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Rui Barradas

2020-May-08 12:07 UTC

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

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

Duncan Murdoch

2020-May-08 12:56 UTC

head link

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

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.
>

Rui Barradas

2020-May-08 13:46 UTC

head link

[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.
>>
>

Rolf Turner

2020-May-08 22:11 UTC

head link

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

Hi Rui.  Doesn't happen to me under Ubuntu 18.04:
> install.packages('cowplot',lib=.Rlib) 
> 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/RtmpG8wb97/downloaded_packages?
My session info is as follows:
> sessionInfo()
> R version 4.0.0 (2020-04-24)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 18.04.4 LTS
> 
> Matrix products: default
> BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
> LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
> 
> Random number generation:
>  RNG:     Mersenne-Twister 
>  Normal:  Inversion 
>  Sample:  Rounding 
>  
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
>  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_GB.UTF-8    
>  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_GB.UTF-8   
>  [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C                 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C       
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] brev_0.0-4
> 
> loaded via a namespace (and not attached):
> [1] compiler_4.0.0 tools_4.0.0  
No idea what to suggest.  Sorry.

cheers,

Rolf

-- 
Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

Rui Barradas

2020-May-10 09:54 UTC

head link

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

Hello,

Thanks for the info.
It was an update issue, I updated to Ubuntu 20.04 and R to 4.0.0 but not 
RStudio. Now that I have all three most recent versions it works as 
before, with no strange warning message.
So I guess this thread is closed.

Thanks to all,

Rui Barradas

?s 23:11 de 08/05/20, Rolf Turner escreveu:> 
> Hi Rui.? Doesn't happen to me under Ubuntu 18.04:
> 
>> install.packages('cowplot',lib=.Rlib) 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/RtmpG8wb97/downloaded_packages?
> 
> My session info is as follows:
> 
>> sessionInfo()
>> R version 4.0.0 (2020-04-24)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 18.04.4 LTS
>>
>> Matrix products: default
>> BLAS:?? /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
>> LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
>>
>> Random number generation:
>> ?RNG:???? Mersenne-Twister ?Normal:? Inversion ?Sample:? Rounding
>> locale:
>> ?[1] LC_CTYPE=en_GB.UTF-8?????? LC_NUMERIC=C ?[3] 
>> LC_TIME=en_NZ.UTF-8??????? LC_COLLATE=en_GB.UTF-8 ?[5] 
>> LC_MONETARY=en_NZ.UTF-8??? LC_MESSAGES=en_GB.UTF-8 ?[7] 
>> LC_PAPER=en_NZ.UTF-8?????? LC_NAME=C ?[9] LC_ADDRESS=C               
>> LC_TELEPHONE=C [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C
>> attached base packages:
>> [1] stats???? graphics? grDevices utils???? datasets? methods?? base
>> other attached packages:
>> [1] brev_0.0-4
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_4.0.0 tools_4.0.0 
> 
> No idea what to suggest.? Sorry.
> 
> cheers,
> 
> Rolf
>

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

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

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