Question: Installing SigneR problem
0
gravatar for taha.valizadeh
11 months ago by
taha.valizadeh0 wrote:

Hi,

 

I hope you are having a good time.

My name is Taha ValizadehAslani. I am a graduate student at EESI lab Drexel University.

We are interested in your software package SigneR, but I have some troubles installing it. My R version 3.5.1. and I am on a windows 7 computer. This is the error that I get when I try to install it.

ERROR: dependencies 'Rcpp', 'later' are not available for package 'httpuv'
* removing 'C:/ProgramData/Anaconda2/envs/mro_env/lib/R/library/httpuv'
In R CMD INSTALL
ERROR: dependencies 'htmlwidgets', 'jsonlite', 'rstudioapi' are not available for package 'r2d3'
* removing 'C:/ProgramData/Anaconda2/envs/mro_env/lib/R/library/r2d3'
In R CMD INSTALL

When I try BiocManager::valid()  I get the following messaage:

* sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RevoUtils_11.0.1     RevoUtilsMath_11.0.0

loaded via a namespace (and not attached):
[1] BiocManager_1.30.4  compiler_3.5.1      tools_3.5.1         BiocParallel_1.16.2

Bioconductor version '3.8'

  * 6 packages out-of-date
  * 2 packages too new

create a valid installation with

  BiocManager::install(c(
    "foreach", "mongolite", "packrat", "rbokeh", "rJava", "RJSONIO", "rsconnect",
    "sparklyr"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
6 packages out-of-date; 2 packages too new 

Can you help me with this?

Thanks,

Taha

signer install error • 264 views
ADD COMMENTlink modified 11 months ago by shepherl ♦♦ 1.7k • written 11 months ago by taha.valizadeh0
Answer: Installing SigneR problem
1
gravatar for shepherl
11 months ago by
shepherl ♦♦ 1.7k
United States
shepherl ♦♦ 1.7k wrote:

The first two ERRORs indicate there are missing dependencies on your system. You could try

BiocManager::install(c('Rcpp', 'later', 'htmlwidgets', 'jsonlite', 'rstudioapi'))

as those were the missing dependencies listed above - then try installing SigneR again

BiocManager::install('SigneR')

You could also try as suggested doing the

  BiocManager::install(c(
    "foreach", "mongolite", "packrat", "rbokeh", "rJava", "RJSONIO", "rsconnect",
    "sparklyr"
  ), update = TRUE, ask = FALSE)

To get a valid installation of packages as some appear to have been updated.

ADD COMMENTlink written 11 months ago by shepherl ♦♦ 1.7k

Thank you very much for your answer.

I did that and it helped. I installed SigneR, but I still keep getting error messages when I try to load the library. This is the error message:

Error: package or namespace load failed for ‘SummarizedExperiment’ in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘Matrix’
Error: package ‘SummarizedExperiment’ could not be loaded

Can you please tell me what to do?

ADD REPLYlink written 11 months ago by taha.valizadeh0

If there are any other ERRORs like there is no package called try installing the missing package with BiocManager::install so in this case try BiocManager::install('Matrix')

ADD REPLYlink written 11 months ago by shepherl ♦♦ 1.7k
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