[R] Surprising behavior and bugs in R 4.0.4

[Jiefei Wang]

FYI, you do not have to provide a full link to the function
"install.packages". Please install the package just by
install.package("package name")

Best,
Jiefei

On Sun, Mar 21, 2021 at 9:41 AM Jiefei Wang <szwjf08 using gmail.com> wrote:

> 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!
>>
>>         [[alternative HTML version deleted]]
>>
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>>

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