Question: install pdInfoBuilder package
0
gravatar for Julie Collet
7.0 years ago by
Julie Collet40
Julie Collet40 wrote:
Dear all, I created an annotation package with pdInfoBuilder. All looked like it worked. I first tried to install it directly with R by - Creating a zip file (with winzip or 7 zip) - Installing it directly with R by install.packages("pd.110608.dser.sc.expr.zip", repos=NULL) All looked like it worked until I call the library and get > library(pd.110608.dser.sc.expr) Error in library(pd.110608.dser.sc.expr) : 'pd.110608.dser.sc.expr' is not a valid installed package I then tried with R tools following http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html And got the following message error on the gcc-4.6.3 session Starting program: CMD INSTALL -build pd.110608.dser.sc.expr No executable specified, use 'target exec'. I played around with various combinations of path that would make sense to me. But 1) I'm not sure this is where the problem come from 2) I have a very limited notion of what 'path' means so I'm not sure what should actually be in the path and in what order. You'd have guessed, I'm on Windows (7). Many thanks for your help, Julie [[alternative HTML version deleted]]
annotation pdinfobuilder • 760 views
ADD COMMENTlink modified 7.0 years ago by Benilton Carvalho4.3k • written 7.0 years ago by Julie Collet40
Answer: install pdInfoBuilder package
0
gravatar for Benilton Carvalho
7.0 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k wrote:
Hi Julie, The first step is to identify where you have the directory (containing the package) created by pdInfoBuilder. I don't have a Windows machine to try with more realistic "names", but suppose you the directory 'pd.110608.dser.sc.expr' is inside the 'folder' "C:/MyDocuments". So, I'd do the following (from within R): setwd("C:/MyDocuments") install.packages('pd.110608.dser.sc.expr', type='source') and that would be it... Can you please try and let me know exactly what output you get? b On 27 November 2012 07:10, Julie Collet <j.collet@uq.edu.au> wrote: > Dear all, > > I created an annotation package with pdInfoBuilder. All looked like it > worked. I first tried to install it directly with R by > - Creating a zip file (with winzip or 7 zip) > - Installing it directly with R by > install.packages("pd.110608.dser.sc.expr.zip", repos=NULL) > All looked like it worked until I call the library and get > > library(pd.110608.dser.sc.expr) > Error in library(pd.110608.dser.sc.expr) : > 'pd.110608.dser.sc.expr' is not a valid installed package > > I then tried with R tools following > http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html > And got the following message error on the gcc-4.6.3 session > Starting program: CMD INSTALL -build pd.110608.dser.sc.expr > No executable specified, use 'target exec'. > I played around with various combinations of path that would make sense to > me. But 1) I'm not sure this is where the problem come from 2) I have a > very limited notion of what 'path' means so I'm not sure what should > actually be in the path and in what order. > > You'd have guessed, I'm on Windows (7). > > Many thanks for your help, > Julie > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 COMMENTlink written 7.0 years ago by Benilton Carvalho4.3k
Hi Benito, Many thanks for your help. I initially tried: > setwd("C:/Users/uqjcol10/Desktop") > install.packages("pd.110608.dser.sc.expr.zip", repos=NULL) > library(pd.110608.dser.sc.expr) Error in library(pd.110608.dser.sc.expr) : 'pd.110608.dser.sc.expr' is not a valid installed package So the installation didn't give any error message, I could just not access the library. Following your message I tried: > install.packages("pd.110608.dser.sc.expr", repos=NULL, type='source') --- Please select a CRAN mirror for use in this session --- * installing *source* package 'pd.110608.dser.sc.expr' ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded *** arch - i386 Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'SQLite' *** arch - x64 Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'SQLite' * DONE (pd.110608.dser.sc.expr) > library(pd.110608.dser.sc.expr) Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'SQLite' Should I worry about the Warning message or is it completely normal? It surely looks much more promising. Many thanks for your help, Julie From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com] Sent: Tuesday, 27 November 2012 8:04 PM To: Julie Collet Cc: bioconductor@r-project.org Subject: Re: [BioC] install pdInfoBuilder package Hi Julie, The first step is to identify where you have the directory (containing the package) created by pdInfoBuilder. I don't have a Windows machine to try with more realistic "names", but suppose you the directory 'pd.110608.dser.sc.expr' is inside the 'folder' "C:/MyDocuments". So, I'd do the following (from within R): setwd("C:/MyDocuments") install.packages('pd.110608.dser.sc.expr', type='source') and that would be it... Can you please try and let me know exactly what output you get? b On 27 November 2012 07:10, Julie Collet <j.collet@uq.edu.au<mailto:j.collet@uq.edu.au>> wrote: Dear all, I created an annotation package with pdInfoBuilder. All looked like it worked. I first tried to install it directly with R by - Creating a zip file (with winzip or 7 zip) - Installing it directly with R by install.packages("pd.110608.dser.sc.expr.zip", repos=NULL) All looked like it worked until I call the library and get > library(pd.110608.dser.sc.expr) Error in library(pd.110608.dser.sc.expr) : 'pd.110608.dser.sc.expr' is not a valid installed package I then tried with R tools following http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html And got the following message error on the gcc-4.6.3 session Starting program: CMD INSTALL -build pd.110608.dser.sc.expr No executable specified, use 'target exec'. I played around with various combinations of path that would make sense to me. But 1) I'm not sure this is where the problem come from 2) I have a very limited notion of what 'path' means so I'm not sure what should actually be in the path and in what order. You'd have guessed, I'm on Windows (7). Many thanks for your help, Julie [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto: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 7.0 years ago by Julie Collet40
Hi Julie, On 11/27/12 8:10 PM, Julie Collet wrote: > Hi Benito, > > Many thanks for your help. > I initially tried: >> setwd("C:/Users/uqjcol10/Desktop") >> install.packages("pd.110608.dser.sc.expr.zip", repos=NULL) >> library(pd.110608.dser.sc.expr) > Error in library(pd.110608.dser.sc.expr) : > 'pd.110608.dser.sc.expr' is not a valid installed package > This is because you used winzip or whatever to zip up the package you made. What you want to be pointing to is the directory that existed before you ran winzip. You might be able to just unzip and then run install.packages(), but you may need to recreate the package first. Also note that Benilton advised you to use the additional argument type = "source". So you should be doing something like install.packages("pd.110608.dser.sc.expr", repos = NULL, type = "source") Best, Jim > So the installation didn't give any error message, I could just not access the library. Following your message I tried: > >> install.packages("pd.110608.dser.sc.expr", repos=NULL, type='source') > --- Please select a CRAN mirror for use in this session --- > * installing *source* package 'pd.110608.dser.sc.expr' ... > ** R > ** data > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > *** arch - i386 > Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : > there is no package called 'SQLite' > *** arch - x64 > Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : > there is no package called 'SQLite' > > > * DONE (pd.110608.dser.sc.expr) >> library(pd.110608.dser.sc.expr) > Warning message: > In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : > there is no package called 'SQLite' > > Should I worry about the Warning message or is it completely normal? > > It surely looks much more promising. Many thanks for your help, > Julie > > > > From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com] > Sent: Tuesday, 27 November 2012 8:04 PM > To: Julie Collet > Cc: bioconductor at r-project.org > Subject: Re: [BioC] install pdInfoBuilder package > > Hi Julie, > > The first step is to identify where you have the directory (containing the package) created by pdInfoBuilder. > > I don't have a Windows machine to try with more realistic "names", but suppose you the directory 'pd.110608.dser.sc.expr' is inside the 'folder' "C:/MyDocuments". > > So, I'd do the following (from within R): > > setwd("C:/MyDocuments") > install.packages('pd.110608.dser.sc.expr', type='source') > > and that would be it... > > Can you please try and let me know exactly what output you get? > > b > > On 27 November 2012 07:10, Julie Collet<j.collet at="" uq.edu.au<mailto:j.collet="" at="" uq.edu.au="">> wrote: > Dear all, > > I created an annotation package with pdInfoBuilder. All looked like it worked. I first tried to install it directly with R by > - Creating a zip file (with winzip or 7 zip) > - Installing it directly with R by install.packages("pd.110608.dser.sc.expr.zip", repos=NULL) > All looked like it worked until I call the library and get >> library(pd.110608.dser.sc.expr) > Error in library(pd.110608.dser.sc.expr) : > 'pd.110608.dser.sc.expr' is not a valid installed package > > I then tried with R tools following http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html > And got the following message error on the gcc-4.6.3 session > Starting program: CMD INSTALL -build pd.110608.dser.sc.expr > No executable specified, use 'target exec'. > I played around with various combinations of path that would make sense to me. But 1) I'm not sure this is where the problem come from 2) I have a very limited notion of what 'path' means so I'm not sure what should actually be in the path and in what order. > > You'd have guessed, I'm on Windows (7). > > Many thanks for your help, > Julie > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org<mailto:bioconductor at="" 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]] > > _______________________________________________ > 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 7.0 years ago by James W. MacDonald51k
I'm pretty sure I had addressed that issue (of SQLite)... what's the result for sessionInfo() ? On 28 November 2012 01:10, Julie Collet <j.collet@uq.edu.au> wrote: > Hi Benito,**** > > ** ** > > Many thanks for your help.**** > > I initially tried:**** > > > setwd("C:/Users/uqjcol10/Desktop")**** > > > install.packages("pd.110608.dser.sc.expr.zip", repos=NULL)**** > > > library(pd.110608.dser.sc.expr)**** > > Error in library(pd.110608.dser.sc.expr) : **** > > ‘pd.110608.dser.sc.expr’ is not a valid installed package**** > > ** ** > > So the installation didn’t give any error message, I could just not access > the library. Following your message I tried:**** > > ** ** > > > install.packages("pd.110608.dser.sc.expr", repos=NULL, type='source')*** > * > > --- Please select a CRAN mirror for use in this session ---**** > > * installing *source* package 'pd.110608.dser.sc.expr' ...**** > > ** R**** > > ** data**** > > ** inst**** > > ** preparing package for lazy loading**** > > ** help**** > > *** installing help indices**** > > ** building package indices**** > > ** testing if installed package can be loaded**** > > *** arch - i386**** > > Warning in library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, :**** > > there is no package called 'SQLite'**** > > *** arch - x64**** > > Warning in library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, :**** > > there is no package called 'SQLite'**** > > ** ** > > ** ** > > * DONE (pd.110608.dser.sc.expr)**** > > > library(pd.110608.dser.sc.expr)**** > > Warning message:**** > > In library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, :**** > > there is no package called ‘SQLite’**** > > ** ** > > Should I worry about the Warning message or is it completely normal?**** > > ** ** > > It surely looks much more promising. Many thanks for your help,**** > > Julie**** > > ** ** > > ** ** > > ** ** > > *From:* Benilton Carvalho [mailto:beniltoncarvalho@gmail.com] > *Sent:* Tuesday, 27 November 2012 8:04 PM > *To:* Julie Collet > *Cc:* bioconductor@r-project.org > *Subject:* Re: [BioC] install pdInfoBuilder package**** > > ** ** > > Hi Julie,**** > > ** ** > > The first step is to identify where you have the directory (containing the > package) created by pdInfoBuilder.**** > > ** ** > > I don't have a Windows machine to try with more realistic "names", but > suppose you the directory 'pd.110608.dser.sc.expr' is inside the 'folder' > "C:/MyDocuments".**** > > ** ** > > So, I'd do the following (from within R):**** > > ** ** > > setwd("C:/MyDocuments")**** > > install.packages('pd.110608.dser.sc.expr', type='source')**** > > ** ** > > and that would be it...**** > > ** ** > > Can you please try and let me know exactly what output you get?**** > > ** ** > > b**** > > ** ** > > On 27 November 2012 07:10, Julie Collet <j.collet@uq.edu.au> wrote:**** > > Dear all, > > I created an annotation package with pdInfoBuilder. All looked like it > worked. I first tried to install it directly with R by > - Creating a zip file (with winzip or 7 zip) > - Installing it directly with R by > install.packages("pd.110608.dser.sc.expr.zip", repos=NULL) > All looked like it worked until I call the library and get > > library(pd.110608.dser.sc.expr) > Error in library(pd.110608.dser.sc.expr) : > 'pd.110608.dser.sc.expr' is not a valid installed package > > I then tried with R tools following > http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html > And got the following message error on the gcc-4.6.3 session > Starting program: CMD INSTALL -build pd.110608.dser.sc.expr > No executable specified, use 'target exec'. > I played around with various combinations of path that would make sense to > me. But 1) I'm not sure this is where the problem come from 2) I have a > very limited notion of what 'path' means so I'm not sure what should > actually be in the path and in what order. > > You'd have guessed, I'm on Windows (7). > > Many thanks for your help, > Julie > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 7.0 years ago by Benilton Carvalho4.3k
sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C [5] LC_TIME=English_Australia.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.110608.dser.sc.expr_0.0.1 pdInfoBuilder_1.20.0 oligo_1.20.4 [4] oligoClasses_1.18.0 affxparser_1.28.1 RSQLite_0.11.2 [7] DBI_0.2-5 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 BiocInstaller_1.4.7 Biostrings_2.24.1 bit_1.1-8 [5] codetools_0.2-8 ff_2.2-7 foreach_1.4.0 IRanges_1.14.4 [9] iterators_1.0.6 preprocessCore_1.18.0 splines_2.15.1 stats4_2.15.1 [13] tools_2.15.1 zlibbioc_1.2.0 From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com] Sent: Wednesday, 28 November 2012 11:17 AM To: Julie Collet Cc: bioconductor@r-project.org Subject: Re: [BioC] install pdInfoBuilder package I'm pretty sure I had addressed that issue (of SQLite)... what's the result for sessionInfo() ? On 28 November 2012 01:10, Julie Collet <j.collet@uq.edu.au<mailto:j.collet@uq.edu.au>> wrote: Hi Benito, Many thanks for your help. I initially tried: > setwd("C:/Users/uqjcol10/Desktop") > install.packages("pd.110608.dser.sc.expr.zip", repos=NULL) > library(pd.110608.dser.sc.expr) Error in library(pd.110608.dser.sc.expr) : 'pd.110608.dser.sc.expr' is not a valid installed package So the installation didn't give any error message, I could just not access the library. Following your message I tried: > install.packages("pd.110608.dser.sc.expr", repos=NULL, type='source') --- Please select a CRAN mirror for use in this session --- * installing *source* package 'pd.110608.dser.sc.expr' ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded *** arch - i386 Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'SQLite' *** arch - x64 Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'SQLite' * DONE (pd.110608.dser.sc.expr) > library(pd.110608.dser.sc.expr) Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'SQLite' Should I worry about the Warning message or is it completely normal? It surely looks much more promising. Many thanks for your help, Julie From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com<mailto:beniltoncarvalho@gmail.com>] Sent: Tuesday, 27 November 2012 8:04 PM To: Julie Collet Cc: bioconductor@r-project.org<mailto:bioconductor@r-project.org> Subject: Re: [BioC] install pdInfoBuilder package Hi Julie, The first step is to identify where you have the directory (containing the package) created by pdInfoBuilder. I don't have a Windows machine to try with more realistic "names", but suppose you the directory 'pd.110608.dser.sc.expr' is inside the 'folder' "C:/MyDocuments". So, I'd do the following (from within R): setwd("C:/MyDocuments") install.packages('pd.110608.dser.sc.expr', type='source') and that would be it... Can you please try and let me know exactly what output you get? b On 27 November 2012 07:10, Julie Collet <j.collet@uq.edu.au<mailto:j.collet@uq.edu.au>> wrote: Dear all, I created an annotation package with pdInfoBuilder. All looked like it worked. I first tried to install it directly with R by - Creating a zip file (with winzip or 7 zip) - Installing it directly with R by install.packages("pd.110608.dser.sc.expr.zip", repos=NULL) All looked like it worked until I call the library and get > library(pd.110608.dser.sc.expr) Error in library(pd.110608.dser.sc.expr) : 'pd.110608.dser.sc.expr' is not a valid installed package I then tried with R tools following http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html And got the following message error on the gcc-4.6.3 session Starting program: CMD INSTALL -build pd.110608.dser.sc.expr No executable specified, use 'target exec'. I played around with various combinations of path that would make sense to me. But 1) I'm not sure this is where the problem come from 2) I have a very limited notion of what 'path' means so I'm not sure what should actually be in the path and in what order. You'd have guessed, I'm on Windows (7). Many thanks for your help, Julie [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto: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 7.0 years ago by Julie Collet40
your installation isn't up-to-date... you need to update the installed packages... the current pdInfoBuilder is 1.22.0... and, if the problem persists, I'll address it asap. b On 28 November 2012 01:19, Julie Collet <j.collet@uq.edu.au> wrote: > sessionInfo()**** > > R version 2.15.1 (2012-06-22)**** > > Platform: x86_64-pc-mingw32/x64 (64-bit)**** > > ** ** > > locale:**** > > [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 * > *** > > [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C * > *** > > [5] LC_TIME=English_Australia.1252 **** > > ** ** > > attached base packages:**** > > [1] stats graphics grDevices utils datasets methods base * > *** > > ** ** > > other attached packages:**** > > [1] pd.110608.dser.sc.expr_0.0.1 pdInfoBuilder_1.20.0 > oligo_1.20.4 **** > > [4] oligoClasses_1.18.0 affxparser_1.28.1 > RSQLite_0.11.2 **** > > [7] DBI_0.2-5 Biobase_2.16.0 > BiocGenerics_0.2.0 **** > > ** ** > > loaded via a namespace (and not attached):**** > > [1] affyio_1.24.0 BiocInstaller_1.4.7 Biostrings_2.24.1 > bit_1.1-8 **** > > [5] codetools_0.2-8 ff_2.2-7 foreach_1.4.0 > IRanges_1.14.4 **** > > [9] iterators_1.0.6 preprocessCore_1.18.0 splines_2.15.1 > stats4_2.15.1 **** > > [13] tools_2.15.1 zlibbioc_1.2.0 **** > > ** ** > > *From:* Benilton Carvalho [mailto:beniltoncarvalho@gmail.com] > *Sent:* Wednesday, 28 November 2012 11:17 AM > > *To:* Julie Collet > *Cc:* bioconductor@r-project.org > *Subject:* Re: [BioC] install pdInfoBuilder package**** > > ** ** > > I'm pretty sure I had addressed that issue (of SQLite)... what's the > result for sessionInfo() ?**** > > ** ** > > On 28 November 2012 01:10, Julie Collet <j.collet@uq.edu.au> wrote:**** > > Hi Benito,**** > > **** > > Many thanks for your help.**** > > I initially tried:**** > > > setwd("C:/Users/uqjcol10/Desktop")**** > > > install.packages("pd.110608.dser.sc.expr.zip", repos=NULL)**** > > > library(pd.110608.dser.sc.expr)**** > > Error in library(pd.110608.dser.sc.expr) : **** > > ‘pd.110608.dser.sc.expr’ is not a valid installed package**** > > **** > > So the installation didn’t give any error message, I could just not access > the library. Following your message I tried:**** > > **** > > > install.packages("pd.110608.dser.sc.expr", repos=NULL, type='source')*** > * > > --- Please select a CRAN mirror for use in this session ---**** > > * installing *source* package 'pd.110608.dser.sc.expr' ...**** > > ** R**** > > ** data**** > > ** inst**** > > ** preparing package for lazy loading**** > > ** help**** > > *** installing help indices**** > > ** building package indices**** > > ** testing if installed package can be loaded**** > > *** arch - i386**** > > Warning in library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, :**** > > there is no package called 'SQLite'**** > > *** arch - x64**** > > Warning in library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, :**** > > there is no package called 'SQLite'**** > > **** > > **** > > * DONE (pd.110608.dser.sc.expr)**** > > > library(pd.110608.dser.sc.expr)**** > > Warning message:**** > > In library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, :**** > > there is no package called ‘SQLite’**** > > **** > > Should I worry about the Warning message or is it completely normal?**** > > **** > > It surely looks much more promising. Many thanks for your help,**** > > Julie**** > > **** > > **** > > **** > > *From:* Benilton Carvalho [mailto:beniltoncarvalho@gmail.com] > *Sent:* Tuesday, 27 November 2012 8:04 PM > *To:* Julie Collet > *Cc:* bioconductor@r-project.org > *Subject:* Re: [BioC] install pdInfoBuilder package**** > > **** > > Hi Julie,**** > > **** > > The first step is to identify where you have the directory (containing the > package) created by pdInfoBuilder.**** > > **** > > I don't have a Windows machine to try with more realistic "names", but > suppose you the directory 'pd.110608.dser.sc.expr' is inside the 'folder' > "C:/MyDocuments".**** > > **** > > So, I'd do the following (from within R):**** > > **** > > setwd("C:/MyDocuments")**** > > install.packages('pd.110608.dser.sc.expr', type='source')**** > > **** > > and that would be it...**** > > **** > > Can you please try and let me know exactly what output you get?**** > > **** > > b**** > > **** > > On 27 November 2012 07:10, Julie Collet <j.collet@uq.edu.au> wrote:**** > > Dear all, > > I created an annotation package with pdInfoBuilder. All looked like it > worked. I first tried to install it directly with R by > - Creating a zip file (with winzip or 7 zip) > - Installing it directly with R by > install.packages("pd.110608.dser.sc.expr.zip", repos=NULL) > All looked like it worked until I call the library and get > > library(pd.110608.dser.sc.expr) > Error in library(pd.110608.dser.sc.expr) : > 'pd.110608.dser.sc.expr' is not a valid installed package > > I then tried with R tools following > http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html > And got the following message error on the gcc-4.6.3 session > Starting program: CMD INSTALL -build pd.110608.dser.sc.expr > No executable specified, use 'target exec'. > I played around with various combinations of path that would make sense to > me. But 1) I'm not sure this is where the problem come from 2) I have a > very limited notion of what 'path' means so I'm not sure what should > actually be in the path and in what order. > > You'd have guessed, I'm on Windows (7). > > Many thanks for your help, > Julie > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 7.0 years ago by Benilton Carvalho4.3k
All good and no more warning message. Thanks a lot for your time and your help, Julie From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com] Sent: Wednesday, 28 November 2012 11:23 AM To: Julie Collet Cc: bioconductor@r-project.org Subject: Re: [BioC] install pdInfoBuilder package your installation isn't up-to-date... you need to update the installed packages... the current pdInfoBuilder is 1.22.0... and, if the problem persists, I'll address it asap. b On 28 November 2012 01:19, Julie Collet <j.collet@uq.edu.au<mailto:j.collet@uq.edu.au>> wrote: sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C [5] LC_TIME=English_Australia.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.110608.dser.sc.expr_0.0.1 pdInfoBuilder_1.20.0 oligo_1.20.4 [4] oligoClasses_1.18.0 affxparser_1.28.1 RSQLite_0.11.2 [7] DBI_0.2-5 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 BiocInstaller_1.4.7 Biostrings_2.24.1 bit_1.1-8 [5] codetools_0.2-8 ff_2.2-7 foreach_1.4.0 IRanges_1.14.4 [9] iterators_1.0.6 preprocessCore_1.18.0 splines_2.15.1 stats4_2.15.1 [13] tools_2.15.1 zlibbioc_1.2.0 From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com<mailto:beniltoncarvalho@gmail.com>] Sent: Wednesday, 28 November 2012 11:17 AM To: Julie Collet Cc: bioconductor@r-project.org<mailto:bioconductor@r-project.org> Subject: Re: [BioC] install pdInfoBuilder package I'm pretty sure I had addressed that issue (of SQLite)... what's the result for sessionInfo() ? On 28 November 2012 01:10, Julie Collet <j.collet@uq.edu.au<mailto:j.collet@uq.edu.au>> wrote: Hi Benito, Many thanks for your help. I initially tried: > setwd("C:/Users/uqjcol10/Desktop") > install.packages("pd.110608.dser.sc.expr.zip", repos=NULL) > library(pd.110608.dser.sc.expr) Error in library(pd.110608.dser.sc.expr) : 'pd.110608.dser.sc.expr' is not a valid installed package So the installation didn't give any error message, I could just not access the library. Following your message I tried: > install.packages("pd.110608.dser.sc.expr", repos=NULL, type='source') --- Please select a CRAN mirror for use in this session --- * installing *source* package 'pd.110608.dser.sc.expr' ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded *** arch - i386 Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'SQLite' *** arch - x64 Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'SQLite' * DONE (pd.110608.dser.sc.expr) > library(pd.110608.dser.sc.expr) Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'SQLite' Should I worry about the Warning message or is it completely normal? It surely looks much more promising. Many thanks for your help, Julie From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com<mailto:beniltoncarvalho@gmail.com>] Sent: Tuesday, 27 November 2012 8:04 PM To: Julie Collet Cc: bioconductor@r-project.org<mailto:bioconductor@r-project.org> Subject: Re: [BioC] install pdInfoBuilder package Hi Julie, The first step is to identify where you have the directory (containing the package) created by pdInfoBuilder. I don't have a Windows machine to try with more realistic "names", but suppose you the directory 'pd.110608.dser.sc.expr' is inside the 'folder' "C:/MyDocuments". So, I'd do the following (from within R): setwd("C:/MyDocuments") install.packages('pd.110608.dser.sc.expr', type='source') and that would be it... Can you please try and let me know exactly what output you get? b On 27 November 2012 07:10, Julie Collet <j.collet@uq.edu.au<mailto:j.collet@uq.edu.au>> wrote: Dear all, I created an annotation package with pdInfoBuilder. All looked like it worked. I first tried to install it directly with R by - Creating a zip file (with winzip or 7 zip) - Installing it directly with R by install.packages("pd.110608.dser.sc.expr.zip", repos=NULL) All looked like it worked until I call the library and get > library(pd.110608.dser.sc.expr) Error in library(pd.110608.dser.sc.expr) : 'pd.110608.dser.sc.expr' is not a valid installed package I then tried with R tools following http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html And got the following message error on the gcc-4.6.3 session Starting program: CMD INSTALL -build pd.110608.dser.sc.expr No executable specified, use 'target exec'. I played around with various combinations of path that would make sense to me. But 1) I'm not sure this is where the problem come from 2) I have a very limited notion of what 'path' means so I'm not sure what should actually be in the path and in what order. You'd have guessed, I'm on Windows (7). Many thanks for your help, Julie [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto: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 7.0 years ago by Julie Collet40
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