Open portiaxu opened 8 years ago
It is rather unfortunate that this upgrade is not backward compatible and will make ngs.plot disabled. However, a lot of users are still using R v3.0.2 with me being one of them. I'll hold off the upgrade for a while until it becomes clearer which parts need to be modified.
On Thu, Nov 12, 2015 at 1:40 AM, portiaxu notifications@github.com wrote:
Hello, our server recently update R from 3.0.2 to 3.2.0 and a new error occur, I have installed shortread but I can't run the software anyway.
Welcome at Thu Nov 12 14:36:05 2015 Configuring variables...Done Loading R librariesBioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install Error in match(x, table, nomatch = 0L) : object 'ShortRead' not found Calls: biocLite -> %in% -> match In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called \u2018ShortRead\u2019 Execution halted
— Reply to this email directly or view it on GitHub https://github.com/shenlab-sinai/ngsplot/issues/51.
Li Shen, Ph.D. Computer Science Associate Professor Department of Neuroscience Icahn School of Medicine at Mount Sinai New York, NY 10029 ################# ngs.plot - the coolest NGS plotting tool: https://code.google.com/p/ngsplot/ Want ChIP-seq differential analysis? Use: https://code.google.com/p/diffreps/
Thank you for your kind reply! ngsplot is very convenient and powerful. I have tried following approach and it worked. Hope it can give you some hints.
I install another version of R in my account(since I'm using a server) and change environment parameters and runs the following command and it worked!
~/R/bin/Rscript ~/ngsplot/bin/ngs.plot.r -G hg19 -R bed -C DMR_4factors.txt -O DMR_4factors
2015-11-14 12:03 GMT+08:00 Li Shen notifications@github.com:
It is rather unfortunate that this upgrade is not backward compatible and will make ngs.plot disabled. However, a lot of users are still using R v3.0.2 with me being one of them. I'll hold off the upgrade for a while until it becomes clearer which parts need to be modified.
On Thu, Nov 12, 2015 at 1:40 AM, portiaxu notifications@github.com wrote:
Hello, our server recently update R from 3.0.2 to 3.2.0 and a new error occur, I have installed shortread but I can't run the software anyway.
Welcome at Thu Nov 12 14:36:05 2015 Configuring variables...Done Loading R librariesBioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install Error in match(x, table, nomatch = 0L) : object 'ShortRead' not found Calls: biocLite -> %in% -> match In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called \u2018ShortRead\u2019 Execution halted
— Reply to this email directly or view it on GitHub https://github.com/shenlab-sinai/ngsplot/issues/51.
Li Shen, Ph.D. Computer Science Associate Professor Department of Neuroscience Icahn School of Medicine at Mount Sinai New York, NY 10029 ################# ngs.plot - the coolest NGS plotting tool: https://code.google.com/p/ngsplot/ Want ChIP-seq differential analysis? Use: https://code.google.com/p/diffreps/
— Reply to this email directly or view it on GitHub https://github.com/shenlab-sinai/ngsplot/issues/51#issuecomment-156623181 .
Siyuan Xu Laboratory of Epigenetics Institutes of Biomedical Sciences Shanghai Medical College of Fudan University
138 Yixueyuan Road Shanghai 200032 P.R. China
Tel: 86-21-54237874 (Lab)
Thank you for the tip! There are certainly several ways to get around this.
Li
On Sun, Nov 15, 2015 at 9:43 AM, portiaxu notifications@github.com wrote:
Thank you for your kind reply! ngsplot is very convenient and powerful. I have tried following approach and it worked. Hope it can give you some hints.
I install another version of R in my account(since I'm using a server) and change environment parameters and runs the following command and it worked!
~/R/bin/Rscript ~/ngsplot/bin/ngs.plot.r -G hg19 -R bed -C DMR_4factors.txt -O DMR_4factors
2015-11-14 12:03 GMT+08:00 Li Shen notifications@github.com:
It is rather unfortunate that this upgrade is not backward compatible and will make ngs.plot disabled. However, a lot of users are still using R v3.0.2 with me being one of them. I'll hold off the upgrade for a while until it becomes clearer which parts need to be modified.
On Thu, Nov 12, 2015 at 1:40 AM, portiaxu notifications@github.com wrote:
Hello, our server recently update R from 3.0.2 to 3.2.0 and a new error occur, I have installed shortread but I can't run the software anyway.
Welcome at Thu Nov 12 14:36:05 2015 Configuring variables...Done Loading R librariesBioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install Error in match(x, table, nomatch = 0L) : object 'ShortRead' not found Calls: biocLite -> %in% -> match In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called \u2018ShortRead\u2019 Execution halted
— Reply to this email directly or view it on GitHub https://github.com/shenlab-sinai/ngsplot/issues/51.
Li Shen, Ph.D. Computer Science Associate Professor Department of Neuroscience Icahn School of Medicine at Mount Sinai New York, NY 10029 ################# ngs.plot - the coolest NGS plotting tool: https://code.google.com/p/ngsplot/ Want ChIP-seq differential analysis? Use: https://code.google.com/p/diffreps/
— Reply to this email directly or view it on GitHub < https://github.com/shenlab-sinai/ngsplot/issues/51#issuecomment-156623181> .
Siyuan Xu Laboratory of Epigenetics Institutes of Biomedical Sciences Shanghai Medical College of Fudan University
138 Yixueyuan Road Shanghai 200032 P.R. China
Tel: 86-21-54237874 (Lab)
— Reply to this email directly or view it on GitHub https://github.com/shenlab-sinai/ngsplot/issues/51#issuecomment-156815557 .
Li Shen, Ph.D. Computer Science Associate Professor Department of Neuroscience Icahn School of Medicine at Mount Sinai New York, NY 10029 ################# ngs.plot - the coolest NGS plotting tool: https://code.google.com/p/ngsplot/ Want ChIP-seq differential analysis? Use: https://code.google.com/p/diffreps/
Hi,
Have you tried to update bioLite.R?
source("https://bioconductor.org/biocLite.R")
biocLite()
It did work for me.
Hello, our server recently update R from 3.0.2 to 3.2.0 and a new error occur, I have installed shortread but I can't run the software anyway.
Welcome at Thu Nov 12 14:36:05 2015 Configuring variables...Done Loading R librariesBioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install Error in match(x, table, nomatch = 0L) : object 'ShortRead' not found Calls: biocLite -> %in% -> match In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called \u2018ShortRead\u2019
Execution halted