Question: how to install package of "rnaseqGene" for R (ver: 3.5.2) for windows
0
gravatar for mheydarpour
10 weeks ago by
mheydarpour10
mheydarpour10 wrote:

I have difficulty to install the package of "rnaseqGene" to my R (3.5.2) in windows desktop. I used the following 4 different ways to install, however none of them is working and give me an error. Is there any comment or solution for this issue?

install.packages("http://bioconductor.org/packages/rnaseqGene/")

install.packages("https://github.com/mikelove/rnaseqGene/")

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("rnaseqGene")

install.packages("C:/Users/name/AppData/Local/Temp/RtmpUfCddW/downloadedpackages/rnaseqGene1.7.1.tar.gz")

rnaseqgene • 99 views
ADD COMMENTlink modified 10 weeks ago by James W. MacDonald49k • written 10 weeks ago by mheydarpour10
Answer: how to install package of "rnaseqGene" for R (ver: 3.5.2) for windows
1
gravatar for James W. MacDonald
10 weeks ago by
United States
James W. MacDonald49k wrote:

Why are you doing all these random things? You evidently know about BiocManager::install, which is the only way you should be installing any Bioconductor package.

> library(BiocManager)
Bioconductor version 3.8 (BiocManager 1.30.4), ?BiocManager::install for help
Warning message:
package 'BiocManager' was built under R version 3.5.1 
> install("rnaseqGene")
<snip>
* DONE (rnaseqGene)
In R CMD INSTALL

> library(rnaseqGene)
<snip, again>
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

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

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] rnaseqGene_1.4.1            fission_1.2.0              
 [3] RUVSeq_1.16.1               edgeR_3.24.3               
 [5] limma_3.38.3                EDASeq_2.16.3              
 [7] ShortRead_1.40.0            sva_3.30.1                 
 [9] mgcv_1.8-23                 nlme_3.1-137               
[11] Gviz_1.26.4                 ReportingTools_2.22.1      
[13] knitr_1.21                  org.Hs.eg.db_3.7.0     

There is one source install in there, which doesn't have any C code, so I think it should install OK on any Windows box. Howeva, I could be wrong, and given that I have Rtools installed, that might be why it works for me and not for you. So you could try installing the Rtools if BiocManager::install doesn't work.

Also, you need in future to show the output from your attempts, as nobody can really help you if you just say 'I tried this thing and it did not work'. That is not a useful thing to tell anybody. Didn't work how? What happened? Did your computer explode?

ADD COMMENTlink written 10 weeks ago by James W. MacDonald49k

Thank you very much James. So informative messages. I installed the package successfully!

ADD REPLYlink written 10 weeks ago by mheydarpour10
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