devel at r-project.org .> mailing list https://stat.ethz.ch/mailman/listinfo/r-devel .>
ADD COMMENTlink written 6.5 years ago by Malcolm Cook1.5k
There are utilities ( e.g. dotkit, and modules) which facilitate version management, basically creating on the fly PATH and env setups, if you are comfortable keeping all that around. David -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Cook, Malcolm Sent: Tuesday, March 05, 2013 6:08 PM To: 'Paul Gilbert' Cc: 'r-devel at r-project.org'; 'bioconductor at r-project.org'; 'r-discussion at listserv.stowers.org' Subject: Re: [BioC] [Rd] enabling reproducible research & R package management & install.package.version & BiocLite Paul, I think your balanced and reasoned approach addresses all my current concerns. Nice! I will likely adopt your methods. Let me ruminate. Thanks for this. ~ Malcolm .-----Original Message----- .From: Paul Gilbert [mailto:pgilbert902 at gmail.com] .Sent: Tuesday, March 05, 2013 4:34 PM .To: Cook, Malcolm .Cc: 'r-devel at r-project.org'; 'bioconductor at r-project.org'; 'r-discussion at listserv.stowers.org' .Subject: Re: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite . .(More on the original question further below.) . .On 13-03-05 09:48 AM, Cook, Malcolm wrote: .> All, .> .> What got me started on this line of inquiry was my attempt at .> balancing the advantages of performing a periodic (daily or weekly) .> update to the 'release' version of locally installed R/Bioconductor .> packages on our institute-wide installation of R with the .> disadvantages of potentially changing the result of an analyst's .> workflow in mid-project. . .I have implemented a strategy to try to address this as follows: . .1/ Install a new version of R when it is released, and packages in the R .version's site-library with package versions as available at the time .the R version is installed. Only upgrade these package versions in the .case they are severely broken. . .2/ Install the same packages in site-library-fresh and upgrade these .package versions on a regular basis (e.g. daily). . .3/ When a new version of R is released, freeze but do not remove the old .R version, at least not for a fairly long time, and freeze .site-library-fresh for the old version. Begin with the new version as in .1/ and 2/. The old version remains available, so "reverting" is trivial. . . .The analysts are then responsible for choosing the R version they use, .and the library they use. This means they do not have to change R and .package version mid-project, but they can if they wish. I think the .above two libraries will cover most cases, but it is possible that a few .projects will need their own special library with a combination of .package versions. In this case the user could create their own library, .or you might prefer some more official mechanism. . .The idea of the above strategy is to provide the stability one might .want for an ongoing project, and the possibility of an upgraded package .if necessary, but not encourage analysts to remain indefinitely with old .versions (by say, putting new packages in an old R version library). . .This strategy has been implemented in a set of make files in the project .RoboAdmin available at http://automater.r-forge.r-project.org/. It can .be done entirely automatically with a cron job. Constructive comments .are always appreciated. . .(IT departments sometimes think that there should be only one version of .everything available, which they test and approve. So the initial .reaction to this approach could be negative. I think they have not .really thought about the advantages. They usually cannot test/approve an .upgrade without user input, and timing is often extremely complicate .because of ongoing user needs. This strategy is simply shifting .responsibility and timing to the users, or user departments, that can .actually do the testing and approving.) . .Regarding NFS mounts, it is relatively robust. There can be occasional .problems, especially for users that have a habit of keeping an R session .open for days at a time and using site-library- fresh packages. In my .experience this did not happen often enough to worry about a "blackout .period". . .Regarding the original question, I would like to think it could be .possible to keep enough information to reproduce the exact environment, .but I think for potentially sensitive numerical problems that is .optimistic. As others have pointed out, results can depend not only on R .and package versions, configuration, OS versions, and library and .compiler versions, but also on the underlying hardware. You might have .some hope using something like an Amazon core instance. (BTW, this .problem is not specific to R.) . .It is true that restricting to a fixed computing environment at your .institution may ease things somewhat, but if you occasionally upgrade .hardware or the OS then you will probably lose reproducibility. . .An alternative that I recommend is that you produce a set of tests that .confirm the results of any important project. These can be conveniently .put in the tests/ directory of an R package, which is then maintained .local, not on CRAN, and built/tested whenever a new R and packages are .installed. (Tools for this are also available at the above indicated web .site.) This approach means that you continue to reproduce the old .results, or if not, discover differences/problems in the old or new .version of R and/or packages that may be important to you. I have been .successfully using a variant of this since about 1993, using R and .package tests/ since they became available. . .Paul . .> .> I just got the "green light" to institute such periodic updates that .> I have been arguing is in our collective best interest. In return, .> I promised my best effort to provide a means for preserving or .> reverting to a working R library configuration. .> .> Please note that the reproducibility I am most eager to provide is .> limited to reproducibility within the computing environment of our .> institute, which perhaps takes away some of the dragon's nests, .> though certainly not all. .> .> There are technical issues of updating package installations on an .> NFS mount that might have files/libraries open on it from running R .> sessions. I am interested in learning of approaches for .> minimizing/eliminating exposure to these issue as well. The .> first/best approach seems to be to institute a 'black out' period .> when users should expect the installed library to change. Perhaps .> there are improvements to this???? .> .> Best, .> .> Malcolm .> .> .> .-----Original Message----- .From: Mike Marchywka .> [mailto:marchywka at hotmail.com] .Sent: Tuesday, March 05, 2013 5:24 .> AM .To: amackey at virginia.edu; Cook, Malcolm .Cc: .> r-devel at r-project.org; bioconductor at r-project.org; .> r-discussion at listserv.stowers.org .Subject: RE: [Rd] [BioC] enabling .> reproducible research & R package management & .> install.package.version & BiocLite . . .I hate to ask what go this .> thread started but it sounds like someone was counting on .exact .> numeric reproducibility or was there a bug in a specific release? In .> actual .fact, the best way to determine reproducibility is run the .> code in a variety of .packages. Alternatively, you can do everything .> in java and not assume .that calculations commute or associate as the .> code is modified but it seems .pointless. Sensitivity determination .> would seem to lead to more reprodicible results .than trying to keep .> a specific set of code quirks. . .I also seem to recall that FPU may .> have random lower order bits in some cases, .same code/data give .> different results. Alsways assume FP is stochastic and plan .on .> anlayzing the "noise." . . .---------------------------------------- .> .> From: amackey at virginia.edu .> Date: Mon, 4 Mar 2013 16:28:48 .> -0500 .> To: MEC at stowers.org .> CC: r-devel at r-project.org; .> bioconductor at r-project.org; r-discussion at listserv.stowers.org .> .> Subject: Re: [Rd] [BioC] enabling reproducible research & R package .> management & install.package.version & BiocLite .> .> On Mon, Mar 4, .> 2013 at 4:13 PM, Cook, Malcolm <mec at="" stowers.org=""> wrote: .> .> > * .> where do the dragons lurk .> > .> .> webs of interconnected .> dynamically loaded libraries, identical versions of .> R compiled .> with different BLAS/LAPACK options, etc. Go with the VM if you .> .> really, truly, want this level of exact reproducibility. .> .> An .> alternative (and arguably more useful) strategy would be to cache .> .> results of each computational step, and report when results differ .> upon .> re-execution with identical inputs; if you cache sessionInfo .> along with .> each result, you can identify which package(s) changed, .> and begin to hunt .> down why the change occurred (possibly for the .> better); couple this with .> the concept of keeping both code *and* .> results in version control, then you .> can move forward with a .> (re)analysis without being crippled by out-of-date .> software. .> .> .> -Aaron .> .> -- .> Aaron J. Mackey, PhD .> Assistant Professor .> .> Center for Public Health Genomics .> University of Virginia .> .> amackey at virginia.edu .> http://www.cphg.virginia.edu/mackey .> .> .> [[alternative HTML version deleted]] .> .> .> ______________________________________________ .> .> R-devel at r-project.org mailing list .> .> https://stat.ethz.ch/mailman/listinfo/r-devel . .> .> ______________________________________________ R-devel at r-project.org .> mailing list https://stat.ethz.ch/mailman/listinfo/r-devel .> _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 6.5 years ago by David Lapointe170
Thanks David, I've looked into them both a bit, and I don't think the provide an approach for R (or Perl, for that matter) library management, which is the wicket I'm trying to get less sticky now. They could be useful to manage the various installations of version of R and analysis files (we're talking allot of NextGenSequencing, so, bowtie, tophat, and friends) quite nicely similarly in service of an approach to enabling reproducible results. THanks for you thoughts, and, if you know of others similar to dotkit/modules I'd be keen to here of them. ~Malcolm .-----Original Message----- .From: Lapointe, David [mailto:David.Lapointe at umassmed.edu] .Sent: Wednesday, March 06, 2013 7:46 AM .To: Cook, Malcolm; 'Paul Gilbert' .Cc: 'r-devel at r-project.org'; 'bioconductor at r-project.org'; 'r-discussion at listserv.stowers.org' .Subject: RE: [BioC] [Rd] enabling reproducible research & R package management & install.package.version & BiocLite . .There are utilities ( e.g. dotkit, and modules) which facilitate version management, basically creating on the fly PATH and env setups, if .you are comfortable keeping all that around. . .David . .-----Original Message----- .From: bioconductor-bounces at r-project.org [mailto:bioconductor- bounces at r-project.org] On Behalf Of Cook, Malcolm .Sent: Tuesday, March 05, 2013 6:08 PM .To: 'Paul Gilbert' .Cc: 'r-devel at r-project.org'; 'bioconductor at r-project.org'; 'r-discussion at listserv.stowers.org' .Subject: Re: [BioC] [Rd] enabling reproducible research & R package management & install.package.version & BiocLite . .Paul, . .I think your balanced and reasoned approach addresses all my current concerns. Nice! I will likely adopt your methods. Let me .ruminate. Thanks for this. . .~ Malcolm . . .-----Original Message----- . .From: Paul Gilbert [mailto:pgilbert902 at gmail.com] . .Sent: Tuesday, March 05, 2013 4:34 PM . .To: Cook, Malcolm . .Cc: 'r-devel at r-project.org'; 'bioconductor at r-project.org'; 'r-discussion at listserv.stowers.org' . .Subject: Re: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite . . .(More on the original question further below.) . . .On 13-03-05 09:48 AM, Cook, Malcolm wrote: . .> All, . .> . .> What got me started on this line of inquiry was my attempt at .> balancing the advantages of performing a periodic (daily or .weekly) .> update to the 'release' version of locally installed R/Bioconductor .> packages on our institute-wide installation of R with .the .> disadvantages of potentially changing the result of an analyst's .> workflow in mid-project. . . . .I have implemented a strategy to try to address this as follows: . . . .1/ Install a new version of R when it is released, and packages in the R .version's site-library with package versions as available at the .time .the R version is installed. Only upgrade these package versions in the .case they are severely broken. . . . .2/ Install the same packages in site-library-fresh and upgrade these .package versions on a regular basis (e.g. daily). . . . .3/ When a new version of R is released, freeze but do not remove the old .R version, at least not for a fairly long time, and freeze ..site-library-fresh for the old version. Begin with the new version as in .1/ and 2/. The old version remains available, so "reverting" is .trivial. . . . . . .The analysts are then responsible for choosing the R version they use, .and the library they use. This means they do not have to .change R and .package version mid-project, but they can if they wish. I think the .above two libraries will cover most cases, but it is .possible that a few .projects will need their own special library with a combination of .package versions. In this case the user could .create their own library, .or you might prefer some more official mechanism. . . . .The idea of the above strategy is to provide the stability one might .want for an ongoing project, and the possibility of an upgraded .package .if necessary, but not encourage analysts to remain indefinitely with old .versions (by say, putting new packages in an old R .version library). . . . .This strategy has been implemented in a set of make files in the project .RoboAdmin available at http://automater.r-forge.r- .project.org/. It can .be done entirely automatically with a cron job. Constructive comments .are always appreciated. . . . .(IT departments sometimes think that there should be only one version of .everything available, which they test and approve. So .the initial .reaction to this approach could be negative. I think they have not .really thought about the advantages. They usually .cannot test/approve an .upgrade without user input, and timing is often extremely complicate .because of ongoing user needs. This .strategy is simply shifting .responsibility and timing to the users, or user departments, that can .actually do the testing and .approving.) . . .Regarding NFS mounts, it is relatively robust. There can be occasional .problems, especially for users that have a habit of keeping an .R session .open for days at a time and using site-library-fresh packages. In my .experience this did not happen often enough to worry .about a "blackout .period". . . . .Regarding the original question, I would like to think it could be .possible to keep enough information to reproduce the exact .environment, .but I think for potentially sensitive numerical problems that is .optimistic. As others have pointed out, results can .depend not only on R .and package versions, configuration, OS versions, and library and .compiler versions, but also on the .underlying hardware. You might have .some hope using something like an Amazon core instance. (BTW, this .problem is not specific .to R.) . . .It is true that restricting to a fixed computing environment at your .institution may ease things somewhat, but if you occasionally .upgrade .hardware or the OS then you will probably lose reproducibility. . . . .An alternative that I recommend is that you produce a set of tests that .confirm the results of any important project. These can be .conveniently .put in the tests/ directory of an R package, which is then maintained .local, not on CRAN, and built/tested whenever a .new R and packages are .installed. (Tools for this are also available at the above indicated web . .site.) This approach means that you continue to reproduce the old .results, or if not, discover differences/problems in the old or new ..version of R and/or packages that may be important to you. I have been .successfully using a variant of this since about 1993, using R .and .package tests/ since they became available. . . . .Paul . . . .> . .> I just got the "green light" to institute such periodic updates that .> I have been arguing is in our collective best interest. In return, ..> I promised my best effort to provide a means for preserving or .> reverting to a working R library configuration. . .> . .> Please note that the reproducibility I am most eager to provide is .> limited to reproducibility within the computing environment of .our .> institute, which perhaps takes away some of the dragon's nests, .> though certainly not all. . .> . .> There are technical issues of updating package installations on an .> NFS mount that might have files/libraries open on it from .running R .> sessions. I am interested in learning of approaches for .> minimizing/eliminating exposure to these issue as well. The .> .first/best approach seems to be to institute a 'black out' period . .> when users should expect the installed library to change. Perhaps . .> there are improvements to this???? . .> . .> Best, . .> . .> Malcolm . .> . .> . .> .-----Original Message----- .From: Mike Marchywka .> [mailto:marchywka at hotmail.com] .Sent: Tuesday, March 05, 2013 5:24 .> .AM .To: amackey at virginia.edu; Cook, Malcolm .Cc: . .> r-devel at r-project.org; bioconductor at r-project.org; .> r-discussion at listserv.stowers.org .Subject: RE: [Rd] [BioC] enabling .> .reproducible research & R package management & .> install.package.version & BiocLite . . .I hate to ask what go this .> thread started .but it sounds like someone was counting on .exact .> numeric reproducibility or was there a bug in a specific release? In .> actual ..fact, the best way to determine reproducibility is run the .> code in a variety of .packages. Alternatively, you can do everything .> in .java and not assume .that calculations commute or associate as the .> code is modified but it seems .pointless. Sensitivity .determination .> would seem to lead to more reprodicible results .than trying to keep .> a specific set of code quirks. . .I also seem to .recall that FPU may .> have random lower order bits in some cases, .same code/data give .> different results. Alsways assume FP is .stochastic and plan .on .> anlayzing the "noise." . . .---------------------------------------- . .> .> From: amackey at virginia.edu .> Date: Mon, 4 Mar 2013 16:28:48 .> -0500 .> To: MEC at stowers.org .> CC: r-devel at r-project.org; ..> bioconductor at r-project.org; r-discussion at listserv.stowers.org .> .> Subject: Re: [Rd] [BioC] enabling reproducible research & R .package .> management & install.package.version & BiocLite .> .> On Mon, Mar 4, .> 2013 at 4:13 PM, Cook, Malcolm .<mec at="" stowers.org=""> wrote: .> .> > * .> where do the dragons lurk .> > .> .> webs of interconnected .> dynamically loaded libraries, .identical versions of .> R compiled .> with different BLAS/LAPACK options, etc. Go with the VM if you .> .> really, truly, want this level .of exact reproducibility. .> .> An .> alternative (and arguably more useful) strategy would be to cache .> .> results of each .computational step, and report when results differ .> upon .> re- execution with identical inputs; if you cache sessionInfo .> along .with .> each result, you can identify which package(s) changed, .> and begin to hunt .> down why the change occurred (possibly for .the .> better); couple this with .> the concept of keeping both code *and* .> results in version control, then you .> can move forward .with a .> (re)analysis without being crippled by out-of-date .> software. .> .> .> -Aaron .> .> -- .> Aaron J. Mackey, PhD .> Assistant .Professor .> .> Center for Public Health Genomics .> University of Virginia .> .> amackey at virginia.edu .> .http://www.cphg.virginia.edu/mackey .> .> .> [[alternative HTML version deleted]] .> .> .> .______________________________________________ .> .> R-devel at r-project.org mailing list .> .> .https://stat.ethz.ch/mailman/listinfo/r-devel . . .> . .> ______________________________________________ R-devel at r-project.org .> mailing list .https://stat.ethz.ch/mailman/listinfo/r-devel . .> . ._______________________________________________ .Bioconductor mailing list .Bioconductor at r-project.org .https://stat.ethz.ch/mailman/listinfo/bioconductor .Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 6.5 years ago by Malcolm Cook1.5k
seen QuasR (and/or gmapR, Rsubread, etc.)? one can run BowTie, gsnap, etc. from R this certainly makes it easier for me to remember how I did some ChIP- seq or BS-seq or RNA-seq processing a year ago, when it turns out I need to add a sample or samples and carry on with an existing analysis pipeline On Wed, Mar 6, 2013 at 10:17 AM, Cook, Malcolm <mec@stowers.org> wrote: > Thanks David, I've looked into them both a bit, and I don't think the > provide an approach for R (or Perl, for that matter) library management, > which is the wicket I'm trying to get less sticky now. > > They could be useful to manage the various installations of version of R > and analysis files (we're talking allot of NextGenSequencing, so, bowtie, > tophat, and friends) quite nicely similarly in service of an approach to > enabling reproducible results. > > THanks for you thoughts, and, if you know of others similar to > dotkit/modules I'd be keen to here of them. > > ~Malcolm > > > .-----Original Message----- > .From: Lapointe, David [mailto:David.Lapointe@umassmed.edu] > .Sent: Wednesday, March 06, 2013 7:46 AM > .To: Cook, Malcolm; 'Paul Gilbert' > .Cc: 'r-devel@r-project.org'; 'bioconductor@r-project.org'; ' > r-discussion@listserv.stowers.org' > .Subject: RE: [BioC] [Rd] enabling reproducible research & R package > management & install.package.version & BiocLite > . > .There are utilities ( e.g. dotkit, and modules) which facilitate version > management, basically creating on the fly PATH and env setups, if > .you are comfortable keeping all that around. > . > .David > . > .-----Original Message----- > .From: bioconductor-bounces@r-project.org [mailto: > bioconductor-bounces@r-project.org] On Behalf Of Cook, Malcolm > .Sent: Tuesday, March 05, 2013 6:08 PM > .To: 'Paul Gilbert' > .Cc: 'r-devel@r-project.org'; 'bioconductor@r-project.org'; ' > r-discussion@listserv.stowers.org' > .Subject: Re: [BioC] [Rd] enabling reproducible research & R package > management & install.package.version & BiocLite > . > .Paul, > . > .I think your balanced and reasoned approach addresses all my current > concerns. Nice! I will likely adopt your methods. Let me > .ruminate. Thanks for this. > . > .~ Malcolm > . > . .-----Original Message----- > . .From: Paul Gilbert [mailto:pgilbert902@gmail.com] > . .Sent: Tuesday, March 05, 2013 4:34 PM > . .To: Cook, Malcolm > . .Cc: 'r-devel@r-project.org'; 'bioconductor@r-project.org'; ' > r-discussion@listserv.stowers.org' > . .Subject: Re: [Rd] [BioC] enabling reproducible research & R package > management & install.package.version & BiocLite . > . .(More on the original question further below.) . > . .On 13-03-05 09:48 AM, Cook, Malcolm wrote: > . .> All, > . .> > . .> What got me started on this line of inquiry was my attempt at .> > balancing the advantages of performing a periodic (daily or > .weekly) .> update to the 'release' version of locally installed > R/Bioconductor .> packages on our institute-wide installation of R with > .the .> disadvantages of potentially changing the result of an analyst's > .> workflow in mid-project. > . . > . .I have implemented a strategy to try to address this as follows: > . . > . .1/ Install a new version of R when it is released, and packages in the > R .version's site-library with package versions as available at the > .time .the R version is installed. Only upgrade these package versions > in the .case they are severely broken. > . . > . .2/ Install the same packages in site-library-fresh and upgrade these > .package versions on a regular basis (e.g. daily). > . . > . .3/ When a new version of R is released, freeze but do not remove the > old .R version, at least not for a fairly long time, and freeze > ..site-library-fresh for the old version. Begin with the new version as > in .1/ and 2/. The old version remains available, so "reverting" is > .trivial. > . . > . . > . .The analysts are then responsible for choosing the R version they use, > .and the library they use. This means they do not have to > .change R and .package version mid-project, but they can if they wish. I > think the .above two libraries will cover most cases, but it is > .possible that a few .projects will need their own special library with > a combination of .package versions. In this case the user could > .create their own library, .or you might prefer some more official > mechanism. > . . > . .The idea of the above strategy is to provide the stability one might > .want for an ongoing project, and the possibility of an upgraded > .package .if necessary, but not encourage analysts to remain > indefinitely with old .versions (by say, putting new packages in an old R > .version library). > . . > . .This strategy has been implemented in a set of make files in the > project .RoboAdmin available at http://automater.r-forge.r- > .project.org/. It can .be done entirely automatically with a cron job. > Constructive comments .are always appreciated. > . . > . .(IT departments sometimes think that there should be only one version > of .everything available, which they test and approve. So > .the initial .reaction to this approach could be negative. I think they > have not .really thought about the advantages. They usually > .cannot test/approve an .upgrade without user input, and timing is often > extremely complicate .because of ongoing user needs. This > .strategy is simply shifting .responsibility and timing to the users, or > user departments, that can .actually do the testing and > .approving.) . > . .Regarding NFS mounts, it is relatively robust. There can be occasional > .problems, especially for users that have a habit of keeping an > .R session .open for days at a time and using site-library-fresh > packages. In my .experience this did not happen often enough to worry > .about a "blackout .period". > . . > . .Regarding the original question, I would like to think it could be > .possible to keep enough information to reproduce the exact > .environment, .but I think for potentially sensitive numerical problems > that is .optimistic. As others have pointed out, results can > .depend not only on R .and package versions, configuration, OS versions, > and library and .compiler versions, but also on the > .underlying hardware. You might have .some hope using something like an > Amazon core instance. (BTW, this .problem is not specific > .to R.) . > . .It is true that restricting to a fixed computing environment at your > .institution may ease things somewhat, but if you occasionally > .upgrade .hardware or the OS then you will probably lose reproducibility. > . . > . .An alternative that I recommend is that you produce a set of tests > that .confirm the results of any important project. These can be > .conveniently .put in the tests/ directory of an R package, which is > then maintained .local, not on CRAN, and built/tested whenever a > .new R and packages are .installed. (Tools for this are also available > at the above indicated web > . .site.) This approach means that you continue to reproduce the old > .results, or if not, discover differences/problems in the old or new > ..version of R and/or packages that may be important to you. I have been > .successfully using a variant of this since about 1993, using R > .and .package tests/ since they became available. > . . > . .Paul > . . > . .> > . .> I just got the "green light" to institute such periodic updates that > .> I have been arguing is in our collective best interest. In return, > ..> I promised my best effort to provide a means for preserving or .> > reverting to a working R library configuration. > . .> > . .> Please note that the reproducibility I am most eager to provide is > .> limited to reproducibility within the computing environment of > .our .> institute, which perhaps takes away some of the dragon's nests, > .> though certainly not all. > . .> > . .> There are technical issues of updating package installations on an > .> NFS mount that might have files/libraries open on it from > .running R .> sessions. I am interested in learning of approaches for > .> minimizing/eliminating exposure to these issue as well. The .> > .first/best approach seems to be to institute a 'black out' period > . .> when users should expect the installed library to change. Perhaps > . .> there are improvements to this???? > . .> > . .> Best, > . .> > . .> Malcolm > . .> > . .> > . .> .-----Original Message----- .From: Mike Marchywka .> [mailto: > marchywka@hotmail.com] .Sent: Tuesday, March 05, 2013 5:24 .> > .AM .To: amackey@virginia.edu; Cook, Malcolm .Cc: > . .> r-devel@r-project.org; bioconductor@r-project.org; .> > r-discussion@listserv.stowers.org .Subject: RE: [Rd] [BioC] enabling .> > .reproducible research & R package management & .> > install.package.version & BiocLite . . .I hate to ask what go this .> > thread started > .but it sounds like someone was counting on .exact .> numeric > reproducibility or was there a bug in a specific release? In .> actual > ..fact, the best way to determine reproducibility is run the .> code in > a variety of .packages. Alternatively, you can do everything .> in > .java and not assume .that calculations commute or associate as the .> > code is modified but it seems .pointless. Sensitivity > .determination .> would seem to lead to more reprodicible results .than > trying to keep .> a specific set of code quirks. . .I also seem to > .recall that FPU may .> have random lower order bits in some cases, > .same code/data give .> different results. Alsways assume FP is > .stochastic and plan .on .> anlayzing the "noise." . . > .---------------------------------------- > . .> .> From: amackey@virginia.edu .> Date: Mon, 4 Mar 2013 16:28:48 .> > -0500 .> To: MEC@stowers.org .> CC: r-devel@r-project.org; > ..> bioconductor@r-project.org; r-discussion@listserv.stowers.org .> .> > Subject: Re: [Rd] [BioC] enabling reproducible research & R > .package .> management & install.package.version & BiocLite .> .> On > Mon, Mar 4, .> 2013 at 4:13 PM, Cook, Malcolm > .<mec@stowers.org> wrote: .> .> > * .> where do the dragons lurk .> > > .> .> webs of interconnected .> dynamically loaded libraries, > .identical versions of .> R compiled .> with different BLAS/LAPACK > options, etc. Go with the VM if you .> .> really, truly, want this level > .of exact reproducibility. .> .> An .> alternative (and arguably more > useful) strategy would be to cache .> .> results of each > .computational step, and report when results differ .> upon .> > re-execution with identical inputs; if you cache sessionInfo .> along > .with .> each result, you can identify which package(s) changed, .> and > begin to hunt .> down why the change occurred (possibly for > .the .> better); couple this with .> the concept of keeping both code > *and* .> results in version control, then you .> can move forward > .with a .> (re)analysis without being crippled by out-of-date .> > software. .> .> .> -Aaron .> .> -- .> Aaron J. Mackey, PhD .> Assistant > .Professor .> .> Center for Public Health Genomics .> University of > Virginia .> .> amackey@virginia.edu .> > .http://www.cphg.virginia.edu/mackey .> .> .> [[alternative HTML > version deleted]] .> .> .> > .______________________________________________ .> .> > R-devel@r-project.org mailing list .> .> > .https://stat.ethz.ch/mailman/listinfo/r-devel . > . .> > . .> ______________________________________________ R-devel@r-project.org .> mailing list > .https://stat.ethz.ch/mailman/listinfo/r-devel > . .> > . > ._______________________________________________ > .Bioconductor mailing list > .Bioconductor@r-project.org > .https://stat.ethz.ch/mailman/listinfo/bioconductor > .Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
ADD REPLYlink written 6.5 years ago by Tim Triche4.2k
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