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malucalle / selbal

selbal: selection of balances for microbial signatures
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selbal install error #7

Open marine11 opened 4 years ago

marine11 commented 4 years ago

hi,

An error occurs during installation.

devtools::install_github(repo = "UVic-omics/selbal")

---- error----- Downloading GitHub repo UVic-omics/selbal@master Warning message in system(paste(TAR, "--version >", tf, "2>&1")): “error in running command”Warning message in system(cmd): “error in running command”Warning message in utils::untar(tarfile, ...): “‘/usr/bin/gzip -dc '/datavd/tmp//RtmpoIDfFk/file371554aced05.tar.gz' | /bin/gtar -xf '-' -C '/data/d/tmp//RtmpoIDfFk/remotes37156a835221'’ returned error code 127”Warning message in system(paste(TAR, "--version >", tf, "2>&1")): “error in running command”

And one more question. What is the average running time of selbal.cv? 400x300 data is still running for 5 hours and I wonder if it is normal.

What's wrong? Thank you.

UVic-omics commented 4 years ago

Hi @marine11,

There have been some changes with devtools, so what used to work before probably now is obsolete. Nevertheless, at the main page you have the following alternative (which seems to work for Windows users):

devtools::install_url(url="https://github.com/UVic-omics/selbal/archive/master.zip", INSTALL_opt= "--no-multiarch")

Try to run it and tell us if it works for you.

About the average time of ruuning selbal, . . . it depends on many things: the number of kernels of your computer, the number of samples and the number of taxa. Having 300 taxa, it is normal to spend so many time. Before running selbal you should wonder if all of them could be relevant in the study; we mean, taxa with a high presence of zeros would not contribute to explaining the response variable; so we recomend you to consider those with a low presence of zero values.

guitar21 commented 4 years ago

Hi,

I have this problem when trying to install this package. Any help would be much appreciated.

devtools::install_url(url="https://github.com/UVic-omics/selbal/archive/master.zip",

1: All
2: CRAN packages only
3: None
4: rlang (0.4.0 -> 0.4.2 ) [CRAN] 5: scales (1.0.0 -> 1.1.0 ) [CRAN] 6: Rcpp (1.0.2 -> 1.0.3 ) [CRAN] 7: data.table (1.12.2 -> 1.12.6 ) [CRAN] 8: igraph (1.2.4.1 -> 1.2.4.2) [CRAN] 9: R6 (2.4.0 -> 2.4.1 ) [CRAN] 10: backports (1.1.4 -> 1.1.5 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1 rlang (0.4.0 -> 0.4.2 ) [CRAN] scales (1.0.0 -> 1.1.0 ) [CRAN] Rcpp (1.0.2 -> 1.0.3 ) [CRAN] data.table (1.12.2 -> 1.12.6 ) [CRAN] igraph (1.2.4.1 -> 1.2.4.2) [CRAN] R6 (2.4.0 -> 2.4.1 ) [CRAN] backports (1.1.4 -> 1.1.5 ) [CRAN] Installing 7 packages: rlang, scales, Rcpp, data.table, igraph, R6, backports Installing packages into ‘C:/R/R-3.5.2/library’ (as ‘lib’ is unspecified)

There is a binary version available but the source version is later: binary source needs_compilation igraph 1.2.4.1 1.2.4.2 TRUE

Error: Failed to install 'unknown package' from URL: Cancelled by user

UVic-omics commented 4 years ago

Hi @guitar21 ! First of all thank you for your comment, we will try to help you solving the issue. Please run the following lines (before running them close RStudio and R and open a new session) and tell us if it works.

# Install devtools if you did not
   library(devtools)
# Install selbal
   install_github("https://github.com/UVic-omics/selbal")

Best regards,
guitar21 commented 4 years ago

Hi there,

I closed the session and ran the above code and this is the output. I always get to this stage but always get different warning messages.

.libPaths("C:/R/R-3.5.2/library")> library(devtools)Loading required package: usethis> library("usethis", lib.loc="C:/R/R-3.5.2/library")> library(devtools)> install_github("https://github.com/UVic-omics/selbal")Downloading GitHub repo UVic-omics/selbal@masterThese packages have more recent versions available. Which would you like to update?

1: All 2: CRAN packages only 3: None 4: igraph (1.2.4.1 -> 1.2.4.2) [CRAN] 5: R6 (2.4.0 -> 2.4.1 ) [CRAN] 6: backports (1.1.4 -> 1.1.5 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:1igraph (1.2.4.1 -> 1.2.4.2) [CRAN] R6 (2.4.0 -> 2.4.1 ) [CRAN] backports (1.1.4 -> 1.1.5 ) [CRAN]Installing 3 packages: igraph, R6, backportsInstalling packages into ‘C:/R/R-3.5.2/library’ (as ‘lib’ is unspecified)trying URL 'https://mirror.aarnet.edu.au/pub/CRAN/bin/windows/contrib/3.5/igraph_1.2.4.2.zip'Content type 'application/zip' length 9162440 bytes (8.7 MB)downloaded 8.7 MB trying URL 'https://mirror.aarnet.edu.au/pub/CRAN/bin/windows/contrib/3.5/R6_2.4.1.zip'Content type 'application/zip' length 58868 bytes (57 KB)downloaded 57 KB trying URL 'https://mirror.aarnet.edu.au/pub/CRAN/bin/windows/contrib/3.5/backports_1.1.5.zip'Content type 'application/zip' length 67825 bytes (66 KB)downloaded 66 KB package ‘igraph’ successfully unpacked and MD5 sums checked package ‘R6’ successfully unpacked and MD5 sums checked package ‘backports’ successfully unpacked and MD5 sums checkedError: Failed to install 'selbal' from GitHub: (converted from warning) cannot remove prior installation of package ‘backports’

Any suggestions?

Cheers,

Liz

On Tue, Dec 10, 2019 at 11:31 PM UVic-omics notifications@github.com wrote:

Hi @guitar21 https://github.com/guitar21 ! First of all thank you for your comment, we will try to help you solving the issue. Please run the following lines (before running them close RStudio and R and open a new session) and tell us if it works.

Install devtools if you did not

library(devtools)

Install selbal

install_github("https://github.com/UVic-omics/selbal")

Best regards,

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/UVic-omics/selbal/issues/7?email_source=notifications&email_token=AN4WJDOILF6WBFERI73W7DTQX6DYVA5CNFSM4JEAM3K2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGPCEYY#issuecomment-564011619, or unsubscribe https://github.com/notifications/unsubscribe-auth/AN4WJDLXFRIIHZCHJWAWUHDQX6DYVANCNFSM4JEAM3KQ .

UVic-omics commented 4 years ago

I think it is a problem because of "backports" package. I have searched it in stackoverflow and read some possible ways to fix it.

One of them suggests to close all the R sessions opened in your computer, remove and reinstall the package (manually). Anyway, I post the link where I found it (just writing in Google "cannot remove prior instalation R"):

https://stackoverflow.com/questions/26570912/error-in-installation-a-r-package