pdInfoBuilder - problem installing the annotation package
1
0
Entering edit mode
@tommaso-raffaello-6470
Last seen 9.6 years ago
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 Annotation pdInfoBuilder • 1.1k views
ADD COMMENT
0
Entering edit mode
@benilton-carvalho-1375
Last seen 4.0 years ago
Brazil/Campinas/UNICAMP
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 COMMENT
0
Entering edit mode
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 REPLY
0
Entering edit mode
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 REPLY

Login before adding your answer.

Traffic: 760 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6