Question: pdInfoBuilder - problem installing the annotation package
0
gravatar for Tommaso Raffaello
5.5 years ago by
Tommaso Raffaello60 wrote:
Hi, in the pdInfoBuilder manual it´s written "After the package is created, the user must install it and not just copy it to the library tree." I have created the annotation file with the pdInfoBuilder package, however I can´t install it. The error message is: Warning in install.packages : package 'C:/HY-data/TORAFFAE/R_projects/Pine Microarray/pd.110224.pinus.fa.exp.modified.zip' is not available (for R version 3.0.2) Installing package into 'C:/Rlibs/3.0.2' (as 'lib' is unspecified) >sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] pdInfoBuilder_1.26.0 affxparser_1.34.2 RSQLite_0.11.4 DBI_0.2-7 oligo_1.26.2 [6] Biostrings_2.30.1 XVector_0.2.0 IRanges_1.20.6 Biobase_2.22.0 oligoClasses_1.24.0 [11] BiocGenerics_0.8.0 BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] affyio_1.30.0 bit_1.1-11 codetools_0.2-8 ff_2.2-12 foreach_1.4.1 [6] GenomicRanges_1.14.4 iterators_1.0.6 preprocessCore_1.24.0 splines_3.0.2 stats4_3.0.2 [11] tools_3.0.2 zlibbioc_1.8.0 I´m quite new in R and Bioconductor, hopefully this is not a stupid problem. Thanks! -- Tommaso Raffaello, PhD University of Helsinki Department of Forest Sciences Latokartanonkaari 7 PO Box 27 00014 Helsinki (Finland) Phone number: +358 9 191 58136 email: tommaso.raffaello@helsinki.fi email: tommaso.raffaello@gmail.com [[alternative HTML version deleted]]
annotation pdinfobuilder • 565 views
ADD COMMENTlink modified 5.5 years ago by Benilton Carvalho4.3k • written 5.5 years ago by Tommaso Raffaello60
Answer: pdInfoBuilder - problem installing the annotation package
0
gravatar for Benilton Carvalho
5.5 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k wrote:
Hi Tommaso, could you please try: install.packages('C:/HY-data/TORAFFAE/R_projects/Pine Microarray/pd.110224.pinus.fa.exp.modified', repo=NULL) and let us know what you get? thank you, benilton 2014-03-27 10:26 GMT-03:00 Tommaso Raffaello <tommaso.raffaello@helsinki.fi> : > Hi, > > in the pdInfoBuilder manual it愀 written "After the package is created, > the user must install it and > not just copy it to the library tree." > > I have created the annotation file with the pdInfoBuilder package, > however I can愒 install it. > > The error message is: > > Warning in install.packages : > package 'C:/HY-data/TORAFFAE/R_projects/Pine > Microarray/pd.110224.pinus.fa.exp.modified.zip' is not available (for R > version 3.0.2) > Installing package into 'C:/Rlibs/3.0.2' > (as 'lib' is unspecified) > > >sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > Kingdom.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] pdInfoBuilder_1.26.0 affxparser_1.34.2 RSQLite_0.11.4 > DBI_0.2-7 oligo_1.26.2 > [6] Biostrings_2.30.1 XVector_0.2.0 IRanges_1.20.6 > Biobase_2.22.0 oligoClasses_1.24.0 > [11] BiocGenerics_0.8.0 BiocInstaller_1.12.0 > > loaded via a namespace (and not attached): > [1] affyio_1.30.0 bit_1.1-11 codetools_0.2-8 > ff_2.2-12 foreach_1.4.1 > [6] GenomicRanges_1.14.4 iterators_1.0.6 preprocessCore_1.24.0 > splines_3.0.2 stats4_3.0.2 > [11] tools_3.0.2 zlibbioc_1.8.0 > > > I惴 quite new in R and Bioconductor, hopefully this is not a stupid problem. > > Thanks! > > -- > Tommaso Raffaello, PhD > > University of Helsinki > Department of Forest Sciences > Latokartanonkaari 7 PO Box 27 > 00014 Helsinki (Finland) > > Phone number: +358 9 191 58136 > email: tommaso.raffaello@helsinki.fi > email: tommaso.raffaello@gmail.com > > > [[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 5.5 years ago by Benilton Carvalho4.3k
And on Windows, you also need to include the argument type = "source" Best, Jim On Thursday, March 27, 2014 9:34:02 AM, Benilton Carvalho wrote: > Hi Tommaso, > > could you please try: > > install.packages('C:/HY-data/TORAFFAE/R_projects/Pine > Microarray/pd.110224.pinus.fa.exp.modified', repo=NULL) > > and let us know what you get? > > thank you, > > benilton > > > 2014-03-27 10:26 GMT-03:00 Tommaso Raffaello <tommaso.raffaello at="" helsinki.fi=""> > : > >> Hi, >> >> in the pdInfoBuilder manual it??? written "After the package is created, >> the user must install it and >> not just copy it to the library tree." >> >> I have created the annotation file with the pdInfoBuilder package, >> however I can??? install it. >> >> The error message is: >> >> Warning in install.packages : >> package 'C:/HY-data/TORAFFAE/R_projects/Pine >> Microarray/pd.110224.pinus.fa.exp.modified.zip' is not available (for R >> version 3.0.2) >> Installing package into 'C:/Rlibs/3.0.2' >> (as 'lib' is unspecified) >> >>> sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United >> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 >> [4] LC_NUMERIC=C LC_TIME=English_United >> Kingdom.1252 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] pdInfoBuilder_1.26.0 affxparser_1.34.2 RSQLite_0.11.4 >> DBI_0.2-7 oligo_1.26.2 >> [6] Biostrings_2.30.1 XVector_0.2.0 IRanges_1.20.6 >> Biobase_2.22.0 oligoClasses_1.24.0 >> [11] BiocGenerics_0.8.0 BiocInstaller_1.12.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.30.0 bit_1.1-11 codetools_0.2-8 >> ff_2.2-12 foreach_1.4.1 >> [6] GenomicRanges_1.14.4 iterators_1.0.6 preprocessCore_1.24.0 >> splines_3.0.2 stats4_3.0.2 >> [11] tools_3.0.2 zlibbioc_1.8.0 >> >> >> I??? quite new in R and Bioconductor, hopefully this is not a stupid problem. >> >> Thanks! >> >> -- >> Tommaso Raffaello, PhD >> >> University of Helsinki >> Department of Forest Sciences >> Latokartanonkaari 7 PO Box 27 >> 00014 Helsinki (Finland) >> >> Phone number: +358 9 191 58136 >> email: tommaso.raffaello at helsinki.fi >> email: tommaso.raffaello at gmail.com >> >> >> [[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 >> > > [[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 -- 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 5.5 years ago by James W. MacDonald51k
Hi, thanks for your help! Apparently I managed to install and load the package. There is still a warning message but probably it´s fine? Here is the output: >install.packages('C:/HY-data/TORAFFAE/R_projects/Pine Microarray/pd.110224.pinus.fa.exp.modified', repo=NULL, type = 'source') Warning in install.packages : package ‘C:/HY-data/TORAFFAE/R_projects/Pine Microarray/pd.110224.pinus.fa.exp.modified’ is not available (for R version 3.0.2) Installing package into ‘C:/Rlibs/3.0.2’ (as ‘lib’ is unspecified) * installing *source* package 'pd.110224.pinus.fa.exp.modified' ... Warning in as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT' ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (pd.110224.pinus.fa.exp.modified) >library("pd.110224.pinus.fa.exp.modified", lib.loc="C:/Rlibs/3.0.2") > Thanks! Tommaso On 27/03/2014 15:40, James W. MacDonald wrote: > And on Windows, you also need to include the argument > > type = "source" > > Best, > > Jim > > > > On Thursday, March 27, 2014 9:34:02 AM, Benilton Carvalho wrote: >> Hi Tommaso, >> >> could you please try: >> >> install.packages('C:/HY-data/TORAFFAE/R_projects/Pine >> Microarray/pd.110224.pinus.fa.exp.modified', repo=NULL) >> >> and let us know what you get? >> >> thank you, >> >> benilton >> >> >> 2014-03-27 10:26 GMT-03:00 Tommaso Raffaello >> <tommaso.raffaello@helsinki.fi> >> : >> >>> Hi, >>> >>> in the pdInfoBuilder manual itæ„€ written "After the package is >>> created, >>> the user must install it and >>> not just copy it to the library tree." >>> >>> I have created the annotation file with the pdInfoBuilder package, >>> however I canæ„’ install it. >>> >>> The error message is: >>> >>> Warning in install.packages : >>> package 'C:/HY-data/TORAFFAE/R_projects/Pine >>> Microarray/pd.110224.pinus.fa.exp.modified.zip' is not available (for R >>> version 3.0.2) >>> Installing package into 'C:/Rlibs/3.0.2' >>> (as 'lib' is unspecified) >>> >>>> sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>> >>> locale: >>> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United >>> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 >>> [4] LC_NUMERIC=C LC_TIME=English_United >>> Kingdom.1252 >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets methods >>> base >>> >>> other attached packages: >>> [1] pdInfoBuilder_1.26.0 affxparser_1.34.2 RSQLite_0.11.4 >>> DBI_0.2-7 oligo_1.26.2 >>> [6] Biostrings_2.30.1 XVector_0.2.0 IRanges_1.20.6 >>> Biobase_2.22.0 oligoClasses_1.24.0 >>> [11] BiocGenerics_0.8.0 BiocInstaller_1.12.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.30.0 bit_1.1-11 codetools_0.2-8 >>> ff_2.2-12 foreach_1.4.1 >>> [6] GenomicRanges_1.14.4 iterators_1.0.6 preprocessCore_1.24.0 >>> splines_3.0.2 stats4_3.0.2 >>> [11] tools_3.0.2 zlibbioc_1.8.0 >>> >>> >>> I惴 quite new in R and Bioconductor, hopefully this is not a stupid >>> problem. >>> >>> Thanks! >>> >>> -- >>> Tommaso Raffaello, PhD >>> >>> University of Helsinki >>> Department of Forest Sciences >>> Latokartanonkaari 7 PO Box 27 >>> 00014 Helsinki (Finland) >>> >>> Phone number: +358 9 191 58136 >>> email: tommaso.raffaello@helsinki.fi >>> email: tommaso.raffaello@gmail.com >>> >>> >>> [[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]] >> >> >> >> _______________________________________________ >> 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 > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 -- Tommaso Raffaello, PhD University of Helsinki Department of Forest Sciences Latokartanonkaari 7 PO Box 27 00014 Helsinki (Finland) Phone number: +358 9 191 58136 email: tommaso.raffaello@helsinki.fi email: tommaso.raffaello@gmail.com [[alternative HTML version deleted]]
ADD REPLYlink written 5.5 years ago by Tommaso Raffaello60
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