[R] Surprising behavior and bugs in R 4.0.4

[Jiefei Wang]

Hi Miso,

It looks like you have a corrupted package library, probably due to some
packages installed from an unofficial repository(e.g. GitHub). I will
suggest first installing the package "spatstat"(This is the package that
should define "markvario"), then try to install "Seurat" again and see if
it works.

If it doesn't work. Please remove all folders under the path shown in
".libPaths()" and reinstall your R, then installing "Seurat" from CRAN
should work.

Best,
Jiefei

On Sun, Mar 21, 2021 at 2:05 AM Miso Na <mna3 using jhu.edu> wrote:

> Thanks for your reply!
>
> Seurat was downloaded from CRAN, with the below code.
>
> > install.packages('Seurat')
>
>
>
> It seems to work, but when I use as library, the error shows up!
>
> > library(Seurat)
>
> Error: package or namespace load failed for ‘Seurat’:
>
> object ‘markvario’ is not exported by 'namespace:spatstat'
>
>
>
> And of course, I tried to download packages ‘markvario’, but
>
>
>
> > install.packages('markvario')
>
> Installing package into ‘C:/Users/user/Documents/R/win-library/4.0’
>
> (as ‘lib’ is unspecified)
>
> Warning message:
>
> package ‘markvario’ is not available for this version of R
>
>
>
> A version of this package for your version of R might be available
> elsewhere,
>
> see the ideas at
>
>
> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
>
> > install.packages('
> https://cran.r-project.org/src/contrib/Archive/spatstat/spatstat_1.64-1.tar.gz',
> repos=NULL,type="source", INSTALL_opts = "--no-lock")
>
> Installing package into ‘C:/Users/user/Documents/R/win-library/4.0’
>
> (as ‘lib’ is unspecified)
>
> trying URL '
> https://cran.r-project.org/src/contrib/Archive/spatstat/spatstat_1.64-1.tar.gz
> '
>
> Content type 'application/x-gzip' length 7943393 bytes (7.6 MB)
>
> downloaded 7.6 MB
>
>
>
> Error: could not find function "api_create"
>
> Execution halted
>
> Warning message:
>
> In install.packages(
> https://cran.r-project.org/src/contrib/Archive/spatstat/spatstat_1.64-1.tar.gz,
> :
>
>   installation of package
> ‘C:/Users/user/AppData/Local/Temp/RtmpWmLFdn/downloaded_packages/spatstat_1.64-1.tar.gz’
> had non-zero exit status
>
>
>
> Thanks,
>
> Miso
>
> *From:* Jiefei Wang <szwjf08 using gmail.com>
> *Sent:* Sunday, March 21, 2021 1:05 AM
> *To:* Miso Na <mna3 using jhu.edu>
> *Cc:* r-help using r-project.org; Ray Cheng <ycheng45 using jhmi.edu>; Patrick Cahan <
> patrick.cahan using jhmi.edu>
> *Subject:* Re: [R] Surprising behavior and bugs in R 4.0.4
>
>
>
>
> *      External Email - Use Caution      *
>
>
>
>
>
> Hi Miso,
>
>
>
> Have you tried to install Seurat from CRAN? What you were using is the
> GitHub version of the package and has been actively updating, so the
> problem might be from the package.
>
>
>
> Best,
>
> Jiefei
>
>
>
> On Sat, Mar 20, 2021 at 10:32 PM Miso Na <mna3 using jhu.edu> wrote:
>
> Dear helpers,
>
> Although I uninstalled and reinstalled R more than 3 times to delete the
> error in api_create, it did not work. The error is representing on the very
> first page on R consol.
> Error: could not find function "api_create"
>
> I guess this error makes impossible to install library 'SCMAP',
> 'SingleCellExperiment' or 'Seurat'.
> For example, I got this error when I tried to install those libraries.
> Installing package into 'C:/Users/user/Documents/R/win-library/4.0'
> (as 'lib' is unspecified)
> Error: could not find function "api_create"
> Execution halted
> Error: Failed to install 'Seurat' from GitHub:
>   (converted from warning) installation of package
> 'C:/Users/user/AppData/Local/Temp/RtmpKYL3Pe/file2c2c6cb0766e/Seurat_4.0.1.tar.gz'
> had non-zero exit status
>
>
> My sessionInfo is here!
>
> > sessionInfo()
> R version 4.0.4 (2021-02-15)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 19041)
>
> 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
> system code page: 949
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] compiler_4.0.4
>
> Thanks for your help!
>
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