difficulty installing pathtrackr in r on github

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I am trying to install the pathtrackr package, I expected when running the code install_github("aharmer/pathtrackr", build_vignettes = TRUE) the package was installed, however when executing the code the output message is:

These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

 1: All                                
 2: CRAN packages only                 
 3: None                               
 4: Rcpp      (1.0.3  -> 1.0.4 ) [CRAN]
 5: testthat  (2.3.0  -> 2.3.2 ) [CRAN]
 6: digest    (0.6.22 -> 0.6.25) [CRAN]
 7: rlang     (0.4.1  -> 0.4.5 ) [CRAN]
 8: glue      (1.3.1  -> 1.4.0 ) [CRAN]
 9: backports (1.1.5  -> 1.1.6 ) [CRAN]
10: processx  (3.4.1  -> 3.4.2 ) [CRAN]
11: ps        (1.3.0  -> 1.3.2 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:

Downloading GitHub repo aoles/EBImage@master
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                                   
2: CRAN packages only                    
3: None                                  
4: BiocGenerics (0.30.0 -> 0.32.0) [CRAN]
5: digest       (0.6.22 -> 0.6.25) [CRAN]
6: Rcpp         (1.0.3  -> 1.0.4 ) [CRAN]
7: rlang        (0.4.1  -> 0.4.5 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:

√  checking for file 'C:\Users\Usuário\AppData\Local\Temp\RtmpauObSg\remotes2c3046934f4\aoles-EBImage-e750cd7/DESCRIPTION' (4.1s)
-  preparing 'EBImage': (1.2s)
√  checking DESCRIPTION meta-information ... 
-  cleaning src
-  installing the package to build vignettes (763ms)
E  creating vignettes (52.3s)
   --- re-building 'EBImage-introduction.Rmd' using rmarkdown
   Error: processing vignette 'EBImage-introduction.Rmd' failed with diagnostics:
   there is no package called 'BiocStyle'
   --- failed re-building 'EBImage-introduction.Rmd'

   SUMMARY: processing the following file failed:
     'EBImage-introduction.Rmd'

   Erro: Vignette re-building failed.
   Execução interrompida
Erro: Failed to install 'pathtrackr' from GitHub:
  Failed to install 'EBImage' from GitHub:
  System command error, exit status: 1, stdout + stderr (last 10 lines):
E> --- re-building 'EBImage-introduction.Rmd' using rmarkdown
E> Error: processing vignette 'EBImage-introduction.Rmd' failed with diagnostics:
E> there is no package called 'BiocStyle'
E> --- failed re-building 'EBImage-introduction.Rmd'
E> 
E> SUMMARY: processing the following file failed:
E>   'EBImage-introduction.Rmd'
E> 
E> Erro: Vignette re-building failed.
E> Execução interrompida
>  

I have limited knowledge of programming and if you can help me with reading guides or tutorials I will be grateful, my operating system is windows 10 home. I tried to update devtools and download ebimage separately, but nothing works.

  • Hello, you’re using Rstudio?

  • The missing package, 'BiocStyle' is a package Bioconductor. Behold here how to install it. Then try installing that Github package again.

  • Hello thank you and I’m sorry for the delay. I use Rstudio and downloaded 'Biocstyle'.

  • I downloaded separately the Ebimage, however the next error found was: Error in file(file, if (append) "a" else "w") : 
 (convertido do aviso) cannot open file 'C:/Users/Usuario/Documents/R/win-library/3.6/00LOCK-reshape2/00new/reshape2/DESCRIPTION': No such file or directory
ERROR: installing package DESCRIPTION failed for package 'reshape2'
* removing 'C:/Users/Usuário/Documents/R/win-library/3.6/reshape2'
Erro: Failed to install 'pathtrackr' from GitHub:
 (convertido do aviso) installation of package ‘reshape2’ had non-zero exit status

  • I was able to install by setting the specific directory install.packages("remotes")
remotes::install_github("aharmer/pathtrackr", lib="C:/Program Files/R/R-3.6.3/library")

  • @Augustogonçalves I’m glad you were able to solve your problem. Now post the solution as an answer here on this topic and then mark it as "answer accepted". So it will help other people who are having the same problem.

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