Question

Installing SigneR problem

0

Entering edit mode

taha.valizadeh • 0

@tahavalizadeh-18960

Last seen 6.0 years ago

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* 6 packages out-of-date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6 packages out-of-date; 2 packages too new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 • 1.2k views

ADD COMMENT • link updated 6.0 years ago by shepherl 4.1k • written 6.0 years ago by taha.valizadeh • 0

score 1 · Answer 1 · 2018-12-20

1

Entering edit mode

shepherl 4.1k

@lshep

Last seen 1 hour ago

United States

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 COMMENT • link 6.0 years ago shepherl 4.1k

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Entering edit mode

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 REPLY • link 6.0 years ago taha.valizadeh • 0

0

Entering edit mode

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 REPLY • link 6.0 years ago shepherl 4.1k