thr3ads.net - R help - [R] Warning in install.packages : converting NULL pointer to R NULL [May 2020]

If this information is useful, please help other people find it:
Share via:

Rui Barradas

2020-May-08 13:46 UTC

[R] Warning in install.packages : converting NULL pointer to R NULL

Hello,

You are right,

Rscript -e 'install.packages("car")'

doesn't give that message, I will ask RStudio support.
And sorry to spam the list with something I should have checked, I'm so 
used to working in GUI 's that I forgot about the command line.

Thanks,

Rui Barradas

?s 13:56 de 08/05/20, Duncan Murdoch escreveu:> That looks like an RStudio message.? Do you get it if you run 
> install.packages() in command line R?
> 
> Duncan Murdoch
> 
> On 08/05/2020 8:07 a.m., Rui Barradas wrote:
>> Hello,
>>
>> R 4.0.0 on Ubuntu 20.04, sessionInfo() below.
>>
>> Since I updated to R 4.0 that every time I try to install a package
with
>> install.packages() the warning in the title shows up at the end, be the
>> installation successful or not. If it is successful, the package loads
>> with no problems, so I'm not very worried but it isn't normal
(expected)
>> behavior, is it?
>>
>> Here is a run of install.packages().
>>
>>
>> install.packages('cowplot')
>> Installing package into ?/usr/local/lib/R/site-library?
>> (as ?lib? is unspecified)
>> trying URL
'https://cloud.r-project.org/src/contrib/cowplot_1.0.0.tar.gz'
>> Content type 'application/x-gzip' length 1275585 bytes (1.2 MB)
>> =================================================>> downloaded
1.2 MB
>>
>> * installing *source* package ?cowplot? ...
>> ** package ?cowplot? successfully unpacked and MD5 sums checked
>> ** using staged installation
>> ** R
>> ** inst
>> ** byte-compile and prepare package for lazy loading
>> ** help
>> *** installing help indices
>> *** copying figures
>> ** building package indices
>> ** installing vignettes
>> ** testing if installed package can be loaded from temporary location
>> ** testing if installed package can be loaded from final location
>> ** testing if installed package keeps a record of temporary
installation
>> path
>> * DONE (cowplot)
>>
>> The downloaded source packages are in
>> ?????/tmp/Rtmp9NXQkt/downloaded_packages?
>> Warning in install.packages :
>> ??? converting NULL pointer to R NULL
>>
>>
>> Also, I'm running this on RStudio and haven't changed the R
library
>> directory.
>>
>>
>> sessionInfo()
>> R version 4.0.0 (2020-04-24)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 20.04 LTS
>>
>> Matrix products: default
>> BLAS:?? /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
>> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
>>
>> locale:
>> ?? [1] LC_CTYPE=pt_PT.UTF-8?????? LC_NUMERIC=C
>> LC_TIME=pt_PT.UTF-8
>> ?? [4] LC_COLLATE=pt_PT.UTF-8???? LC_MONETARY=pt_PT.UTF-8
>> LC_MESSAGES=pt_PT.UTF-8
>> ?? [7] LC_PAPER=pt_PT.UTF-8?????? LC_NAME=C?????????????????
LC_ADDRESS=C
>>
>> [10] LC_TELEPHONE=C???????????? LC_MEASUREMENT=pt_PT.UTF-8
>> LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats???? graphics? grDevices utils???? datasets? methods?? base
>>
>> other attached packages:
>> [1] MASS_7.3-51.6? ggthemes_4.2.0 ggrepel_0.8.2? dplyr_0.8.5
>> ggplot2_3.3.0
>>
>> loaded via a namespace (and not attached):
>> ?? [1] zoo_1.8-8????????? tidyselect_1.0.0?? purrr_0.3.4
>> reshape2_1.4.4???? haven_2.2.0
>> ?? [6] lattice_0.20-41??? sodium_1.1???????? carData_3.0-3
>> colorspace_1.4-1?? vctrs_0.2.4
>> [11] yaml_2.2.1???????? rlang_0.4.6??????? pillar_1.4.3
>> withr_2.2.0??????? foreign_0.8-79
>> [16] glue_1.4.0???????? readxl_1.3.1?????? lifecycle_0.2.0???
plyr_1.8.6
>> ????????? stringr_1.4.0
>> [21] MatrixModels_0.4-1 munsell_0.5.0????? gtable_0.3.0
>> cellranger_1.1.0?? zip_2.0.4
>> [26] rio_0.5.16???????? forcats_0.5.0????? SparseM_1.78
>> quantreg_5.55????? curl_4.3
>> [31] tis_1.38?????????? Rcpp_1.0.4.6?????? readr_1.3.1
>> scales_1.1.0?????? abind_1.4-5
>> [36] farver_2.0.3?????? sos_2.0-0????????? brew_1.0-6
>> digest_0.6.25????? hms_0.5.3
>> [41] png_0.1-7????????? stringi_1.4.6????? openxlsx_4.1.4????
grid_4.0.0
>> ????????? tools_4.0.0
>> [46] magrittr_1.5?????? tibble_3.0.1?????? pacman_0.5.1
>> crayon_1.3.4?????? car_3.0-7
>> [51] pkgconfig_2.0.3??? ellipsis_0.3.0???? Matrix_1.2-18
>> data.table_1.12.8? assertthat_0.2.1
>> [56] httr_1.4.1???????? rstudioapi_0.11??? R6_2.4.1
>> compiler_4.0.0
>>
>>
>> Thanks in advance,
>>
>> Rui Barradas
>>
>> ______________________________________________
>> R-help at 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.
>>
>

Martin Maechler

2020-May-08 14:30 UTC

head link

[R] Warning in install.packages : converting NULL pointer to R NULL

>>>>> Rui Barradas 
>>>>>     on Fri, 8 May 2020 14:46:45 +0100 writes:
    > Hello, You are right,

    > Rscript -e 'install.packages("car")'

    > doesn't give that message, I will ask RStudio support.
    > And sorry to spam the list with something I should have
    > checked, I'm so used to working in GUI 's that I forgot
    > about the command line.

Well, you forgot that Rstudio wraps quite a bit around R.
If you use install.packages() inside Rstudio you get their own
version instead of R's ... :
> install.packagesfunction (...) 
.rs.callAs(name, hook, original, ...)
<environment: 0x55a548da49f0>>
And they have really tweaked R in a way that it behaves
illogically, and even I don't see how they kept their version of
install.packages hidden from the conflicts() and find()
functions :
> find("install.packages")[1] "package:utils"

But of course
> identical(install.packages, utils::install.packages)[1] FALSE

(Now closing Rstudio again .. and revert to use ESS)

Martin

    > Thanks,

    > Rui Barradas

    > ?s 13:56 de 08/05/20, Duncan Murdoch escreveu:
    >> That looks like an RStudio message.? Do you get it if you
    >> run install.packages() in command line R?
    >> 
    >> Duncan Murdoch
    >> 
    >> On 08/05/2020 8:07 a.m., Rui Barradas wrote:
    >>> Hello,
    >>> 
    >>> R 4.0.0 on Ubuntu 20.04, sessionInfo() below.
    >>> 
    >>> Since I updated to R 4.0 that every time I try to
    >>> install a package with install.packages() the warning in
    >>> the title shows up at the end, be the installation
    >>> successful or not. If it is successful, the package
    >>> loads with no problems, so I'm not very worried but it
    >>> isn't normal (expected) behavior, is it?
    >>> 
    >>> Here is a run of install.packages().
    >>> 
    >>> 
    >>> install.packages('cowplot') Installing package into
    >>> ?/usr/local/lib/R/site-library? (as ?lib? is
    >>> unspecified) trying URL
    >>>
'https://cloud.r-project.org/src/contrib/cowplot_1.0.0.tar.gz'
    >>> Content type 'application/x-gzip' length 1275585 bytes
    >>> (1.2 MB)
    >>> =================================================   
>>> downloaded 1.2 MB
    >>> 
    >>> * installing *source* package ?cowplot? ...  ** package
    >>> ?cowplot? successfully unpacked and MD5 sums checked **
    >>> using staged installation ** R ** inst ** byte-compile
    >>> and prepare package for lazy loading ** help ***
    >>> installing help indices *** copying figures ** building
    >>> package indices ** installing vignettes ** testing if
    >>> installed package can be loaded from temporary location
    >>> ** testing if installed package can be loaded from final
    >>> location ** testing if installed package keeps a record
    >>> of temporary installation path * DONE (cowplot)
    >>> 
    >>> The downloaded source packages are in
    >>> ?????/tmp/Rtmp9NXQkt/downloaded_packages? Warning in
    >>> install.packages : ??? converting NULL pointer to R NULL
    >>> 
    >>> 
    >>> Also, I'm running this on RStudio and haven't changed
    >>> the R library directory.
    >>> 
    >>> 
    >>> sessionInfo() R version 4.0.0 (2020-04-24) Platform:
    >>> x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04
    >>> LTS
    >>> 
    >>> Matrix products: default BLAS:??
    >>> /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK:
    >>> /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
    >>> 
    >>> locale: ?? [1] LC_CTYPE=pt_PT.UTF-8?????? LC_NUMERIC=C
    >>> LC_TIME=pt_PT.UTF-8 ?? [4] LC_COLLATE=pt_PT.UTF-8????
    >>> LC_MONETARY=pt_PT.UTF-8 LC_MESSAGES=pt_PT.UTF-8 ?? [7]
    >>> LC_PAPER=pt_PT.UTF-8?????? LC_NAME=C?????????????????
    >>> LC_ADDRESS=C
    >>> 
    >>> [10] LC_TELEPHONE=C????????????
    >>> LC_MEASUREMENT=pt_PT.UTF-8 LC_IDENTIFICATION=C
    >>> 
    >>> attached base packages: [1] stats???? graphics?
    >>> grDevices utils???? datasets? methods?? base
    >>> 
    >>> other attached packages: [1] MASS_7.3-51.6?
    >>> ggthemes_4.2.0 ggrepel_0.8.2? dplyr_0.8.5 ggplot2_3.3.0
    >>> 
    >>> loaded via a namespace (and not attached): ?? [1]
    >>> zoo_1.8-8????????? tidyselect_1.0.0?? purrr_0.3.4
    >>> reshape2_1.4.4???? haven_2.2.0 ?? [6] lattice_0.20-41???
    >>> sodium_1.1???????? carData_3.0-3 colorspace_1.4-1??
    >>> vctrs_0.2.4 [11] yaml_2.2.1???????? rlang_0.4.6???????
    >>> pillar_1.4.3 withr_2.2.0??????? foreign_0.8-79 [16]
    >>> glue_1.4.0???????? readxl_1.3.1?????? lifecycle_0.2.0???
    >>> plyr_1.8.6 ????????? stringr_1.4.0 [21]
    >>> MatrixModels_0.4-1 munsell_0.5.0????? gtable_0.3.0
    >>> cellranger_1.1.0?? zip_2.0.4 [26] rio_0.5.16????????
    >>> forcats_0.5.0????? SparseM_1.78 quantreg_5.55?????
    >>> curl_4.3 [31] tis_1.38?????????? Rcpp_1.0.4.6??????
    >>> readr_1.3.1 scales_1.1.0?????? abind_1.4-5 [36]
    >>> farver_2.0.3?????? sos_2.0-0????????? brew_1.0-6
    >>> digest_0.6.25????? hms_0.5.3 [41] png_0.1-7?????????
    >>> stringi_1.4.6????? openxlsx_4.1.4???? grid_4.0.0
    >>> ????????? tools_4.0.0 [46] magrittr_1.5??????
    >>> tibble_3.0.1?????? pacman_0.5.1 crayon_1.3.4??????
    >>> car_3.0-7 [51] pkgconfig_2.0.3??? ellipsis_0.3.0????
    >>> Matrix_1.2-18 data.table_1.12.8? assertthat_0.2.1 [56]
    >>> httr_1.4.1???????? rstudioapi_0.11??? R6_2.4.1
    >>> compiler_4.0.0
    >>> 
    >>> 
    >>> Thanks in advance,
    >>> 
    >>> Rui Barradas
    >>> 
    >>> ______________________________________________
    >>> R-help at 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.
    >>> 
    >> 

    > ______________________________________________
    > R-help at 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.

Rui Barradas

2020-May-08 15:51 UTC

head link

[R] Warning in install.packages : converting NULL pointer to R NULL

Hello,

My main error was that this is the first time it happens and I didn't do 
any real thinking, I just assumed that it was an upgrade both R and 
Ubuntu issue.

Thanks, the reminder of the differences between R and RStudio was very 
helpful.

Rui Barradas

?s 15:30 de 08/05/20, Martin Maechler escreveu:>>>>>> Rui Barradas
>>>>>>      on Fri, 8 May 2020 14:46:45 +0100 writes:
> 
>      > Hello, You are right,
> 
>      > Rscript -e 'install.packages("car")'
> 
>      > doesn't give that message, I will ask RStudio support.
>      > And sorry to spam the list with something I should have
>      > checked, I'm so used to working in GUI 's that I forgot
>      > about the command line.
> 
> Well, you forgot that Rstudio wraps quite a bit around R.
> If you use install.packages() inside Rstudio you get their own
> version instead of R's ... :
> 
>> install.packages
> function (...)
> .rs.callAs(name, hook, original, ...)
> <environment: 0x55a548da49f0>
>>
> 
> And they have really tweaked R in a way that it behaves
> illogically, and even I don't see how they kept their version of
> install.packages hidden from the conflicts() and find()
> functions :
> 
>> find("install.packages")
> [1] "package:utils"
> 
> But of course
> 
>> identical(install.packages, utils::install.packages)
> [1] FALSE
> 
> (Now closing Rstudio again .. and revert to use ESS)
> 
> Martin
> 
>      > Thanks,
> 
>      > Rui Barradas
> 
>      > ?s 13:56 de 08/05/20, Duncan Murdoch escreveu:
>      >> That looks like an RStudio message.? Do you get it if you
>      >> run install.packages() in command line R?
>      >>
>      >> Duncan Murdoch
>      >>
>      >> On 08/05/2020 8:07 a.m., Rui Barradas wrote:
>      >>> Hello,
>      >>>
>      >>> R 4.0.0 on Ubuntu 20.04, sessionInfo() below.
>      >>>
>      >>> Since I updated to R 4.0 that every time I try to
>      >>> install a package with install.packages() the warning in
>      >>> the title shows up at the end, be the installation
>      >>> successful or not. If it is successful, the package
>      >>> loads with no problems, so I'm not very worried but
it
>      >>> isn't normal (expected) behavior, is it?
>      >>>
>      >>> Here is a run of install.packages().
>      >>>
>      >>>
>      >>> install.packages('cowplot') Installing package
into
>      >>> ?/usr/local/lib/R/site-library? (as ?lib? is
>      >>> unspecified) trying URL
>      >>>
'https://cloud.r-project.org/src/contrib/cowplot_1.0.0.tar.gz'
>      >>> Content type 'application/x-gzip' length 1275585
bytes
>      >>> (1.2 MB)
>      >>> =================================================>    
>>> downloaded 1.2 MB
>      >>>
>      >>> * installing *source* package ?cowplot? ...  ** package
>      >>> ?cowplot? successfully unpacked and MD5 sums checked **
>      >>> using staged installation ** R ** inst ** byte-compile
>      >>> and prepare package for lazy loading ** help ***
>      >>> installing help indices *** copying figures ** building
>      >>> package indices ** installing vignettes ** testing if
>      >>> installed package can be loaded from temporary location
>      >>> ** testing if installed package can be loaded from final
>      >>> location ** testing if installed package keeps a record
>      >>> of temporary installation path * DONE (cowplot)
>      >>>
>      >>> The downloaded source packages are in
>      >>> ?????/tmp/Rtmp9NXQkt/downloaded_packages? Warning in
>      >>> install.packages : ??? converting NULL pointer to R NULL
>      >>>
>      >>>
>      >>> Also, I'm running this on RStudio and haven't
changed
>      >>> the R library directory.
>      >>>
>      >>>
>      >>> sessionInfo() R version 4.0.0 (2020-04-24) Platform:
>      >>> x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04
>      >>> LTS
>      >>>
>      >>> Matrix products: default BLAS:
>      >>> /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK:
>      >>> /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
>      >>>
>      >>> locale: ?? [1] LC_CTYPE=pt_PT.UTF-8?????? LC_NUMERIC=C
>      >>> LC_TIME=pt_PT.UTF-8 ?? [4] LC_COLLATE=pt_PT.UTF-8
>      >>> LC_MONETARY=pt_PT.UTF-8 LC_MESSAGES=pt_PT.UTF-8 ?? [7]
>      >>> LC_PAPER=pt_PT.UTF-8?????? LC_NAME=C
>      >>> LC_ADDRESS=C
>      >>>
>      >>> [10] LC_TELEPHONE=C
>      >>> LC_MEASUREMENT=pt_PT.UTF-8 LC_IDENTIFICATION=C
>      >>>
>      >>> attached base packages: [1] stats???? graphics
>      >>> grDevices utils???? datasets? methods?? base
>      >>>
>      >>> other attached packages: [1] MASS_7.3-51.6
>      >>> ggthemes_4.2.0 ggrepel_0.8.2? dplyr_0.8.5 ggplot2_3.3.0
>      >>>
>      >>> loaded via a namespace (and not attached): ?? [1]
>      >>> zoo_1.8-8????????? tidyselect_1.0.0?? purrr_0.3.4
>      >>> reshape2_1.4.4???? haven_2.2.0 ?? [6] lattice_0.20-41
>      >>> sodium_1.1???????? carData_3.0-3 colorspace_1.4-1
>      >>> vctrs_0.2.4 [11] yaml_2.2.1???????? rlang_0.4.6
>      >>> pillar_1.4.3 withr_2.2.0??????? foreign_0.8-79 [16]
>      >>> glue_1.4.0???????? readxl_1.3.1?????? lifecycle_0.2.0
>      >>> plyr_1.8.6 ????????? stringr_1.4.0 [21]
>      >>> MatrixModels_0.4-1 munsell_0.5.0????? gtable_0.3.0
>      >>> cellranger_1.1.0?? zip_2.0.4 [26] rio_0.5.16
>      >>> forcats_0.5.0????? SparseM_1.78 quantreg_5.55
>      >>> curl_4.3 [31] tis_1.38?????????? Rcpp_1.0.4.6
>      >>> readr_1.3.1 scales_1.1.0?????? abind_1.4-5 [36]
>      >>> farver_2.0.3?????? sos_2.0-0????????? brew_1.0-6
>      >>> digest_0.6.25????? hms_0.5.3 [41] png_0.1-7
>      >>> stringi_1.4.6????? openxlsx_4.1.4???? grid_4.0.0
>      >>> ????????? tools_4.0.0 [46] magrittr_1.5
>      >>> tibble_3.0.1?????? pacman_0.5.1 crayon_1.3.4
>      >>> car_3.0-7 [51] pkgconfig_2.0.3??? ellipsis_0.3.0
>      >>> Matrix_1.2-18 data.table_1.12.8? assertthat_0.2.1 [56]
>      >>> httr_1.4.1???????? rstudioapi_0.11??? R6_2.4.1
>      >>> compiler_4.0.0
>      >>>
>      >>>
>      >>> Thanks in advance,
>      >>>
>      >>> Rui Barradas
>      >>>
>      >>> ______________________________________________
>      >>> R-help at 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.
>      >>>
>      >>
> 
>      > ______________________________________________
>      > R-help at 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.
>

R help - May 2020 - Warning in install.packages : converting NULL pointer to R NULL

[R] Warning in install.packages : converting NULL pointer to R NULL

[R] Warning in install.packages : converting NULL pointer to R NULL

[R] Warning in install.packages : converting NULL pointer to R NULL