[R] unable to install source packages with Rtools installed

Jim Lemon drj|m|emon @end|ng |rom gm@||@com
Wed Aug 25 07:56:08 CEST 2021


Hi Xiaoyu,
"non-zero exit status" is just a fancy way of saying something went
wrong. An old computing convention is for a function to return zero
(FALSE) for success or some positive integer that tells you what the
error was. In general, when you have a sequence of interdependent
functions or programs, if one goes wrong, all subsequent ones usually
do, too.

Jim

On Wed, Aug 25, 2021 at 11:16 AM Xiaoyu Zeng <xiaoyuzengpsy using gmail.com> wrote:
>
> Thanks for replying, Jim and Bert.
>
> I installed proxy and reinstalled jsonlite, but it failed again. I even tried setting ''dependencies = TRUE", and it turned out with the same error "had non-zero exit status". Session info and error information were enclosed.
>
> I need to ensure Rtool work and I can install package from source as I need to install a package from Github. But I had no clue about the error "had non-zero exit status". Any ideas?
>
> Best regards,
> Xiaoyu
>
> Error info:
> install.packages("jsonlite", type = "source",dependencies = TRUE)
> 还安装相依关系‘e1071’, ‘wk’, ‘tinytex’, ‘R.cache’, ‘classInt’, ‘DBI’, ‘s2’, ‘units’, ‘rmarkdown’, ‘R.rsp’, ‘sf’
>
> trying URL 'https://cran.rstudio.com/src/contrib/e1071_1.7-8.tar.gz'
> Content type 'application/x-gzip' length 581347 bytes (567 KB)
> downloaded 567 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/wk_0.5.0.tar.gz'
> Content type 'application/x-gzip' length 138686 bytes (135 KB)
> downloaded 135 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/tinytex_0.33.tar.gz'
> Content type 'application/x-gzip' length 30085 bytes (29 KB)
> downloaded 29 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/R.cache_0.15.0.tar.gz'
> Content type 'application/x-gzip' length 34692 bytes (33 KB)
> downloaded 33 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/classInt_0.4-3.tar.gz'
> Content type 'application/x-gzip' length 403884 bytes (394 KB)
> downloaded 394 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/DBI_1.1.1.tar.gz'
> Content type 'application/x-gzip' length 743802 bytes (726 KB)
> downloaded 726 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/s2_1.0.6.tar.gz'
> Content type 'application/x-gzip' length 1605788 bytes (1.5 MB)
> downloaded 1.5 MB
>
> trying URL 'https://cran.rstudio.com/src/contrib/units_0.7-2.tar.gz'
> Content type 'application/x-gzip' length 855840 bytes (835 KB)
> downloaded 835 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/rmarkdown_2.10.tar.gz'
> Content type 'application/x-gzip' length 3248794 bytes (3.1 MB)
> downloaded 3.1 MB
>
> trying URL 'https://cran.rstudio.com/src/contrib/R.rsp_0.44.0.tar.gz'
> Content type 'application/x-gzip' length 823684 bytes (804 KB)
> downloaded 804 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/sf_1.0-2.tar.gz'
> Content type 'application/x-gzip' length 3645982 bytes (3.5 MB)
> downloaded 3.5 MB
>
> trying URL 'https://cran.rstudio.com/src/contrib/jsonlite_1.7.2.tar.gz'
> Content type 'application/x-gzip' length 421716 bytes (411 KB)
> downloaded 411 KB
>
> Warning in install.packages :
>   installation of package ‘e1071’ had non-zero exit status
> Warning in install.packages :
>   installation of package ‘wk’ had non-zero exit status
> Warning in install.packages :
>   installation of package ‘tinytex’ had non-zero exit status
> Warning in install.packages :
>   installation of package ‘R.cache’ had non-zero exit status
> Warning in install.packages :
>   installation of package ‘DBI’ had non-zero exit status
> Warning in install.packages :
>   installation of package ‘units’ had non-zero exit status
> Warning in install.packages :
>   installation of package ‘jsonlite’ had non-zero exit status
> Warning in install.packages :
>   installation of package ‘classInt’ had non-zero exit status
> Warning in install.packages :
>   installation of package ‘s2’ had non-zero exit status
> Warning in install.packages :
>   installation of package ‘rmarkdown’ had non-zero exit status
> Warning in install.packages :
>   installation of package ‘R.rsp’ had non-zero exit status
> Warning in install.packages :
>   installation of package ‘sf’ had non-zero exit status
>
> The downloaded source packages are in
> ‘C:\Users\xiaoy\AppData\Local\Temp\RtmpoPSf4N\downloaded_packages’
>
> Session info:
> > sessionInfo()
> R version 4.1.1 (2021-08-10)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 18363)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936
> [3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
> [5] LC_TIME=Chinese (Simplified)_China.936
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] compiler_4.1.1 tools_4.1.1
>
>
> Xiaoyu Zeng
>
> Graduate student, Social and Affective NeuroPharmacology (SANP) Lab
>
> State Key Laboratory of Cognitive Neuroscience and Learning
>
> Beijing Normal University
>
> http://brain.bnu.edu.cn/home/yinama/
>
>
>
> Jim Lemon <drjimlemon using gmail.com> 于2021年8月25日周三 上午7:09写道:
>>
>> Hi Xiaoyu,
>> From your github posting, it seems that the "proxy" package failed for
>> some reason. As the following packages probably depend upon "proxy",
>> installation for them will usually fail, too. Maybe "proxy" or some of
>> the other packages aren't source but require compiling? Have you tried
>> install.packages()? I see that "proxy" is available on CRAN.
>>
>> Jim
>>
>> On Wed, Aug 25, 2021 at 7:24 AM Xiaoyu Zeng <xiaoyuzengpsy using gmail.com> wrote:
>> >
>> > Hi all.
>> >
>> > I installed the latest R and Rtools, and I followed the guidelines to test
>> > the installation of Rtools (rtools40v2-x86_64.exe for windows10). I
>> > verified that *make* can be found, but I still could not install an R
>> > package from the source.
>> >
>> > Any ideas?
>> >
>> > *More detailed info:*
>> > https://github.com/r-windows/rtools-packages/issues/222
>> >
>> > Best regards,
>> > Xiaoyu
>> >
>> > Xiaoyu Zeng
>> >
>> > Graduate student, Social and Affective NeuroPharmacology (SANP) Lab
>> >
>> > State Key Laboratory of Cognitive Neuroscience and Learning
>> >
>> > Beijing Normal University
>> >
>> > http://brain.bnu.edu.cn/home/yinama/
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.



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