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