How to install packages "mapsnp" in R?

Question

[Sherry]

Hi, I found the article about how to draw snp map: https://scfbm.biomedcentral.com/articles/10.1186/s13029-016-0052-z

However, no matter how hard I tried, R still shows to me "package ‘mapsnp’ is not available (for R version 3.4.0)".

Please help me if you know how to solve the problem.

[venu]

From this page (reference - 8 from paper), you should be able to install, it syays R > 2.15.*

Did you try downloading *tar.gz file and install ? May be it is not in CRAN. Download manually and install.

[Sherry]

Hi Venu, I downloaded the *tar.gz file, but I don't know how to install in R. (I'm strange to Linux.) If you can teach me how to install, that would be great. Thank you.

Answer 1

[venu]

Ok, but first move your answer as a comment to original post. (moderate -> Move post to a comment on the top level post).

And check this, Installing an R package

In future, please use ADD COMMENT or ADD REPLY button to comment something.

UPDATE

Authors haven't configured the repository properly. Do the following

library("devtools")

install_github("csuzfq/mapsnp_pkg/mapsnp")

It works fine

Downloading GitHub repo csuzfq/mapsnp_pkg@master
from URL https://api.github.com/repos/csuzfq/mapsnp_pkg/zipball/master
Installing mapsnp
'/usr/local/Cellar/r/3.3.3/R.framework/Resources/bin/R' --no-site-file  \
  --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/1z/4hxh0srn2c73cws8pc19_6ym0000gn/T/RtmpfTVCip/devtools16a41e50b597/csuzfq-mapsnp_pkg-cb6c8bf/mapsnp'  \
  --library='/usr/local/lib/R/3.3/site-library' --install-tests

* installing *binary* package ‘mapsnp’ ...
* DONE (mapsnp)

[WouterDeCoster]

Hi venu

If it turns out that this solves the issue, please repost your solution (both comments together) as an answer, as such this solution can get accepted.

Cheers, Wouter

[Sherry]

Hi venu,

I input

> install.packages("devtools")
> require(devtools)
> install_github("mapsnp","csuzfq")

---

Here are the address of the package：https://github.com/csuzfq/mapsnp_pkg

but R gives me ：

Downloading GitHub repo csuzfq/mapsnp@master from URL https://api.github.com/repos/csuzfq/mapsnp/zipball/master Error: Does not appear to be an R package (no DESCRIPTION) In addition: Warning message: Username parameter is deprecated. Please use csuzfq/mapsnp

---

what is wrong with my code?

Thank you.

[venu]

@pompompurin2004 - check the update.

[Sherry]

Hi @venu, Thank you for your reply. It is really clear and helpful. I learn a lot. I followed what you have written to me. But R shows me:

Downloading GitHub repo csuzfq/mapsnp_pkg@master from URL https://api.github.com/repos/csuzfq/mapsnp_pkg/zipball/master Installing mapsnp Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) && : missing value where TRUE/FALSE needed

What happened to it? I don't understand what it means.

Could you help me? Thank you.

[venu]

@Sherry, I don't know why this error is showing up. It installed properly in my machine. Try this

getOption("unzip")
options(unzip="internal")
install_github("csuzfq/mapsnp_pkg/mapsnp")

Also what R version are you using? Posting sessionInfo() output might help.

[Sherry]

Hi @venu, I have tried the code you gave, but it seems not working. Here is my R version:

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Traditional)_Hong Kong SAR.950 
[2] LC_CTYPE=Chinese (Traditional)_Hong Kong SAR.950   
[3] LC_MONETARY=Chinese (Traditional)_Hong Kong SAR.950
[4] LC_NUMERIC=C                                       
[5] LC_TIME=Chinese (Traditional)_Hong Kong SAR.950    

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

other attached packages:
[1] devtools_1.12.0

loaded via a namespace (and not attached):
[1] httr_1.2.1     compiler_3.4.0 R6_2.2.0       tools_3.4.0    withr_1.0.2    curl_2.6      
[7] memoise_1.1.0  git2r_0.18.0   digest_0.6.12

Maybe my computer has too many problems, I can try it on my friend's computer tomorrow. Thank you. :))

[Sherry]

When I run the code, the R shows：

> install_github("csuzfq/mapsnp_pkg/mapsnp")
Downloading GitHub repo csuzfq/mapsnp_pkg@master
from URL https://api.github.com/repos/csuzfq/mapsnp_pkg/zipball/master
Installing mapsnp
"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD  \
  INSTALL  \
  "C:/Users/user/AppData/Local/Temp/Rtmp0EekOl/devtools4186c8b64e8/csuzfq-mapsnp_pkg-cb6c8bf/mapsnp"  \
  --library="C:/Users/user/Documents/R/win-library/3.4" --install-tests 

* installing *binary* package 'mapsnp' ...
Warning: 執行中命令 'cp -R . "C:/Users/user/Documents/R/win-library/3.4/mapsnp" || ( internal cd - .| (cd "C:/Users/user/Documents/R/win-library/3.4/mapsnp" && internal -xf -))' 已有狀態 127
ERROR: installing binary package failed
* removing 'C:/Users/user/Documents/R/win-library/3.4/mapsnp'
Error: Command failed (1)

[venu]

I'm strange to Linux

from this comment on original thread, I thought you are using Linux machine but from the error above it seems you are using windows machine. I don't know how to install these packages (atleast how to debug) in windows machine. I think you can't install from Github in a windows machine but I'm not sure.

P.S - Better switch to linux :)

[WouterDeCoster]

I can confirm that your Linux solution works for me.

[Sherry]

That's right. My teacher also uses window system, but he can not install it. Thank you for your clear and helpful reply and suggestion. :))

[WouterDeCoster]

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below: