Question: Unable to use GEOquery (SOLVED)
0
gravatar for Juan C Oliveros Collazos
11.6 years ago by
Juan C Oliveros Collazos190 wrote:
Sean, I did what you said and now GEOquery is running properly. I think biocLite also installs a number of additional packages needed for GEOquery to work. Thanks a lot! Best, Juan Carlos Sean Davis wrote: > On Thu, Apr 17, 2008 at 6:21 AM, Juan C Oliveros Collazos > <oliveros at="" cnb.csic.es=""> wrote: >> Hi all, >> >> I just downloadad and installed the package "GEOquery" from bioconductor >> web site. The installation carried-out with no errors. > > Hi, Juan. You might want to try again. First, remove the package > with remove.packages('GEOquery'). Then, type: > > source('http://bioconductor.org/biocLite.R') > biocLite('GEOquery') > > Does this fix the problem? > > Sean > > >> However, when I try to load the library: "library(GEOquery)", I get the >> following error: >> >> ------------------------------------------------------------------ ------- >> > library(GEOquery); >> Error in makeClassRepresentation(Class, properties, superClasses, >> prototype, : >> element 2 is empty; >> the part of the args list of 'list' being evaluated was: >> (header = list(), ) >> Error : unable to load R code in package 'GEOquery' >> Error: package/namespace load failed for 'GEOquery' >> ------------------------------------------------------------------ ------ >> >> >> This is the sessionInfo() output: >> ------------------------------------------------------------------ ------ >> > sessionInfo(); >> R version 2.6.0 (2007-10-03) >> i686-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en _US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.U TF-8;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] Biobase_1.16.1 limma_2.12.0 >> >> loaded via a namespace (and not attached): >> [1] rcompgen_0.1-15 >> ---------------------------------------------------------------------- >> >> Looking at this output, It seems that the package is not installed. >> However, when i do "installed.packages()" GEOquery appears in the list! >> >> I can not figure-out where the error is... >> >> Any help? >> >> Thanks in advance! >> >> Best, >> >> Juan Carlos >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > -- Juan Carlos Oliveros BioinfoGP, CNB-CSIC ** NEW EMAIL ADDRESS: oliveros at cnb.csic.es **
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ADD COMMENTlink modified 11.6 years ago by Sean Davis21k • written 11.6 years ago by Juan C Oliveros Collazos190
Answer: Unable to use GEOquery (SOLVED)
0
gravatar for Sean Davis
11.6 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Thu, Apr 17, 2008 at 9:39 AM, Juan C Oliveros Collazos <oliveros at="" cnb.csic.es=""> wrote: > Sean, > > I did what you said and now GEOquery is running properly. > > I think biocLite also installs a number of additional packages needed for > GEOquery to work. > > Thanks a lot! That is great to hear, Juan. Just to be clear, you should ALWAYS use biocLite to install packages. It will save you a great deal of headache in the future. Sean > Sean Davis wrote: > > > On Thu, Apr 17, 2008 at 6:21 AM, Juan C Oliveros Collazos > > <oliveros at="" cnb.csic.es=""> wrote: > > > > > Hi all, > > > > > > I just downloadad and installed the package "GEOquery" from > bioconductor > > > web site. The installation carried-out with no errors. > > > > > > > Hi, Juan. You might want to try again. First, remove the package > > with remove.packages('GEOquery'). Then, type: > > > > source('http://bioconductor.org/biocLite.R') > > biocLite('GEOquery') > > > > Does this fix the problem? > > > > Sean > > > > > > > > > However, when I try to load the library: "library(GEOquery)", I get the > > > following error: > > > > > > > -------------------------------------------------------------------- ----- > > > > library(GEOquery); > > > Error in makeClassRepresentation(Class, properties, superClasses, > > > prototype, : > > > element 2 is empty; > > > the part of the args list of 'list' being evaluated was: > > > (header = list(), ) > > > Error : unable to load R code in package 'GEOquery' > > > Error: package/namespace load failed for 'GEOquery' > > > > -------------------------------------------------------------------- ---- > > > > > > > > > This is the sessionInfo() output: > > > > -------------------------------------------------------------------- ---- > > > > sessionInfo(); > > > R version 2.6.0 (2007-10-03) > > > i686-pc-linux-gnu > > > > > > locale: > > > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > > > > > attached base packages: > > > [1] tools stats graphics grDevices utils datasets methods > > > [8] base > > > > > > other attached packages: > > > [1] Biobase_1.16.1 limma_2.12.0 > > > > > > loaded via a namespace (and not attached): > > > [1] rcompgen_0.1-15 > > > ---------------------------------------------------------------------- > > > > > > Looking at this output, It seems that the package is not installed. > > > However, when i do "installed.packages()" GEOquery appears in the list! > > > > > > I can not figure-out where the error is... > > > > > > Any help? > > > > > > Thanks in advance! > > > > > > Best, > > > > > > Juan Carlos > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > > > -- > Juan Carlos Oliveros > BioinfoGP, CNB-CSIC > > ** NEW EMAIL ADDRESS: oliveros at cnb.csic.es ** >
ADD COMMENTlink written 11.6 years ago by Sean Davis21k
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