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shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases
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R 3.2 Bioconductor 3.2 updated problem #51

Open portiaxu opened 8 years ago

portiaxu commented 8 years ago

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

lishen commented 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/

portiaxu commented 8 years ago

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)

lishen commented 8 years ago

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/

pajanne commented 8 years ago

Hi,

Have you tried to update bioLite.R?

source("https://bioconductor.org/biocLite.R")
biocLite()

It did work for me.