Dear Kasper : Thanks for your explanation. However, I opened the shell from Rstudio and type the command R --vanilla, seems it works fine, but still not sure about efficiency of using R -vanilla. I am not confident about using R commands, so is there any quick example that I can practice and understand this in depth ? Thanks a lot
Best regards: Jurat On Fri, Nov 11, 2016 at 7:22 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > You're bing asked to use > R --vanilla > because you have a non-standard problem, exemplified by the fact that what > you have problems with (installing CRAN packages) works for thousands of > users of Bioconductor (certainly for me). This suggests that there is > something wrong with something on your computer. Starting R with R > --vanilla disables loading of some user-specific component. If it works > with R --vanilla the conclusion is that whatever made it fail was something > loaded by R but not R --vanilla. If it doesn't work with R --vanilla the > conclusion is that your problem is elsewhere. > > Best, > Kasper > > On Fri, Nov 11, 2016 at 12:09 PM, Jurat Shayidin <juratb...@gmail.com> > wrote: > >> sorry for this simple question. why use R vanilla ? not familiar enough >> with this term. >> >> On Fri, Nov 11, 2016 at 5:51 PM, Martin Morgan < >> martin.mor...@roswellpark.org> wrote: >> >> > On 11/11/2016 11:42 AM, Jurat Shayidin wrote: >> > >> >> I'll keep this in mind. Thanks for reminding. Could you please >> elaborate >> >> your answer on my doubt ? Thanks >> >> >> >> On Fri, Nov 11, 2016 at 5:27 PM, Martin Morgan < >> >> martin.mor...@roswellpark.org> wrote: >> >> >> >> Please respond on the mailing list, so that others in similar >> situations >> >>> can benefit / contribute. >> >>> >> >>> On 11/11/2016 10:39 AM, Jurat Shayidin wrote: >> >>> >> >>> Dear Martin : >> >>>> >> >>>> Thanks for your prompt hit . I used to have R release version, so >> after >> >>>> I installed devel version of R, I removed R released version, while >> only >> >>>> keep devel version instead. Is this correct ? I didn't clean R >> session, >> >>>> >> >>> >> > this is not related to your original question. I personally need both a >> > release and devel version of R and have both installed. >> > >> > how can I make it happen on windows? Plus, How to make R session >> >>>> vanilla ? What's right configuration both R devel and Bioc devel >> before >> >>>> >> >>> >> > open a Windows shell ('cmd') and type >> > >> > R --vanilla >> > >> > or perhaps >> > >> > Rgui --vanilla >> > >> > building my packages ? Could you elaborate your answer please? Thank you >> >>>> >> >>> >> > again, this isn't related to your original question. See the section >> > 'Which version of R?' in >> > >> > http://bioconductor.org/developers/how-to/useDevel/ >> > >> > Martin >> > >> > >> > very much >> >>>> >> >>>> Best regards : >> >>>> >> >>>> On Fri, Nov 11, 2016 at 4:04 PM, Martin Morgan >> >>>> <martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org >> >> >> >>>> >> >>>> wrote: >> >>>> >> >>>> On 11/11/2016 09:44 AM, Jurat Shayidin wrote: >> >>>> >> >>>> Dear BiocDevel: >> >>>> >> >>>> I ran into the issue after installed devel version of R and >> Bioc >> >>>> 3.4. >> >>>> Because my packages depends on some packages from CRAN >> >>>> repository, now I >> >>>> failed to installed paclages from CRAN. I don't have problem >> >>>> when I used >> >>>> released version of R. Because new packages must coordinate >> with >> >>>> devel >> >>>> version of Bioc and R, so I did it. But can't installl >> packages >> >>>> from CRAN >> >>>> like dplyr. How can I overcome this issue ? Any quick >> solution >> >>>> ? I got >> >>>> error as follow: >> >>>> >> >>>> >> >>>> BiocInstaller::useDevel() >> >>>> >> >>>> Error: 'devel' version already in use >> >>>> >> >>>> install.packages("dplyr") >> >>>> >> >>>> Error in install.packages : missing value where TRUE/FALSE >> >>>> needed >> >>>> >> >>>> >> >>>> this does not happen for me; you'll need to debug on your end, >> >>>> minimally, reporting the output of traceback() after the error >> >>>> occurs. >> >>>> >> >>>> are you in a clean R session with no .RData or other objects >> loaded >> >>>> that might interfere with R? >> >>>> >> >>>> R --vanilla >> >>>> >> >>>> Martin >> >>>> >> >>>> PS -- please do not 'close' questions that have been answered on >> >>>> support.bioconductor.org <http://support.bioconductor.org>. >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> sessionInfo() >> >>>> >> >>>> R Under development (unstable) (2016-11-09 r71642) >> >>>> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >>>> Running under: Windows >= 8 x64 (build 9200) >> >>>> >> >>>> locale: >> >>>> [1] LC_COLLATE=English_United States.1252 >> >>>> [2] LC_CTYPE=English_United States.1252 >> >>>> [3] LC_MONETARY=English_United States.1252 >> >>>> [4] LC_NUMERIC=C >> >>>> [5] LC_TIME=English_United States.1252 >> >>>> >> >>>> attached base packages: >> >>>> [1] parallel stats4 stats graphics grDevices >> >>>> [6] utils datasets methods base >> >>>> >> >>>> other attached packages: >> >>>> [1] SummarizedExperiment_1.5.2 Biobase_2.35.0 >> >>>> [3] XVector_0.15.0 rtracklayer_1.35.1 >> >>>> [5] GenomicRanges_1.27.5 GenomeInfoDb_1.11.3 >> >>>> [7] IRanges_2.9.7 S4Vectors_0.13.2 >> >>>> [9] BiocGenerics_0.21.0 BiocInstaller_1.25.2 >> >>>> >> >>>> loaded via a namespace (and not attached): >> >>>> [1] lattice_0.20-34 XML_3.98-1.5 >> >>>> [3] Rsamtools_1.27.2 Biostrings_2.43.0 >> >>>> [5] GenomicAlignments_1.11.0 bitops_1.0-6 >> >>>> [7] grid_3.4.0 zlibbioc_1.21.0 >> >>>> [9] Matrix_1.2-7.1 BiocParallel_1.9.1 >> >>>> [11] tools_3.4.0 RCurl_1.95-4.8 >> >>>> [13] compiler_3.4.0 >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> This email message may contain legally privileged and/or >> >>>> confidential information. If you are not the intended >> recipient(s), >> >>>> or the employee or agent responsible for the delivery of this >> >>>> message to the intended recipient(s), you are hereby notified >> that >> >>>> any disclosure, copying, distribution, or use of this email >> message >> >>>> is prohibited. If you have received this message in error, >> please >> >>>> notify the sender immediately by e-mail and delete this email >> >>>> message from your computer. Thank you. >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> -- >> >>>> Jurat Shahidin >> >>>> >> >>>> Dipartimento di Elettronica, Informazione e Bioingegneria >> >>>> Politecnico di Milano >> >>>> Piazza Leonardo da Vinci 32 - 20133 Milano, Italy >> >>>> Mobile : +39 3279366608 >> >>>> >> >>>> >> >>> >> >>> This email message may contain legally privileged and/or confidential >> >>> information. If you are not the intended recipient(s), or the >> employee >> >>> or >> >>> agent responsible for the delivery of this message to the intended >> >>> recipient(s), you are hereby notified that any disclosure, copying, >> >>> distribution, or use of this email message is prohibited. If you have >> >>> received this message in error, please notify the sender immediately >> by >> >>> e-mail and delete this email message from your computer. Thank you. >> >>> >> >>> >> >> >> >> >> >> >> > >> > This email message may contain legally privileged and/or confidential >> > information. If you are not the intended recipient(s), or the employee >> or >> > agent responsible for the delivery of this message to the intended >> > recipient(s), you are hereby notified that any disclosure, copying, >> > distribution, or use of this email message is prohibited. If you have >> > received this message in error, please notify the sender immediately by >> > e-mail and delete this email message from your computer. Thank you. >> > >> >> >> >> -- >> Jurat Shahidin >> >> Dipartimento di Elettronica, Informazione e Bioingegneria >> Politecnico di Milano >> Piazza Leonardo da Vinci 32 - 20133 Milano, Italy >> Mobile : +39 3279366608 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > -- Jurat Shahidin Dipartimento di Elettronica, Informazione e Bioingegneria Politecnico di Milano Piazza Leonardo da Vinci 32 - 20133 Milano, Italy Mobile : +39 3279366608 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel