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

7 messages · Duncan Murdoch, Martin Maechler, Rolf Turner +1 more

Rui Barradas
# 
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
# 
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:
Rui Barradas
# 
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:
Martin Maechler
# 
> 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 ... :
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 :
[1] "package:utils"

But of course
[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
# 
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:
Rolf Turner
# 
Hi Rui.  Doesn't happen to me under Ubuntu 18.04:
My session info is as follows:
No idea what to suggest.  Sorry.

cheers,

Rolf
1 day later
Rui Barradas
# 
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: