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Having issue installing #1

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shk44 opened this issue Apr 18, 2020 · 1 comment
Open

Having issue installing #1

shk44 opened this issue Apr 18, 2020 · 1 comment

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@shk44
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shk44 commented Apr 18, 2020

Looking to use the wrapper trim_fastq for R. Trying to install the package on Windows.

> remotes::install_github("anilchalisey/rseqR", force=TRUE)
I get the error:

Downloading GitHub repo anilchalisey/rseqR@master
....
Error in parse(outFile) : 
  C:/Users/.../AppData/Local/Temp/Rtmp270b2M/R.INSTALL56286f931d24/rseqR/R/pathway_analysis.R:76:12: unexpected '{'
75:   # if plotting then do so here - we plot the top 3 upregulated and downregulated
76:   if (plot {
               ^
ERROR: unable to collate and parse R files for package 'rseqR'
* removing 'D:/R_library/rseqR'
* restoring previous 'D:/R_library/rseqR'
Error: Failed to install 'rseqR' from GitHub:
  (converted from warning) installation of package ‘C:/Users/.../AppData/Local/Temp/RtmpQ37IIz/file59983ea65739/rseqR_0.0.1.1.tar.gz’ had non-zero exit status

Tried to manually unpack the package and delete the pathway_analysis file, but that didn't work either.

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    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] remotes_2.1.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6      rstudioapi_0.11   magrittr_1.5      usethis_1.5.1     devtools_2.2.1    pkgload_1.0.2     R6_2.4.1          rlang_0.4.5       fansi_0.4.1      
[10] tools_3.6.0       pkgbuild_1.0.6    sessioninfo_1.1.1 cli_2.0.2         withr_2.1.2       ellipsis_0.3.0    assertthat_0.2.1  digest_0.6.25     rprojroot_1.3-2  
[19] crayon_1.3.4      processx_3.4.2    callr_3.4.3       fs_1.3.1          ps_1.3.2          curl_4.3          testthat_2.3.2    memoise_1.1.0     glue_1.4.0       
[28] compiler_3.6.0    desc_1.2.0        backports_1.1.6   prettyunits_1.1.1
@jliu678
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jliu678 commented Dec 9, 2020

I just submit a pull request for this

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