search

benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
464 stars 142 forks source link

Cannot install ‘RcppParallel’ #259

Closed tvkarpinets closed 7 years ago

tvkarpinets commented 7 years ago

I want to install dada2 in my directory on a parallel server. It is failed because I was not able to install ‘RcppParallel’. I have a message installation path not writeable, unable to update packages: assertthat, backports, BiocParallel, boot, circlize, curl, dplyr, foreign, gdata, ggpubr, ggsci, Hmisc, HMMcopy, htmltools, jsonlite, knitr, markdown, MASS, Matrix, matrixStats, memoise, R6, Rcpp, readr, rmarkdown, rpart, Rsamtools, shiny, squash, stringi, survminer, tibble, XML

spholmes commented 7 years ago

Could you tell us what OS and what version of R and bioconductor you have by giving the sessionInfo

Thanks Susan

On Tue, Jun 13, 2017 at 1:39 PM, tvkarpinets notifications@github.com wrote:

I want to install dada2 in my directory on a parallel server. It is failed because I was not able to install ‘RcppParallel’. I have a message installation path not writeable, unable to update packages: assertthat, backports, BiocParallel, boot, circlize, curl, dplyr, foreign, gdata, ggpubr, ggsci, Hmisc, HMMcopy, htmltools, jsonlite, knitr, markdown, MASS, Matrix, matrixStats, memoise, R6, Rcpp, readr, rmarkdown, rpart, Rsamtools, shiny, squash, stringi, survminer, tibble, XML

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/259, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvUjKzxxJPSAgZBOgK0YZa-JWEwnbks5sDvOKgaJpZM4N5Dcs .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

tvkarpinets commented 7 years ago

Wow, It is so fast response. Thank you very much.

LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch

Distributor ID: RedHatEnterpriseServer

Description: Red Hat Enterprise Linux Server release 6.4 (Santiago)

Release: 6.4

Codename: Santiago

R version 3.3.3 (2017-03-06)

Bioconductor version 3.4 (BiocInstaller 1.24.0)

sessionInfo()

R version 3.3.3 (2017-03-06)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Red Hat Enterprise Linux Server release 6.4 (Santiago)

locale:

[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C

[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8

[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8

[7] LC_PAPER=en_US.UTF-8 LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:

[1] BiocInstaller_1.24.0

From: Susan Holmes notifications@github.com<mailto:notifications@github.com> Reply-To: benjjneb/dada2 reply@reply.github.com<mailto:reply@reply.github.com> Date: Tuesday, June 13, 2017 at 4:40 PM To: benjjneb/dada2 dada2@noreply.github.com<mailto:dada2@noreply.github.com> Cc: Tatiana Karpinets tvkarpinets@mdanderson.org<mailto:tvkarpinets@mdanderson.org>, Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [benjjneb/dada2] Cannot install ‘RcppParallel’ (#259)

Could you tell us what OS and what version of R and bioconductor you have by giving the sessionInfo

Thanks Susan

On Tue, Jun 13, 2017 at 1:39 PM, tvkarpinets notifications@github.com<mailto:notifications@github.com> wrote:

I want to install dada2 in my directory on a parallel server. It is failed because I was not able to install ‘RcppParallel’. I have a message installation path not writeable, unable to update packages: assertthat, backports, BiocParallel, boot, circlize, curl, dplyr, foreign, gdata, ggpubr, ggsci, Hmisc, HMMcopy, htmltools, jsonlite, knitr, markdown, MASS, Matrix, matrixStats, memoise, R6, Rcpp, readr, rmarkdown, rpart, Rsamtools, shiny, squash, stringi, survminer, tibble, XML

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/259, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvUjKzxxJPSAgZBOgK0YZa-JWEwnbks5sDvOKgaJpZM4N5Dcs .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/benjjneb/dada2/issues/259#issuecomment-308256895, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ANBGYsnKXUmJKp0U2tAA9y8bkGA11SUlks5sDwHfgaJpZM4N5Dcs. The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

spholmes commented 7 years ago

If you do not have writing permission, you have to use local libraries by installing everything using:

biocLite(pkgs, lib.loc = "~/R/local_library", lib="~/R/local_library")

For cran: (to install in your home directory pkgs

install.packages("ggplot2", lib="~/pkgs/Rpackages/")

Then when you want to call them up:

library(ggplot2, lib.loc="~/pkgs/Rpackages/")

On Tue, Jun 13, 2017 at 1:39 PM, tvkarpinets notifications@github.com wrote:

I want to install dada2 in my directory on a parallel server. It is failed because I was not able to install ‘RcppParallel’. I have a message installation path not writeable, unable to update packages: assertthat, backports, BiocParallel, boot, circlize, curl, dplyr, foreign, gdata, ggpubr, ggsci, Hmisc, HMMcopy, htmltools, jsonlite, knitr, markdown, MASS, Matrix, matrixStats, memoise, R6, Rcpp, readr, rmarkdown, rpart, Rsamtools, shiny, squash, stringi, survminer, tibble, XML

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/259, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvUjKzxxJPSAgZBOgK0YZa-JWEwnbks5sDvOKgaJpZM4N5Dcs .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

spholmes commented 7 years ago

See my next message for instructions because you are using a linux server on which you do not have write permssions you have to tel Bioconductor and R to install and use a library that is in your your home directory where you are allowed to install packages.

On Tue, Jun 13, 2017 at 2:52 PM, tvkarpinets notifications@github.com wrote:

Wow, It is so fast response. Thank you very much.

LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4. 0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing- 4.0-amd64:printing-4.0-noarch

Distributor ID: RedHatEnterpriseServer

Description: Red Hat Enterprise Linux Server release 6.4 (Santiago)

Release: 6.4

Codename: Santiago

R version 3.3.3 (2017-03-06)

Bioconductor version 3.4 (BiocInstaller 1.24.0)

sessionInfo()

R version 3.3.3 (2017-03-06)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Red Hat Enterprise Linux Server release 6.4 (Santiago)

locale:

[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C

[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8

[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8

[7] LC_PAPER=en_US.UTF-8 LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:

[1] BiocInstaller_1.24.0

From: Susan Holmes <notifications@github.com<mailto:notifications@github. com>> Reply-To: benjjneb/dada2 <reply@reply.github.com<mailto: reply@reply.github.com>> Date: Tuesday, June 13, 2017 at 4:40 PM To: benjjneb/dada2 <dada2@noreply.github.com<mailto:dada2@noreply.github. com>> Cc: Tatiana Karpinets <tvkarpinets@mdanderson.org<mailto: tvkarpinets@mdanderson.org>>, Author <author@noreply.github.com<mailto: author@noreply.github.com>> Subject: Re: [benjjneb/dada2] Cannot install ‘RcppParallel’ (#259)

Could you tell us what OS and what version of R and bioconductor you have by giving the sessionInfo

Thanks Susan

On Tue, Jun 13, 2017 at 1:39 PM, tvkarpinets <notifications@github.com< mailto:notifications@github.com>> wrote:

I want to install dada2 in my directory on a parallel server. It is failed because I was not able to install ‘RcppParallel’. I have a message installation path not writeable, unable to update packages: assertthat, backports, BiocParallel, boot, circlize, curl, dplyr, foreign, gdata, ggpubr, ggsci, Hmisc, HMMcopy, htmltools, jsonlite, knitr, markdown, MASS, Matrix, matrixStats, memoise, R6, Rcpp, readr, rmarkdown, rpart, Rsamtools, shiny, squash, stringi, survminer, tibble, XML

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/259, or mute the thread https://github.com/notifications/unsubscribe-auth/ ABJcvUjKzxxJPSAgZBOgK0YZa-JWEwnbks5sDvOKgaJpZM4N5Dcs .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ benjjneb/dada2/issues/259#issuecomment-308256895, or mute the thread< https://github.com/notifications/unsubscribe-auth/ ANBGYsnKXUmJKp0U2tAA9y8bkGA11SUlks5sDwHfgaJpZM4N5Dcs>. The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/259#issuecomment-308259680, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvYoG9U6zreff4oPus1jbuYn81wyOks5sDwScgaJpZM4N5Dcs .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

tvkarpinets commented 7 years ago

Thanks, Susan. Your recommendations are very clear. I hope it will work. Thank you very much. Tatiana.

From: Susan Holmes notifications@github.com<mailto:notifications@github.com> Reply-To: benjjneb/dada2 reply@reply.github.com<mailto:reply@reply.github.com> Date: Tuesday, June 13, 2017 at 4:58 PM To: benjjneb/dada2 dada2@noreply.github.com<mailto:dada2@noreply.github.com> Cc: Tatiana Karpinets tvkarpinets@mdanderson.org<mailto:tvkarpinets@mdanderson.org>, Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [benjjneb/dada2] Cannot install ‘RcppParallel’ (#259)

If you do not have writing permission, you have to use local libraries by installing everything using:

biocLite(pkgs, lib.loc = "~/R/local_library", lib="~/R/local_library")

For cran: (to install in your home directory pkgs

install.packages("ggplot2", lib="~/pkgs/Rpackages/")

Then when you want to call them up:

library(ggplot2, lib.loc="~/pkgs/Rpackages/")

On Tue, Jun 13, 2017 at 1:39 PM, tvkarpinets notifications@github.com<mailto:notifications@github.com> wrote:

I want to install dada2 in my directory on a parallel server. It is failed because I was not able to install ‘RcppParallel’. I have a message installation path not writeable, unable to update packages: assertthat, backports, BiocParallel, boot, circlize, curl, dplyr, foreign, gdata, ggpubr, ggsci, Hmisc, HMMcopy, htmltools, jsonlite, knitr, markdown, MASS, Matrix, matrixStats, memoise, R6, Rcpp, readr, rmarkdown, rpart, Rsamtools, shiny, squash, stringi, survminer, tibble, XML

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/259, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvUjKzxxJPSAgZBOgK0YZa-JWEwnbks5sDvOKgaJpZM4N5Dcs .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/benjjneb/dada2/issues/259#issuecomment-308260938, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ANBGYhgPrAaLhJjw35eV9qrEBiZRyQzyks5sDwXsgaJpZM4N5Dcs. The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

tvkarpinets commented 7 years ago

I am sorry,Susan, it works for most packages, but it doesn’t work for

RcppParallel, at least on our server.

From: Susan Holmes notifications@github.com<mailto:notifications@github.com> Reply-To: benjjneb/dada2 reply@reply.github.com<mailto:reply@reply.github.com> Date: Tuesday, June 13, 2017 at 4:59 PM To: benjjneb/dada2 dada2@noreply.github.com<mailto:dada2@noreply.github.com> Cc: Tatiana Karpinets tvkarpinets@mdanderson.org<mailto:tvkarpinets@mdanderson.org>, Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [benjjneb/dada2] Cannot install ‘RcppParallel’ (#259)

See my next message for instructions because you are using a linux server on which you do not have write permssions you have to tel Bioconductor and R to install and use a library that is in your your home directory where you are allowed to install packages.

On Tue, Jun 13, 2017 at 2:52 PM, tvkarpinets notifications@github.com<mailto:notifications@github.com> wrote:

Wow, It is so fast response. Thank you very much.

LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4. 0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing- 4.0-amd64:printing-4.0-noarch

Distributor ID: RedHatEnterpriseServer

Description: Red Hat Enterprise Linux Server release 6.4 (Santiago)

Release: 6.4

Codename: Santiago

R version 3.3.3 (2017-03-06)

Bioconductor version 3.4 (BiocInstaller 1.24.0)

sessionInfo()

R version 3.3.3 (2017-03-06)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Red Hat Enterprise Linux Server release 6.4 (Santiago)

locale:

[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C

[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8

[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8

[7] LC_PAPER=en_US.UTF-8 LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:

[1] BiocInstaller_1.24.0

From: Susan Holmes notifications@github.com<mailto:notifications@github.com<mailto:notifications@github. com>> Reply-To: benjjneb/dada2 reply@reply.github.com<mailto:reply@reply.github.com<mailto: reply@reply.github.commailto:reply@reply.github.com>> Date: Tuesday, June 13, 2017 at 4:40 PM To: benjjneb/dada2 dada2@noreply.github.com<mailto:dada2@noreply.github.com<mailto:dada2@noreply.github. com>> Cc: Tatiana Karpinets tvkarpinets@mdanderson.org<mailto:tvkarpinets@mdanderson.org<mailto: tvkarpinets@mdanderson.orgmailto:tvkarpinets@mdanderson.org>>, Author author@noreply.github.com<mailto:author@noreply.github.com<mailto: author@noreply.github.commailto:author@noreply.github.com>> Subject: Re: [benjjneb/dada2] Cannot install ‘RcppParallel’ (#259)

Could you tell us what OS and what version of R and bioconductor you have by giving the sessionInfo

Thanks Susan

On Tue, Jun 13, 2017 at 1:39 PM, tvkarpinets notifications@github.com<mailto:notifications@github.com< mailto:notifications@github.com>> wrote:

I want to install dada2 in my directory on a parallel server. It is failed because I was not able to install ‘RcppParallel’. I have a message installation path not writeable, unable to update packages: assertthat, backports, BiocParallel, boot, circlize, curl, dplyr, foreign, gdata, ggpubr, ggsci, Hmisc, HMMcopy, htmltools, jsonlite, knitr, markdown, MASS, Matrix, matrixStats, memoise, R6, Rcpp, readr, rmarkdown, rpart, Rsamtools, shiny, squash, stringi, survminer, tibble, XML

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/259, or mute the thread https://github.com/notifications/unsubscribe-auth/ ABJcvUjKzxxJPSAgZBOgK0YZa-JWEwnbks5sDvOKgaJpZM4N5Dcs .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ benjjneb/dada2/issues/259#issuecomment-308256895, or mute the thread< https://github.com/notifications/unsubscribe-auth/ ANBGYsnKXUmJKp0U2tAA9y8bkGA11SUlks5sDwHfgaJpZM4N5Dcs>. The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/259#issuecomment-308259680, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvYoG9U6zreff4oPus1jbuYn81wyOks5sDwScgaJpZM4N5Dcs .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/benjjneb/dada2/issues/259#issuecomment-308261263, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ANBGYnVMITrkdW2RnnwwSIyz1Fm2bXmgks5sDwZGgaJpZM4N5Dcs. The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

benjjneb commented 7 years ago

Installing other R packages in the absence of write permissions is a bit beyond my expertise. Since this is a general R question (not really a dada2 question) have you considered asking at a more general forum, perhaps the Bioconductor support forum?