Question: problem with loading DESeq after upgrading from R 2.14 to R 2.15
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gravatar for Yue Li
7.4 years ago by
Yue Li370
USA
Yue Li370 wrote:
Dear List, I have some problem loading DESeq after I upgraded from R 2.14 to R .2.15 on Mac OS 10.7.3. Basically, I have my own library directory separate from the default library directory (/Library/Frameworks/R.framework/Versions/2.14/Resources/library) to avoid having to re-instally all the packages after changing from 2.14 to 2.15. I also set up my .libPaths("/Library/RLib") in the ~/.Rprofile and R_LIBS=/Library/RLib in my .profile at $HOME. After that, I installed the binary build R 2.15 and upgraded all packages. Under terminal window, I can load all of the packages including DESeq and DEXSeq. Under R64.app GUI, however, I can load all packages except for DESeq and DEXSeq in R GUI. Please anyone has some suggestions? Thanks very much! ###################################################################### ########## Under terminal: > library(DESeq) Loading required package: Biobase Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are masked from ‘package:base’: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: locfit locfit 1.5-7 2012-03-22 > ###################################################################### ########## Under R64 or R32 GUI: > library(DESeq) Loading required package: Biobase Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are masked from ‘package:base’: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: locfit locfit 1.5-7 2012-03-22 Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so Reason: image not found Error: package/namespace load failed for ‘DESeq’ [[alternative HTML version deleted]]
gui deseq dexseq • 1.4k views
ADD COMMENTlink modified 7.4 years ago by Yue Li60 • written 7.4 years ago by Yue Li370
Answer: problem with loading DESeq after upgrading from R 2.14 to R 2.15
0
gravatar for Yue Li
7.4 years ago by
Yue Li60
Yue Li60 wrote:
Dear List, I have some problem loading DESeq after I upgraded from R 2.14 to R .2.15 on Mac OS 10.7.3. Basically, I have my own library directory separate from the default library directory (/Library/Frameworks/R.framework/Versions/2.14/Resources/library) to avoid having to re-instally all the packages after changing from 2.14 to 2.15. I also set up my .libPaths("/Library/RLib") in the ~/.Rprofile and R_LIBS=/Library/RLib in my .profile at $HOME. After that, I installed the binary build R 2.15 and upgraded all packages. Under terminal window, I can load all of the packages including DESeq and DEXSeq. Under R64.app GUI, however, I can load all packages except for DESeq and DEXSeq in R GUI. Please anyone has some suggestions? Thanks very much! ###################################################################### ########## Under terminal: > library(DESeq) Loading required package: Biobase Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are masked from ‘package:base’: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: locfit locfit 1.5-7 2012-03-22 > ###################################################################### ########## Under R64 or R32 GUI: > library(DESeq) Loading required package: Biobase Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are masked from ‘package:base’: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: locfit locfit 1.5-7 2012-03-22 Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so Reason: image not found Error: package/namespace load failed for ‘DESeq’ [[alternative HTML version deleted]]
ADD COMMENTlink written 7.4 years ago by Yue Li60
Hi, The way you are trying to maintain your libraries is generally frowned upon. You shouldn't be trying to use R-2.14 packages with your R-2.14 install. You are exposing yourself to weird and hard to explain problems. Look at the error message you are getting: On Mon, Apr 23, 2012 at 3:36 PM, Yue Li <yueli at="" cs.toronto.edu=""> wrote: [snip] > Loading required package: locfit > locfit 1.5-7 ? ? 2012-03-22 > Error in dyn.load(file, DLLpath = DLLpath, ...) : > ?unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': > ?dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib > ?Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so > ?Reason: image not found > Error: package/namespace load failed for ?DESeq? Your trying to load a package from your 2.14 repo ... I'm not sure why this works from the terminal and not the GUI (are you sure you are firing up 2.15 from the terminal?), but I'm also not too inclined to smoke this out, because ... well, you shouldn't be doing this ;-) and also it will likely take you less time to just install things "the normal way". If you really have some compelling reason to have a custom library structure, I like the way the bioc folks suggest developers to keep bioc-devel package separate from bioc-release (now that R is on an annual release cycle), eg: http://www.bioconductor.org/developers/useDevel/ You could imagine having R-2.14 and R-2.15 in separate dirs instead of 2.15-release and 2.15-devel if working w/ devel libraries isn't your cup of tea -- but note they still keep different versions different. Anyway, the "normal" R install does this for you anyway on OS X, so dollars-to-donuts you'll have less hassles just going "the normal" route, and installing the package you need via biocLite again in your "clean" 2.15 library path will likely cost less time than trying to debug your custom library path woes. HTH, -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 REPLYlink written 7.4 years ago by Steve Lianoglou12k
Hi Steve, Thanks for prompt reply! It's just that having to re-install all of the packages for every upgrade of R is also a hassle, don't u think? But you're right that installing it improperly is even disastrous like what I am experiencing now. I wish in the future, someone could just make the upgrade of R as easy as upgrading iTunes or something like that. Yue On 2012-04-23, at 3:53 PM, Steve Lianoglou wrote: > Hi, > > The way you are trying to maintain your libraries is generally frowned > upon. You shouldn't be trying to use R-2.14 packages with your R-2.14 > install. You are exposing yourself to weird and hard to explain > problems. > > Look at the error message you are getting: > > On Mon, Apr 23, 2012 at 3:36 PM, Yue Li <yueli at="" cs.toronto.edu=""> wrote: > [snip] >> Loading required package: locfit >> locfit 1.5-7 2012-03-22 >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': >> dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib >> Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so >> Reason: image not found >> Error: package/namespace load failed for ?DESeq? > > Your trying to load a package from your 2.14 repo ... I'm not sure why > this works from the terminal and not the GUI (are you sure you are > firing up 2.15 from the terminal?), but I'm also not too inclined to > smoke this out, because ... well, you shouldn't be doing this ;-) and > also it will likely take you less time to just install things "the > normal way". > > If you really have some compelling reason to have a custom library > structure, I like the way the bioc folks suggest developers to keep > bioc-devel package separate from bioc-release (now that R is on an > annual release cycle), eg: > > http://www.bioconductor.org/developers/useDevel/ > > You could imagine having R-2.14 and R-2.15 in separate dirs instead of > 2.15-release and 2.15-devel if working w/ devel libraries isn't your > cup of tea -- but note they still keep different versions different. > > Anyway, the "normal" R install does this for you anyway on OS X, so > dollars-to-donuts you'll have less hassles just going "the normal" > route, and installing the package you need via biocLite again in your > "clean" 2.15 library path will likely cost less time than trying to > debug your custom library path woes. > > HTH, > -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 REPLYlink written 7.4 years ago by Yue Li370
Hi Yue, On Mon, Apr 23, 2012 at 1:10 PM, Yue Li <gorillayue at="" gmail.com=""> wrote: > Hi Steve, > > Thanks for prompt reply! It's just that having to re-install all of the packages for every upgrade of R is also a hassle, don't u think? But you're right that installing it improperly is even disastrous like what I am experiencing now. When you say "all of the packages," what do you mean? You only need to install the packages that you work with. There is no requirement to install all of them. Dan > > I wish in the future, someone could just make the upgrade of R as easy as upgrading iTunes or something like that. > > Yue > > > On 2012-04-23, at 3:53 PM, Steve Lianoglou wrote: > >> Hi, >> >> The way you are trying to maintain your libraries is generally frowned >> upon. You shouldn't be trying to use R-2.14 packages with your R-2.14 >> install. You are exposing yourself to weird and hard to explain >> problems. >> >> Look at the error message you are getting: >> >> On Mon, Apr 23, 2012 at 3:36 PM, Yue Li <yueli at="" cs.toronto.edu=""> wrote: >> [snip] >>> Loading required package: locfit >>> locfit 1.5-7 ? ? 2012-03-22 >>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>> unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': >>> dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib >>> Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so >>> Reason: image not found >>> Error: package/namespace load failed for ?DESeq? >> >> Your trying to load a package from your 2.14 repo ... I'm not sure why >> this works from the terminal and not the GUI (are you sure you are >> firing up 2.15 from the terminal?), but I'm also not too inclined to >> smoke this out, because ... well, you shouldn't be doing this ;-) and >> also it will likely take you less time to just install things "the >> normal way". >> >> If you really have some compelling reason to have a custom library >> structure, I like the way the bioc folks suggest developers to keep >> bioc-devel package separate from bioc-release (now that R is on an >> annual release cycle), eg: >> >> http://www.bioconductor.org/developers/useDevel/ >> >> You could imagine having R-2.14 and R-2.15 in separate dirs instead of >> 2.15-release and 2.15-devel if working w/ devel libraries isn't your >> cup of tea -- but note they still keep different versions different. >> >> Anyway, the "normal" R install does this for you anyway on OS X, so >> dollars-to-donuts you'll have less hassles just going "the normal" >> route, and installing the package you need via biocLite again in your >> "clean" 2.15 library path will likely cost less time than trying to >> debug your custom library path woes. >> >> HTH, >> -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 > > _______________________________________________ > 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 7.4 years ago by Dan Tenenbaum8.2k
Hi Dan, By "all of the packages", I meant the packages installed for R 2.14 not all of the packages from CRAN or Bioconductors. They work fine under terminal as shown below and most work fine in R GUI except for DESeq and DEXSeq ... Yue On 2012-04-23, at 4:39 PM, Dan Tenenbaum wrote: > Hi Yue, > > On Mon, Apr 23, 2012 at 1:10 PM, Yue Li <gorillayue at="" gmail.com=""> wrote: >> Hi Steve, >> >> Thanks for prompt reply! It's just that having to re-install all of the packages for every upgrade of R is also a hassle, don't u think? But you're right that installing it improperly is even disastrous like what I am experiencing now. > > When you say "all of the packages," what do you mean? You only need to > install the packages that you work with. There is no requirement to > install all of them. > > Dan > > > >> >> I wish in the future, someone could just make the upgrade of R as easy as upgrading iTunes or something like that. >> >> Yue >> >> >> On 2012-04-23, at 3:53 PM, Steve Lianoglou wrote: >> >>> Hi, >>> >>> The way you are trying to maintain your libraries is generally frowned >>> upon. You shouldn't be trying to use R-2.14 packages with your R-2.14 >>> install. You are exposing yourself to weird and hard to explain >>> problems. >>> >>> Look at the error message you are getting: >>> >>> On Mon, Apr 23, 2012 at 3:36 PM, Yue Li <yueli at="" cs.toronto.edu=""> wrote: >>> [snip] >>>> Loading required package: locfit >>>> locfit 1.5-7 2012-03-22 >>>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>>> unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': >>>> dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib >>>> Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so >>>> Reason: image not found >>>> Error: package/namespace load failed for ?DESeq? >>> >>> Your trying to load a package from your 2.14 repo ... I'm not sure why >>> this works from the terminal and not the GUI (are you sure you are >>> firing up 2.15 from the terminal?), but I'm also not too inclined to >>> smoke this out, because ... well, you shouldn't be doing this ;-) and >>> also it will likely take you less time to just install things "the >>> normal way". >>> >>> If you really have some compelling reason to have a custom library >>> structure, I like the way the bioc folks suggest developers to keep >>> bioc-devel package separate from bioc-release (now that R is on an >>> annual release cycle), eg: >>> >>> http://www.bioconductor.org/developers/useDevel/ >>> >>> You could imagine having R-2.14 and R-2.15 in separate dirs instead of >>> 2.15-release and 2.15-devel if working w/ devel libraries isn't your >>> cup of tea -- but note they still keep different versions different. >>> >>> Anyway, the "normal" R install does this for you anyway on OS X, so >>> dollars-to-donuts you'll have less hassles just going "the normal" >>> route, and installing the package you need via biocLite again in your >>> "clean" 2.15 library path will likely cost less time than trying to >>> debug your custom library path woes. >>> >>> HTH, >>> -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 >> >> _______________________________________________ >> 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 7.4 years ago by Yue Li370
On Mon, Apr 23, 2012 at 1:47 PM, Yue Li <gorillayue at="" gmail.com=""> wrote: > Hi Dan, > > By "all of the packages", I meant the packages installed for R 2.14 not all of the packages from CRAN or Bioconductors. > > They work fine under terminal as shown below and most work fine in R GUI except for DESeq and DEXSeq ... OK, thanks for the clarification. Dan > > Yue > > On 2012-04-23, at 4:39 PM, Dan Tenenbaum wrote: > >> Hi Yue, >> >> On Mon, Apr 23, 2012 at 1:10 PM, Yue Li <gorillayue at="" gmail.com=""> wrote: >>> Hi Steve, >>> >>> Thanks for prompt reply! It's just that having to re-install all of the packages for every upgrade of R is also a hassle, don't u think? But you're right that installing it improperly is even disastrous like what I am experiencing now. >> >> When you say "all of the packages," what do you mean? You only need to >> install the packages that you work with. There is no requirement to >> install all of them. >> >> Dan >> >> >> >>> >>> I wish in the future, someone could just make the upgrade of R as easy as upgrading iTunes or something like that. >>> >>> Yue >>> >>> >>> On 2012-04-23, at 3:53 PM, Steve Lianoglou wrote: >>> >>>> Hi, >>>> >>>> The way you are trying to maintain your libraries is generally frowned >>>> upon. You shouldn't be trying to use R-2.14 packages with your R-2.14 >>>> install. You are exposing yourself to weird and hard to explain >>>> problems. >>>> >>>> Look at the error message you are getting: >>>> >>>> On Mon, Apr 23, 2012 at 3:36 PM, Yue Li <yueli at="" cs.toronto.edu=""> wrote: >>>> [snip] >>>>> Loading required package: locfit >>>>> locfit 1.5-7 ? ? 2012-03-22 >>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>>>> unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': >>>>> dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib >>>>> Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so >>>>> Reason: image not found >>>>> Error: package/namespace load failed for ?DESeq? >>>> >>>> Your trying to load a package from your 2.14 repo ... I'm not sure why >>>> this works from the terminal and not the GUI (are you sure you are >>>> firing up 2.15 from the terminal?), but I'm also not too inclined to >>>> smoke this out, because ... well, you shouldn't be doing this ;-) and >>>> also it will likely take you less time to just install things "the >>>> normal way". >>>> >>>> If you really have some compelling reason to have a custom library >>>> structure, I like the way the bioc folks suggest developers to keep >>>> bioc-devel package separate from bioc-release (now that R is on an >>>> annual release cycle), eg: >>>> >>>> http://www.bioconductor.org/developers/useDevel/ >>>> >>>> You could imagine having R-2.14 and R-2.15 in separate dirs instead of >>>> 2.15-release and 2.15-devel if working w/ devel libraries isn't your >>>> cup of tea -- but note they still keep different versions different. >>>> >>>> Anyway, the "normal" R install does this for you anyway on OS X, so >>>> dollars-to-donuts you'll have less hassles just going "the normal" >>>> route, and installing the package you need via biocLite again in your >>>> "clean" 2.15 library path will likely cost less time than trying to >>>> debug your custom library path woes. >>>> >>>> HTH, >>>> -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 >>> >>> _______________________________________________ >>> 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 7.4 years ago by Dan Tenenbaum8.2k
Any helps on not having to manually re-install the packages for each R upgrade would be greatly appreciated! I followed this post but apparently not be able to make the upgrade seamless ... https://stat.ethz.ch/pipermail/r-sig-mac/2008-August/005276.html On 2012-04-23, at 4:54 PM, Dan Tenenbaum wrote: > On Mon, Apr 23, 2012 at 1:47 PM, Yue Li <gorillayue@gmail.com> wrote: >> Hi Dan, >> >> By "all of the packages", I meant the packages installed for R 2.14 not all of the packages from CRAN or Bioconductors. >> >> They work fine under terminal as shown below and most work fine in R GUI except for DESeq and DEXSeq ... > > OK, thanks for the clarification. > > Dan > > >> >> Yue >> >> On 2012-04-23, at 4:39 PM, Dan Tenenbaum wrote: >> >>> Hi Yue, >>> >>> On Mon, Apr 23, 2012 at 1:10 PM, Yue Li <gorillayue@gmail.com> wrote: >>>> Hi Steve, >>>> >>>> Thanks for prompt reply! It's just that having to re-install all of the packages for every upgrade of R is also a hassle, don't u think? But you're right that installing it improperly is even disastrous like what I am experiencing now. >>> >>> When you say "all of the packages," what do you mean? You only need to >>> install the packages that you work with. There is no requirement to >>> install all of them. >>> >>> Dan >>> >>> >>> >>>> >>>> I wish in the future, someone could just make the upgrade of R as easy as upgrading iTunes or something like that. >>>> >>>> Yue >>>> >>>> >>>> On 2012-04-23, at 3:53 PM, Steve Lianoglou wrote: >>>> >>>>> Hi, >>>>> >>>>> The way you are trying to maintain your libraries is generally frowned >>>>> upon. You shouldn't be trying to use R-2.14 packages with your R-2.14 >>>>> install. You are exposing yourself to weird and hard to explain >>>>> problems. >>>>> >>>>> Look at the error message you are getting: >>>>> >>>>> On Mon, Apr 23, 2012 at 3:36 PM, Yue Li <yueli@cs.toronto.edu> wrote: >>>>> [snip] >>>>>> Loading required package: locfit >>>>>> locfit 1.5-7 2012-03-22 >>>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>>>>> unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': >>>>>> dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib >>>>>> Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so >>>>>> Reason: image not found >>>>>> Error: package/namespace load failed for ‘DESeq’ >>>>> >>>>> Your trying to load a package from your 2.14 repo ... I'm not sure why >>>>> this works from the terminal and not the GUI (are you sure you are >>>>> firing up 2.15 from the terminal?), but I'm also not too inclined to >>>>> smoke this out, because ... well, you shouldn't be doing this ;-) and >>>>> also it will likely take you less time to just install things "the >>>>> normal way". >>>>> >>>>> If you really have some compelling reason to have a custom library >>>>> structure, I like the way the bioc folks suggest developers to keep >>>>> bioc-devel package separate from bioc-release (now that R is on an >>>>> annual release cycle), eg: >>>>> >>>>> http://www.bioconductor.org/developers/useDevel/ >>>>> >>>>> You could imagine having R-2.14 and R-2.15 in separate dirs instead of >>>>> 2.15-release and 2.15-devel if working w/ devel libraries isn't your >>>>> cup of tea -- but note they still keep different versions different. >>>>> >>>>> Anyway, the "normal" R install does this for you anyway on OS X, so >>>>> dollars-to-donuts you'll have less hassles just going "the normal" >>>>> route, and installing the package you need via biocLite again in your >>>>> "clean" 2.15 library path will likely cost less time than trying to >>>>> debug your custom library path woes. >>>>> >>>>> HTH, >>>>> -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 >>>> >>>> _______________________________________________ >>>> 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 >> [[alternative HTML version deleted]]
ADD REPLYlink written 7.4 years ago by Yue Li370
On Mon, Apr 23, 2012 at 2:11 PM, Yue Li <gorillayue at="" gmail.com=""> wrote: > Any helps on not having to manually re-install the packages for each R > upgrade would be greatly appreciated! I followed this post but apparently > not be able to make the upgrade seamless ... > I echo Steve in saying this is not really recommended. For a given version of R, you should be using the appropriate version of Bioconductor. If it makes it easier, you can go into R 2.14 and get a list of the packages you have installed with pkgs <- installed.packages()[,"Package"] You can then take this list and use it as an argument to biocLite() in R 2.15. However, the list will include packages that are part of R so these will not install properly. Dan > https://stat.ethz.ch/pipermail/r-sig-mac/2008-August/005276.html > > > On 2012-04-23, at 4:54 PM, Dan Tenenbaum wrote: > > On Mon, Apr 23, 2012 at 1:47 PM, Yue Li <gorillayue at="" gmail.com=""> wrote: > > Hi Dan, > > > By "all of the packages", I meant the packages installed for R 2.14 not all > of the packages from CRAN or Bioconductors. > > > They work fine under terminal as shown below and most work fine in R GUI > except for DESeq and DEXSeq ... > > > OK, thanks for the clarification. > > Dan > > > > Yue > > > On 2012-04-23, at 4:39 PM, Dan Tenenbaum wrote: > > > Hi Yue, > > > On Mon, Apr 23, 2012 at 1:10 PM, Yue Li <gorillayue at="" gmail.com=""> wrote: > > Hi Steve, > > > Thanks for prompt reply! It's just that having to re-install all of the > packages for every upgrade of R is also a hassle, don't u think? But you're > right that installing it improperly is even disastrous like what I am > experiencing now. > > > When you say "all of the packages," what do you mean? You only need to > > install the packages that you work with. There is no requirement to > > install all of them. > > > Dan > > > > > > I wish in the future, someone could just make the upgrade of R as easy as > upgrading iTunes or something like that. > > > Yue > > > > On 2012-04-23, at 3:53 PM, Steve Lianoglou wrote: > > > Hi, > > > The way you are trying to maintain your libraries is generally frowned > > upon. You shouldn't be trying to use R-2.14 packages with your R-2.14 > > install. You are exposing yourself to weird and hard to explain > > problems. > > > Look at the error message you are getting: > > > On Mon, Apr 23, 2012 at 3:36 PM, Yue Li <yueli at="" cs.toronto.edu=""> wrote: > > [snip] > > Loading required package: locfit > > locfit 1.5-7 ? ? 2012-03-22 > > Error in dyn.load(file, DLLpath = DLLpath, ...) : > > unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': > > dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: > /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib > > Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so > > Reason: image not found > > Error: package/namespace load failed for ?DESeq? > > > Your trying to load a package from your 2.14 repo ... I'm not sure why > > this works from the terminal and not the GUI (are you sure you are > > firing up 2.15 from the terminal?), but I'm also not too inclined to > > smoke this out, because ... well, you shouldn't be doing this ;-) and > > also it will likely take you less time to just install things "the > > normal way". > > > If you really have some compelling reason to have a custom library > > structure, I like the way the bioc folks suggest developers to keep > > bioc-devel package separate from bioc-release (now that R is on an > > annual release cycle), eg: > > > http://www.bioconductor.org/developers/useDevel/ > > > You could imagine having R-2.14 and R-2.15 in separate dirs instead of > > 2.15-release and 2.15-devel if working w/ devel libraries isn't your > > cup of tea -- but note they still keep different versions different. > > > Anyway, the "normal" R install does this for you anyway on OS X, so > > dollars-to-donuts you'll have less hassles just going "the normal" > > route, and installing the package you need via biocLite again in your > > "clean" 2.15 library path will likely cost less time than trying to > > debug your custom library path woes. > > > HTH, > > -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 > > > _______________________________________________ > > 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 7.4 years ago by Dan Tenenbaum8.2k
On 4/23/2012 5:17 PM, Dan Tenenbaum wrote: > On Mon, Apr 23, 2012 at 2:11 PM, Yue Li<gorillayue at="" gmail.com=""> wrote: >> Any helps on not having to manually re-install the packages for each R >> upgrade would be greatly appreciated! I followed this post but apparently >> not be able to make the upgrade seamless ... >> > I echo Steve in saying this is not really recommended. > For a given version of R, you should be using the appropriate version > of Bioconductor. > > If it makes it easier, you can go into R 2.14 and get a list of the > packages you have installed with > pkgs<- installed.packages()[,"Package"] > > You can then take this list and use it as an argument to biocLite() in R 2.15. > However, the list will include packages that are part of R so these > will not install properly. Or alternatively, x <- installed.packages() y <- row.names(x)[-grep("Part", x[,11])] Then you can write that out and scan() it back into your new R version. Best, Jim > > Dan > > >> https://stat.ethz.ch/pipermail/r-sig-mac/2008-August/005276.html >> >> >> On 2012-04-23, at 4:54 PM, Dan Tenenbaum wrote: >> >> On Mon, Apr 23, 2012 at 1:47 PM, Yue Li<gorillayue at="" gmail.com=""> wrote: >> >> Hi Dan, >> >> >> By "all of the packages", I meant the packages installed for R 2.14 not all >> of the packages from CRAN or Bioconductors. >> >> >> They work fine under terminal as shown below and most work fine in R GUI >> except for DESeq and DEXSeq ... >> >> >> OK, thanks for the clarification. >> >> Dan >> >> >> >> Yue >> >> >> On 2012-04-23, at 4:39 PM, Dan Tenenbaum wrote: >> >> >> Hi Yue, >> >> >> On Mon, Apr 23, 2012 at 1:10 PM, Yue Li<gorillayue at="" gmail.com=""> wrote: >> >> Hi Steve, >> >> >> Thanks for prompt reply! It's just that having to re-install all of the >> packages for every upgrade of R is also a hassle, don't u think? But you're >> right that installing it improperly is even disastrous like what I am >> experiencing now. >> >> >> When you say "all of the packages," what do you mean? You only need to >> >> install the packages that you work with. There is no requirement to >> >> install all of them. >> >> >> Dan >> >> >> >> >> >> I wish in the future, someone could just make the upgrade of R as easy as >> upgrading iTunes or something like that. >> >> >> Yue >> >> >> >> On 2012-04-23, at 3:53 PM, Steve Lianoglou wrote: >> >> >> Hi, >> >> >> The way you are trying to maintain your libraries is generally frowned >> >> upon. You shouldn't be trying to use R-2.14 packages with your R-2.14 >> >> install. You are exposing yourself to weird and hard to explain >> >> problems. >> >> >> Look at the error message you are getting: >> >> >> On Mon, Apr 23, 2012 at 3:36 PM, Yue Li<yueli at="" cs.toronto.edu=""> wrote: >> >> [snip] >> >> Loading required package: locfit >> >> locfit 1.5-7 2012-03-22 >> >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> >> unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': >> >> dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: >> /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib >> >> Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so >> >> Reason: image not found >> >> Error: package/namespace load failed for ?DESeq? >> >> >> Your trying to load a package from your 2.14 repo ... I'm not sure why >> >> this works from the terminal and not the GUI (are you sure you are >> >> firing up 2.15 from the terminal?), but I'm also not too inclined to >> >> smoke this out, because ... well, you shouldn't be doing this ;-) and >> >> also it will likely take you less time to just install things "the >> >> normal way". >> >> >> If you really have some compelling reason to have a custom library >> >> structure, I like the way the bioc folks suggest developers to keep >> >> bioc-devel package separate from bioc-release (now that R is on an >> >> annual release cycle), eg: >> >> >> http://www.bioconductor.org/developers/useDevel/ >> >> >> You could imagine having R-2.14 and R-2.15 in separate dirs instead of >> >> 2.15-release and 2.15-devel if working w/ devel libraries isn't your >> >> cup of tea -- but note they still keep different versions different. >> >> >> Anyway, the "normal" R install does this for you anyway on OS X, so >> >> dollars-to-donuts you'll have less hassles just going "the normal" >> >> route, and installing the package you need via biocLite again in your >> >> "clean" 2.15 library path will likely cost less time than trying to >> >> debug your custom library path woes. >> >> >> HTH, >> >> -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 >> >> >> _______________________________________________ >> >> 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 >> >> >> > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD REPLYlink written 7.4 years ago by James W. MacDonald51k
Thanks Jim! That seems more automated upgrade. So basically we reinstall all existing packages that are NOT "Part of R 2.14.1" when upgrading to "Part of R 2.15". I will try that out and let you guys know how that goes! On 2012-04-23, at 5:23 PM, James W. MacDonald wrote: > > > On 4/23/2012 5:17 PM, Dan Tenenbaum wrote: >> On Mon, Apr 23, 2012 at 2:11 PM, Yue Li<gorillayue at="" gmail.com=""> wrote: >>> Any helps on not having to manually re-install the packages for each R >>> upgrade would be greatly appreciated! I followed this post but apparently >>> not be able to make the upgrade seamless ... >>> >> I echo Steve in saying this is not really recommended. >> For a given version of R, you should be using the appropriate version >> of Bioconductor. >> >> If it makes it easier, you can go into R 2.14 and get a list of the >> packages you have installed with >> pkgs<- installed.packages()[,"Package"] >> >> You can then take this list and use it as an argument to biocLite() in R 2.15. >> However, the list will include packages that are part of R so these >> will not install properly. > > Or alternatively, > > x <- installed.packages() > y <- row.names(x)[-grep("Part", x[,11])] > > Then you can write that out and scan() it back into your new R version. > > Best, > > Jim > > > > >> >> Dan >> >> >>> https://stat.ethz.ch/pipermail/r-sig-mac/2008-August/005276.html >>> >>> >>> On 2012-04-23, at 4:54 PM, Dan Tenenbaum wrote: >>> >>> On Mon, Apr 23, 2012 at 1:47 PM, Yue Li<gorillayue at="" gmail.com=""> wrote: >>> >>> Hi Dan, >>> >>> >>> By "all of the packages", I meant the packages installed for R 2.14 not all >>> of the packages from CRAN or Bioconductors. >>> >>> >>> They work fine under terminal as shown below and most work fine in R GUI >>> except for DESeq and DEXSeq ... >>> >>> >>> OK, thanks for the clarification. >>> >>> Dan >>> >>> >>> >>> Yue >>> >>> >>> On 2012-04-23, at 4:39 PM, Dan Tenenbaum wrote: >>> >>> >>> Hi Yue, >>> >>> >>> On Mon, Apr 23, 2012 at 1:10 PM, Yue Li<gorillayue at="" gmail.com=""> wrote: >>> >>> Hi Steve, >>> >>> >>> Thanks for prompt reply! It's just that having to re-install all of the >>> packages for every upgrade of R is also a hassle, don't u think? But you're >>> right that installing it improperly is even disastrous like what I am >>> experiencing now. >>> >>> >>> When you say "all of the packages," what do you mean? You only need to >>> >>> install the packages that you work with. There is no requirement to >>> >>> install all of them. >>> >>> >>> Dan >>> >>> >>> >>> >>> >>> I wish in the future, someone could just make the upgrade of R as easy as >>> upgrading iTunes or something like that. >>> >>> >>> Yue >>> >>> >>> >>> On 2012-04-23, at 3:53 PM, Steve Lianoglou wrote: >>> >>> >>> Hi, >>> >>> >>> The way you are trying to maintain your libraries is generally frowned >>> >>> upon. You shouldn't be trying to use R-2.14 packages with your R-2.14 >>> >>> install. You are exposing yourself to weird and hard to explain >>> >>> problems. >>> >>> >>> Look at the error message you are getting: >>> >>> >>> On Mon, Apr 23, 2012 at 3:36 PM, Yue Li<yueli at="" cs.toronto.edu=""> wrote: >>> >>> [snip] >>> >>> Loading required package: locfit >>> >>> locfit 1.5-7 2012-03-22 >>> >>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>> >>> unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': >>> >>> dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: >>> /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib >>> >>> Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so >>> >>> Reason: image not found >>> >>> Error: package/namespace load failed for ?DESeq? >>> >>> >>> Your trying to load a package from your 2.14 repo ... I'm not sure why >>> >>> this works from the terminal and not the GUI (are you sure you are >>> >>> firing up 2.15 from the terminal?), but I'm also not too inclined to >>> >>> smoke this out, because ... well, you shouldn't be doing this ;-) and >>> >>> also it will likely take you less time to just install things "the >>> >>> normal way". >>> >>> >>> If you really have some compelling reason to have a custom library >>> >>> structure, I like the way the bioc folks suggest developers to keep >>> >>> bioc-devel package separate from bioc-release (now that R is on an >>> >>> annual release cycle), eg: >>> >>> >>> http://www.bioconductor.org/developers/useDevel/ >>> >>> >>> You could imagine having R-2.14 and R-2.15 in separate dirs instead of >>> >>> 2.15-release and 2.15-devel if working w/ devel libraries isn't your >>> >>> cup of tea -- but note they still keep different versions different. >>> >>> >>> Anyway, the "normal" R install does this for you anyway on OS X, so >>> >>> dollars-to-donuts you'll have less hassles just going "the normal" >>> >>> route, and installing the package you need via biocLite again in your >>> >>> "clean" 2.15 library path will likely cost less time than trying to >>> >>> debug your custom library path woes. >>> >>> >>> HTH, >>> >>> -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 >>> >>> >>> _______________________________________________ >>> >>> 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 >>> >>> >>> >> _______________________________________________ >> 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 > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 >
ADD REPLYlink written 7.4 years ago by Yue Li370
Just to let you guys know that the tips suggested by Jim work gracefully, and I would recommend all R users (at least Unix users) to follow that when upgrading their R! Thanks very much. On 2012-04-23, at 5:30 PM, Yue Li wrote: > Thanks Jim! That seems more automated upgrade. So basically we reinstall all existing packages that are NOT "Part of R 2.14.1" when upgrading to "Part of R 2.15". > > I will try that out and let you guys know how that goes! > > > On 2012-04-23, at 5:23 PM, James W. MacDonald wrote: > >> >> >> On 4/23/2012 5:17 PM, Dan Tenenbaum wrote: >>> On Mon, Apr 23, 2012 at 2:11 PM, Yue Li<gorillayue at="" gmail.com=""> wrote: >>>> Any helps on not having to manually re-install the packages for each R >>>> upgrade would be greatly appreciated! I followed this post but apparently >>>> not be able to make the upgrade seamless ... >>>> >>> I echo Steve in saying this is not really recommended. >>> For a given version of R, you should be using the appropriate version >>> of Bioconductor. >>> >>> If it makes it easier, you can go into R 2.14 and get a list of the >>> packages you have installed with >>> pkgs<- installed.packages()[,"Package"] >>> >>> You can then take this list and use it as an argument to biocLite() in R 2.15. >>> However, the list will include packages that are part of R so these >>> will not install properly. >> >> Or alternatively, >> >> x <- installed.packages() >> y <- row.names(x)[-grep("Part", x[,11])] >> >> Then you can write that out and scan() it back into your new R version. >> >> Best, >> >> Jim >> >> >> >> >>> >>> Dan >>> >>> >>>> https://stat.ethz.ch/pipermail/r-sig-mac/2008-August/005276.html >>>> >>>> >>>> On 2012-04-23, at 4:54 PM, Dan Tenenbaum wrote: >>>> >>>> On Mon, Apr 23, 2012 at 1:47 PM, Yue Li<gorillayue at="" gmail.com=""> wrote: >>>> >>>> Hi Dan, >>>> >>>> >>>> By "all of the packages", I meant the packages installed for R 2.14 not all >>>> of the packages from CRAN or Bioconductors. >>>> >>>> >>>> They work fine under terminal as shown below and most work fine in R GUI >>>> except for DESeq and DEXSeq ... >>>> >>>> >>>> OK, thanks for the clarification. >>>> >>>> Dan >>>> >>>> >>>> >>>> Yue >>>> >>>> >>>> On 2012-04-23, at 4:39 PM, Dan Tenenbaum wrote: >>>> >>>> >>>> Hi Yue, >>>> >>>> >>>> On Mon, Apr 23, 2012 at 1:10 PM, Yue Li<gorillayue at="" gmail.com=""> wrote: >>>> >>>> Hi Steve, >>>> >>>> >>>> Thanks for prompt reply! It's just that having to re-install all of the >>>> packages for every upgrade of R is also a hassle, don't u think? But you're >>>> right that installing it improperly is even disastrous like what I am >>>> experiencing now. >>>> >>>> >>>> When you say "all of the packages," what do you mean? You only need to >>>> >>>> install the packages that you work with. There is no requirement to >>>> >>>> install all of them. >>>> >>>> >>>> Dan >>>> >>>> >>>> >>>> >>>> >>>> I wish in the future, someone could just make the upgrade of R as easy as >>>> upgrading iTunes or something like that. >>>> >>>> >>>> Yue >>>> >>>> >>>> >>>> On 2012-04-23, at 3:53 PM, Steve Lianoglou wrote: >>>> >>>> >>>> Hi, >>>> >>>> >>>> The way you are trying to maintain your libraries is generally frowned >>>> >>>> upon. You shouldn't be trying to use R-2.14 packages with your R-2.14 >>>> >>>> install. You are exposing yourself to weird and hard to explain >>>> >>>> problems. >>>> >>>> >>>> Look at the error message you are getting: >>>> >>>> >>>> On Mon, Apr 23, 2012 at 3:36 PM, Yue Li<yueli at="" cs.toronto.edu=""> wrote: >>>> >>>> [snip] >>>> >>>> Loading required package: locfit >>>> >>>> locfit 1.5-7 2012-03-22 >>>> >>>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>>> >>>> unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': >>>> >>>> dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: >>>> /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib >>>> >>>> Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so >>>> >>>> Reason: image not found >>>> >>>> Error: package/namespace load failed for ?DESeq? >>>> >>>> >>>> Your trying to load a package from your 2.14 repo ... I'm not sure why >>>> >>>> this works from the terminal and not the GUI (are you sure you are >>>> >>>> firing up 2.15 from the terminal?), but I'm also not too inclined to >>>> >>>> smoke this out, because ... well, you shouldn't be doing this ;-) and >>>> >>>> also it will likely take you less time to just install things "the >>>> >>>> normal way". >>>> >>>> >>>> If you really have some compelling reason to have a custom library >>>> >>>> structure, I like the way the bioc folks suggest developers to keep >>>> >>>> bioc-devel package separate from bioc-release (now that R is on an >>>> >>>> annual release cycle), eg: >>>> >>>> >>>> http://www.bioconductor.org/developers/useDevel/ >>>> >>>> >>>> You could imagine having R-2.14 and R-2.15 in separate dirs instead of >>>> >>>> 2.15-release and 2.15-devel if working w/ devel libraries isn't your >>>> >>>> cup of tea -- but note they still keep different versions different. >>>> >>>> >>>> Anyway, the "normal" R install does this for you anyway on OS X, so >>>> >>>> dollars-to-donuts you'll have less hassles just going "the normal" >>>> >>>> route, and installing the package you need via biocLite again in your >>>> >>>> "clean" 2.15 library path will likely cost less time than trying to >>>> >>>> debug your custom library path woes. >>>> >>>> >>>> HTH, >>>> >>>> -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 >>>> >>>> >>>> _______________________________________________ >>>> >>>> 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 >>>> >>>> >>>> >>> _______________________________________________ >>> 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 >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >
ADD REPLYlink written 7.4 years ago by Yue Li370
On Mon, Apr 23, 2012 at 2:11 PM, Yue Li <gorillayue at="" gmail.com=""> wrote: > Any helps on not having to manually re-install the packages for each R > upgrade would be greatly appreciated! I followed this post but apparently > not be able to make the upgrade seamless ... > I echo Steve in saying this is not really recommended. For a given version of R, you should be using the appropriate version of Bioconductor. If it makes it easier, you can go into R 2.14 and get a list of the packages you have installed with pkgs <- installed.packages()[,"Package"] You can then take this list and use it as an argument to biocLite() in R 2.15. However, the list will include packages that are part of R so these will not install properly. Dan > https://stat.ethz.ch/pipermail/r-sig-mac/2008-August/005276.html > > > On 2012-04-23, at 4:54 PM, Dan Tenenbaum wrote: > > On Mon, Apr 23, 2012 at 1:47 PM, Yue Li <gorillayue at="" gmail.com=""> wrote: > > Hi Dan, > > > By "all of the packages", I meant the packages installed for R 2.14 not all > of the packages from CRAN or Bioconductors. > > > They work fine under terminal as shown below and most work fine in R GUI > except for DESeq and DEXSeq ... > > > OK, thanks for the clarification. > > Dan > > > > Yue > > > On 2012-04-23, at 4:39 PM, Dan Tenenbaum wrote: > > > Hi Yue, > > > On Mon, Apr 23, 2012 at 1:10 PM, Yue Li <gorillayue at="" gmail.com=""> wrote: > > Hi Steve, > > > Thanks for prompt reply! It's just that having to re-install all of the > packages for every upgrade of R is also a hassle, don't u think? But you're > right that installing it improperly is even disastrous like what I am > experiencing now. > > > When you say "all of the packages," what do you mean? You only need to > > install the packages that you work with. There is no requirement to > > install all of them. > > > Dan > > > > > > I wish in the future, someone could just make the upgrade of R as easy as > upgrading iTunes or something like that. > > > Yue > > > > On 2012-04-23, at 3:53 PM, Steve Lianoglou wrote: > > > Hi, > > > The way you are trying to maintain your libraries is generally frowned > > upon. You shouldn't be trying to use R-2.14 packages with your R-2.14 > > install. You are exposing yourself to weird and hard to explain > > problems. > > > Look at the error message you are getting: > > > On Mon, Apr 23, 2012 at 3:36 PM, Yue Li <yueli at="" cs.toronto.edu=""> wrote: > > [snip] > > Loading required package: locfit > > locfit 1.5-7 ? ? 2012-03-22 > > Error in dyn.load(file, DLLpath = DLLpath, ...) : > > unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': > > dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: > /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib > > Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so > > Reason: image not found > > Error: package/namespace load failed for ?DESeq? > > > Your trying to load a package from your 2.14 repo ... I'm not sure why > > this works from the terminal and not the GUI (are you sure you are > > firing up 2.15 from the terminal?), but I'm also not too inclined to > > smoke this out, because ... well, you shouldn't be doing this ;-) and > > also it will likely take you less time to just install things "the > > normal way". > > > If you really have some compelling reason to have a custom library > > structure, I like the way the bioc folks suggest developers to keep > > bioc-devel package separate from bioc-release (now that R is on an > > annual release cycle), eg: > > > http://www.bioconductor.org/developers/useDevel/ > > > You could imagine having R-2.14 and R-2.15 in separate dirs instead of > > 2.15-release and 2.15-devel if working w/ devel libraries isn't your > > cup of tea -- but note they still keep different versions different. > > > Anyway, the "normal" R install does this for you anyway on OS X, so > > dollars-to-donuts you'll have less hassles just going "the normal" > > route, and installing the package you need via biocLite again in your > > "clean" 2.15 library path will likely cost less time than trying to > > debug your custom library path woes. > > > HTH, > > -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 > > > _______________________________________________ > > 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 7.4 years ago by Dan Tenenbaum8.2k
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