Question: Installing SigneR problem
0
gravatar for taha.valizadeh
7 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  * 6 packages out-of-date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6 packages out-of-date; 2 packages too new 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 • 211 views
ADD COMMENTlink modified 7 months ago by shepherl ♦♦ 1.4k • written 7 months ago by taha.valizadeh0
Answer: Installing SigneR problem
1
gravatar for shepherl
7 months ago by
shepherl ♦♦ 1.4k
United States
shepherl ♦♦ 1.4k 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 7 months ago by shepherl ♦♦ 1.4k

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 6 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 6 months ago by shepherl ♦♦ 1.4k
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