Nice fortune.
In retrospect, maybe it would have worked to re-build the user library. Things
were acting so strangely to me I opted for the direct, if more dangerous
approach. :-)
> On Oct 7, 2021, at 11:37 AM, Jeff Newmiller <jdnewmil at
dcn.davis.ca.us> wrote:
>
> Sad, more like.
>
> fortunes::fortune(337)
>
> You would have done just as well to delete the user library and let R
prompt you to re-create it if things were that bad. Note that the default R
configuration always looks first in the user library and only falls back to the
system library if the desired package is not found in the user library. In most
user-administered R installations you are better off acting as though the system
library wasn't there.
>
> On October 7, 2021 7:56:05 AM PDT, Kevin Thorpe <kevin.thorpe at
utoronto.ca> wrote:
>> I thought I would close the loop on this. It was really weird and I
don?t understand everything that went on.
>>
>> First, it was indeed the case that the main library was not writeable
so packages were being installed in a user library.
>>
>> Here is where it gets confusing to me. Both library paths did appear in
.libPaths(). I could not figure out where that was being set since there was no
user .Rprofile and Rprofile.site was not modified. To start over I got the user
to delete the local library and started R as an administrator and forced
installation in the main library with the lib argument. However, even with
dependencies=TRUE in install.packages() everything was not getting installed. I
then had the user start RStudio as an admin and use the install packages from
the menu, again specifying the main library and asking for dependencies. When
this was done, many additional packages were then installed that were not
installed when running the native R application. Eventually, after that,
tidyverse loaded (I realize it is a wrapper to load a bunch of other packages).
I also had the user install rms (which we use) and again, various bits did not
get installed and had to be manually requested (I don?t remember which ones).
>>
>> Anyway, in the end we got his system functioning. I realize that
running as admin to install packages is probably not best practice, but it was
the only way I saw to get things working. I _think_ some of the problems were
because his home directory is synced with OneDrive and the user library path was
to a OneDrive folder.
>>
>> I am often shocked by the difficulties students have installing
packages. They manage to get errors that I have never seen in all my user of
using R. On a Win10 box of my own, I installed R and packages with no
difficulties so, naturally am surprised when things go this haywire with an
installation.
>>
>> That?s my story. Hope it was entertaining. :-)
>>
>> Kevin
>>
>>
>>> On Sep 24, 2021, at 3:26 PM, Duncan Murdoch <murdoch.duncan at
gmail.com> wrote:
>>>
>>> It is worth checking that the library where things were most
recently installed is the first place R looks, i.e. the first entry in
.libPaths(). Often R is installed by an administrator, and users can't
write to the main library, so when they install packages they go somewhere else.
If "somewhere else" isn't first in .libPaths(), R won't see
the new installs.
>>>
>>> Duncan Murdoch
>>>
>>> On 24/09/2021 2:04 p.m., Kevin Thorpe wrote:
>>>> I did try installing xml2 and it appeared to complete. I will
ask him to try again and send me the output.
>>>>> On Sep 24, 2021, at 1:58 PM, Jeff Newmiller <jdnewmil at
dcn.davis.ca.us> wrote:
>>>>>
>>>>> Seems like they should install the xml2 package before
proceeding to load whatever (tidyverse).
>>>>>
>>>>> This kind of "dependency missing" problem tends
to be a recurring problem particularly on Windows but in general when some
deeply-embedded dependency fails to load or is removed in preparation for
upgrading.
>>>>>
>>>>> On September 24, 2021 10:40:41 AM PDT, Kevin Thorpe
<kevin.thorpe at utoronto.ca> wrote:
>>>>>> Below is some output from one of my students. I have
never seen this error and tried a few things (updating packages for one) but am
at a loss to help further. Would appreciate suggestions that I can pass along.
>>>>>>
>>>>>> Here is the error. I tried an install.packages(?xml2?)
which appeared to complete but the error persists.
>>>>>>
>>>>>>> library("tidyverse")
>>>>>> Error: package or namespace load failed for ?tidyverse?
in library.dynam(lib, package, package.lib):
>>>>>> DLL ?xml2? not found: maybe not installed for this
architecture?
>>>>>>
>>>>>> Here is the sessionInfo()
>>>>>>
>>>>>>> sessionInfo()
>>>>>> R version 4.1.1 (2021-08-10)
>>>>>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>>>> Running under: Windows 10 x64 (build 19042)
>>>>>>
>>>>>> Matrix products: default
>>>>>>
>>>>>> locale:
>>>>>> [1] LC_COLLATE=English_Canada.1252
LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
>>>>>> [5] LC_TIME=English_Canada.1252
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] stats graphics grDevices utils datasets methods
base
>>>>>>
>>>>>> loaded via a namespace (and not attached):
>>>>>> [1] Rcpp_1.0.7 cellranger_1.1.0 pillar_1.6.2
compiler_4.1.1 dbplyr_2.1.1 forcats_0.5.1 tools_4.1.1
>>>>>> [8] jsonlite_1.7.2 lubridate_1.7.10 lifecycle_1.0.0
tibble_3.1.4 gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.11
>>>>>> [15] reprex_2.0.1 DBI_1.1.1 haven_2.4.3 withr_2.4.2
dplyr_1.0.7 httr_1.4.2 fs_1.5.0
>>>>>> [22] generics_0.1.0 vctrs_0.3.8 hms_1.1.0 grid_4.1.1
tidyselect_1.1.1 glue_1.4.2 R6_2.5.1
>>>>>> [29] fansi_0.5.0 readxl_1.3.1 tzdb_0.1.2 tidyr_1.1.3
ggplot2_3.3.5 purrr_0.3.4 readr_2.0.1
>>>>>> [36] modelr_0.1.8 magrittr_2.0.1 backports_1.2.1
scales_1.1.1 ellipsis_0.3.2 assertthat_0.2.1 colorspace_2.0-2
>>>>>> [43] utf8_1.2.2 munsell_0.5.0 broom_0.7.9 crayon_1.4.1
>>>>>>
>>>>>
>>>>> --
>>>>> Sent from my phone. Please excuse my brevity.
>>>
>>
>
> --
> Sent from my phone. Please excuse my brevity.
--
Kevin E. Thorpe
Head of Biostatistics, Applied Health Research Centre (AHRC)
Li Ka Shing Knowledge Institute of St. Michael?s Hospital
Assistant Professor, Dalla Lana School of Public Health
University of Toronto
email: kevin.thorpe at utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016