The-Bioinformatics-Group / Albiorix

Code used for configuration and administration of the bioinformatics computer cluster Albiorix at the Department of Biological and Environmental Sciences and Marine sciences, University of Gothenburg.

http://albiorix.bioenv.gu.se/

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Rscript #102

Closed paolaferreira closed 6 years ago

paolaferreira commented 6 years ago

Hello everyone, I found this error when I was trying to do the R script (secapr_env) [paola@albiorix trimming_default]$ Rscript fastqc_visualization.r -i /nobackup/data14/paola/barna_sequences/trimming_default/fastq-results -o /nobackup/data14/paola/barna_sequences/trimming_default/fastq-results/fastq-result.pdf Loading required package: optparse Loading required package: tidyverse Warning in install.packages("tidyverse", repos = "http://cran.us.r-project.org") : 'lib = "/state/partition1/home/local/packages/R-3.1.3/library"' is not writable Error in install.packages("tidyverse", repos = "http://cran.us.r-project.org") : unable to install packages In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'tidyverse' Execution halted

How can I fix it?

Thanks..

mtop commented 6 years ago

Hi @paolaferreira I have installed tidyverse for version 3.2.3 of R. Hope that is fine? Uou can access that version by furst running the command module load R/v.3.2.3. There might be other dependencies missing so give it a try and let me know if it doesn't work.

Cheers

Mats

paolaferreira commented 6 years ago

Now, the script is requesting another package

[paola@albiorix trimming_default]$ Rscript fastqc_visualization.r -i /nobackup/data14/paola/barna_sequences/trimming_default/ -o /nobackup/data14/paola/barna_sequences/trimming_default/fastq-results/summary_all_samples_default.pdf Loading required package: optparse Warning in install.packages("optparse", repos = "http://cran.us.r-project.org") : 'lib = "/state/partition1/home/local/packages/R-3.2.3/library"' is not writable Error in install.packages("optparse", repos = "http://cran.us.r-project.org") : unable to install packages In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'optparse' Execution halted

mtop commented 6 years ago

OK, installed that now. Try again.

Mats

paolaferreira commented 6 years ago

[paola@albiorix trimming_default]$ Rscript fastqc_visualization.r -i /nobackup/data14/paola/barna_sequences/trimming_default/ -o /nobackup/data14/paola/barna_sequences/trimming_default/fastq-results/summary_all_samples_default.pdf Loading required package: optparse Loading required package: tidyverse Warning: program compiled against libxml 209 using older 207 Loading tidyverse: ggplot2 Loading tidyverse: tibble Loading tidyverse: tidyr Loading tidyverse: readr Loading tidyverse: purrr Loading tidyverse: dplyr Conflicts with tidy packages --------------------------------------------------- filter(): dplyr, stats lag(): dplyr, stats Warning message: In .doLoadActions(where, attach) : trying to execute load actions without 'methods' package Error in overscope_eval_next(overscope, expr) : object 'sample_id' not found Calls: %>% ... map -> lapply -> FUN -> overscope_eval_next -> .Call Execution halted

mtop commented 6 years ago

Hi again Not sure what causes this, but found something similar at https://github.com/STAT545-UBC/Discussion/issues/331. I think you should contact the developer of this package to see if you can get some help.

Alternatively you can try the version installed under version 3.3.2 /module load R/v.3.3.2.

Cheers