I'm facing a similar problem to Rstudio keeps flashing after fedora 35 update. Code and console panels and rstudio popup windows keep flashing in and out of view, frequently enough to make rstudio very difficult to use. (The popup windows vanish from view. The code and console panels go blank.)
I'm using this version of rstudio, from the rstudio-desktop-bin AUR package (which uses official rstudio binaries):
RStudio 2021.09.1+372 "Ghost Orchid" Release (8b9ced188245155642d024aa3630363df611088a, 2021-11-08) for Ubuntu Bionic
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Platform: x86_64-pc-linux-gnu (64-bit)
X11, no wayland session running
Linux kernel 5.15.12, Manjaro GNOME
I'm attaching the top of the rstudio diagnostics report output, below. (It's too long to add in the whole file, and I can't upload a PDF as a new user.)
Doing this:
maybe it would be worth to move ~/.config/rstudio and ~/.local/share/rstudio out of the way for a moment to ensure you don't have any left-over legacy configuration in there
didn't help.
I've tried changing the Graphics Device settings to no avail. Unlike the user in the Fedora 35 update issue linked above, setting the Rendering Engine to Software seems to have solved the problem.
RStudio Diagnostics Report
==========================
WARNING: This report may contain sensitive security information and / or
personally identifiable information. Please audit the below and redact any
sensitive information before submitting your diagnostics report.
Generated: Mon Jan 10 13:35:11 2022
RStudio Version
--------------------------------------------------
2021.09.1+372
Session Information
--------------------------------------------------
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux
Matrix products: default
BLAS: /usr/lib/libopenblasp-r0.3.19.so
LAPACK: /usr/lib/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8
[4] LC_COLLATE=en_CA.UTF-8 LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2
System Information
--------------------------------------------------
sysname : Linux
release : 5.15.12-1-MANJARO
version : #1 SMP PREEMPT Wed Dec 29 18:08:07 UTC 2021
nodename : ggill-linux
machine : x86_64
login : graham
user : graham
effective_user : graham
Platform Information
--------------------------------------------------
OS.type : unix
file.sep : /
dynlib.ext : .so
GUI : RStudio
endian : little
pkgType : source
path.sep : :
r_arch :
Environment Variables
--------------------------------------------------
CLICOLOR_FORCE : 1
DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/1000/bus
DESKTOP_SESSION : gnome
DISPLAY : :1
EDITOR : /usr/bin/nano
force_s3tc_enable : true
GDM_LANG : en_CA.UTF-8
GDMSESSION : gnome
GIO_LAUNCHED_DESKTOP_FILE : /usr/share/applications/rstudio.desktop
GIO_LAUNCHED_DESKTOP_FILE_PID : 357197
GIT_ASKPASS : rpostback-askpass
GJS_DEBUG_OUTPUT : stderr
GJS_DEBUG_TOPICS : JS ERROR;JS LOG
GRADLE_HOME : /usr/share/java/gradle
GTK3_MODULES : xapp-gtk3-module
HOME : /home/graham
INVOCATION_ID : 74cb3cdddc254d588858c71b24f6f440
JOURNAL_STREAM : 8:21493
KDEDIRS : /usr
LANG : en_CA.UTF-8
LC_ADDRESS : en_CA.UTF-8
LC_MEASUREMENT : en_CA.UTF-8
LC_MESSAGES : en_CA.UTF-8
LC_MONETARY : en_CA.UTF-8
LC_PAPER : en_CA.UTF-8
LC_TIME : en_CA.UTF-8
LD_LIBRARY_PATH : /usr/lib64/R/lib:/lib:/usr/lib/jvm/java-17-openjdk/lib/server
LN_S : ln -s
LOGNAME : *** redacted ***
MAIL : /var/spool/mail/graham
MAKE : make
MANAGERPID : 7431
MOTD_SHOWN : pam
MPLENGINE : tkAgg
PAGER : /usr/bin/less
PATH : /home/graham/.local/bin:/usr/local/bin:/usr/bin:/var/lib/snapd/snap/bin:/usr/local/sbin:/var/lib/flatpak/exports/bin:/usr/lib/jvm/default/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/usr/lib/rstudio/bin/postback
PWD : *** redacted ***
PYTHONIOENCODING : utf-8
QT_DIR : /usr/lib/rstudio
QT_IM_MODULE : ibus
QT_PLUGIN_PATH : /usr/lib/rstudio/plugins
QT_QPA_PLATFORM_PLUGIN_PATH : /usr/lib/rstudio/plugins/platforms
QT_QPA_PLATFORMTHEME : qt5ct
R_BROWSER :
R_BZIPCMD : /usr/bin/bzip2
R_DOC_DIR : /usr/share/doc/R/
R_GZIPCMD : /usr/bin/gzip
R_HOME : /usr/lib64/R
R_INCLUDE_DIR : /usr/include/R/
R_LIBS_SITE :
R_LIBS_USER : ~/R/x86_64-pc-linux-gnu-library/4.1
R_PAPERSIZE : letter
R_PDFVIEWER :
R_PLATFORM : x86_64-pc-linux-gnu
R_PRINTCMD :
R_RD4PDF : times,hyper
R_SESSION_TMPDIR : /tmp/RtmpmG9HrT
R_SHARE_DIR : /usr/share/R/
R_STRIP_SHARED_LIB : strip --strip-unneeded
R_STRIP_STATIC_LIB : strip --strip-debug
R_SYSTEM_ABI : linux,gcc,gxx,gfortran,gfortran
R_TEXI2DVICMD : /usr/bin/texi2dvi
R_UNZIPCMD : /usr/bin/unzip
R_ZIPCMD : /usr/bin/zip
RMARKDOWN_MATHJAX_PATH : /usr/lib/rstudio/resources/mathjax-27
RS_PPM_FD_READ : 88
RS_PPM_FD_WRITE : 92
RS_RPOSTBACK_PATH : /usr/lib/rstudio/bin/rpostback
RS_SHARED_SECRET : *** redacted ***
RSTUDIO : 1
RSTUDIO_CONSOLE_COLOR : 256
RSTUDIO_CONSOLE_WIDTH : 108
RSTUDIO_PANDOC : /usr/lib/rstudio/bin/pandoc
RSTUDIO_PROGRAM_MODE : desktop
RSTUDIO_SESSION_PORT : 17563
RSTUDIO_USER_IDENTITY : graham
RSTUDIO_WINUTILS : bin/winutils
SED : /usr/bin/sed
SESSION_MANAGER : local/ggill-linux:@/tmp/.ICE-unix/7533,unix/ggill-linux:/tmp/.ICE-unix/7533
SHELL : /usr/bin/fish
SHLVL : 0
SSH_AUTH_SOCK : *** redacted ***
SYSTEMD_EXEC_PID : 7550
TAR : /usr/bin/tar
TERM : xterm-256color
USER : graham
USERNAME : *** redacted ***
WINDOWPATH : 2
XAUTHORITY : /run/user/1000/gdm/Xauthority
XDG_CURRENT_DESKTOP : GNOME
XDG_DATA_DIRS : /home/graham/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop
XDG_MENU_PREFIX : gnome-
XDG_RUNTIME_DIR : /run/user/1000
XDG_SESSION_CLASS : user
XDG_SESSION_DESKTOP : gnome
XDG_SESSION_TYPE : x11
XMODIFIERS : @im=ibus
R Version
--------------------------------------------------
platform : x86_64-pc-linux-gnu
arch : x86_64
os : linux-gnu
system : x86_64, linux-gnu
status :
major : 4
minor : 1.2
year : 2021
month : 11
day : 01
svn rev : 81115
language : R
version.string : R version 4.1.2 (2021-11-01)
nickname : Bird Hippie
R Home
--------------------------------------------------
/usr/lib64/R
R Search Path
--------------------------------------------------
.GlobalEnv
tools:rstudio
package:stats
package:graphics
package:grDevices
package:utils
package:datasets
package:methods
Autoloads
package:base
R Library Paths
--------------------------------------------------
/home/graham/R/x86_64-pc-linux-gnu-library/4.1
/usr/lib/R/library
Loaded Packages
--------------------------------------------------
compiler : /usr/lib/R/library/compiler
datasets : /usr/lib/R/library/datasets
graphics : /usr/lib/R/library/graphics
grDevices : /usr/lib/R/library/grDevices
methods : /usr/lib/R/library/methods
stats : /usr/lib/R/library/stats
tools : /usr/lib/R/library/tools
utils : /usr/lib/R/library/utils
base : /usr/lib64/R/library/base
Installed Packages
--------------------------------------------------
Package LibPath Version
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2 base64enc /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.1-3
3 BH /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.78.0-0
4 bit /home/graham/R/x86_64-pc-linux-gnu-library/4.1 4.0.4
5 bit64 /home/graham/R/x86_64-pc-linux-gnu-library/4.1 4.0.5
6 blob /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.2.2
7 cachem /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.0.6
8 classInt /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.4-3
9 clipr /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.7.1
10 collections /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.3.5
11 colorspace /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.0-2
12 cpp11 /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.4.2
13 credentials /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.3.2
14 curl /home/graham/R/x86_64-pc-linux-gnu-library/4.1 4.3.2
15 data.table /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.14.2
16 DBI /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.1.2
17 dplyr /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.0.7
18 e1071 /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.7-9
19 farver /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.1.0
20 fastdigest /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.6-3
21 fastmap /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.1.0
22 fasttime /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.0-2
23 foreach /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.5.1
24 fpCompare /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.2.3
25 fs /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.5.2
26 gargle /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.2.0
27 gdalUtilities /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.2.0
28 generics /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.1.1
29 gert /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.5.0
30 ggplot2 /home/graham/R/x86_64-pc-linux-gnu-library/4.1 3.3.5
31 gh /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.3.0
32 git2r /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.29.0
33 gitcreds /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.1.1
34 googledrive /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.0.0
35 gridBase /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.4-7
36 gtable /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.3.0
37 gtools /home/graham/R/x86_64-pc-linux-gnu-library/4.1 3.9.2
38 highr /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.9
39 hms /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.1.1
40 htmltools /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.5.2
41 htmlwidgets /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.5.4
42 httr /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.4.2
43 igraph /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.2.11
44 ini /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.3.1
45 isoband /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.2.5
46 iterators /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.0.13
47 jquerylib /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.1.4
48 jsonlite /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.7.2
49 knitr /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.37
50 labeling /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.4.2
51 lifecycle /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.0.1
52 lobstr /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.1.1
53 lubridate /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.8.0
54 Matrix /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.4-0
55 memoise /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.0.1
56 mgcv /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.8-38
57 mime /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.12
58 munsell /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.5.0
59 openssl /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.4.6
60 pillar /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.6.4
61 pkgconfig /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.0.3
62 plogr /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.2.0
63 plyr /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.8.6
64 profvis /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.3.7
65 progress /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.2.2
66 proxy /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.4-26
67 pryr /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.1.5
68 purrr /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.3.4
69 qs /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.25.2
70 quickPlot /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.1.6
71 R.methodsS3 /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.8.1
72 R.oo /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.24.0
73 R.utils /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.11.0
74 ragg /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.2.1
75 RApiSerialize /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.1.0
76 rappdirs /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.3.3
77 raster /home/graham/R/x86_64-pc-linux-gnu-library/4.1 3.5-11
78 RColorBrewer /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.1-2
79 Rcpp /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.0.7
80 RcppParallel /home/graham/R/x86_64-pc-linux-gnu-library/4.1 5.1.5
81 readr /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.1.1
82 rematch2 /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.1.2
83 remotes /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.4.2
84 renv /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.15.0
85 reproducible /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.2.8
86 Require /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.0.13
87 rgdal /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.5-28
88 rgeos /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.5-9
89 rmarkdown /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.11
90 rootSolve /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.8.2.3
91 RSQLite /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.2.9
92 s2 /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.0.7
93 scales /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.1.1
94 sf /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.0-5
95 sp /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.4-6
96 stringfish /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.15.5
97 stringi /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.7.6
98 stringr /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.4.0
99 sys /home/graham/R/x86_64-pc-linux-gnu-library/4.1 3.4
100 systemfonts /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.0.3
101 terra /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.4-22
102 textshaping /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.3.6
103 tibble /home/graham/R/x86_64-pc-linux-gnu-library/4.1 3.1.6
104 tidyr /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.1.4
105 tidyselect /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.1.1
106 tinytex /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.36
107 tzdb /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.2.0
108 units /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.7-2
109 usethis /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.1.5
110 utf8 /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.2.2
111 uuid /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.0-3
112 vctrs /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.3.8
113 versions /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.3
114 viridisLite /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.4.0
115 vroom /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.5.7
116 whisker /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.4
117 wk /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.6.0
118 xfun /home/graham/R/x86_64-pc-linux-gnu-library/4.1 0.29
119 xml2 /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.3.3
120 yaml /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.2.1
121 zip /home/graham/R/x86_64-pc-linux-gnu-library/4.1 2.2.0
122 zoo /home/graham/R/x86_64-pc-linux-gnu-library/4.1 1.8-9
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125 base /usr/lib/R/library 4.1.2
126 boot /usr/lib/R/library 1.3-28
127 brio /usr/lib/R/library 1.1.3
128 callr /usr/lib/R/library 3.7.0
129 class /usr/lib/R/library 7.3-19
130 cli /usr/lib/R/library 3.1.0
131 cluster /usr/lib/R/library 2.1.2
132 codetools /usr/lib/R/library 0.2-18
133 compiler /usr/lib/R/library 4.1.2
134 crayon /usr/lib/R/library 1.4.2
135 curl /usr/lib/R/library 4.3.2
136 datasets /usr/lib/R/library 4.1.2
137 desc /usr/lib/R/library 1.4.0
138 diffobj /usr/lib/R/library 0.3.5
139 digest /usr/lib/R/library 0.6.29
140 ellipsis /usr/lib/R/library 0.3.2
141 evaluate /usr/lib/R/library 0.14
142 fansi /usr/lib/R/library 0.5.0
143 foreign /usr/lib/R/library 0.8-81
144 glue /usr/lib/R/library 1.6.0
145 graphics /usr/lib/R/library 4.1.2
146 grDevices /usr/lib/R/library 4.1.2
147 grid /usr/lib/R/library 4.1.2
148 httpuv /usr/lib/R/library 1.6.4
149 jsonlite /usr/lib/R/library 1.7.2
150 KernSmooth /usr/lib/R/library 2.23-20
151 later /usr/lib/R/library 1.3.0
152 lattice /usr/lib/R/library 0.20-45
153 lifecycle /usr/lib/R/library 1.0.1
154 magrittr /usr/lib/R/library 2.0.1
155 MASS /usr/lib/R/library 7.3-54
156 Matrix /usr/lib/R/library 1.3-4
157 methods /usr/lib/R/library 4.1.2
158 mgcv /usr/lib/R/library 1.8-38
159 nlme /usr/lib/R/library 3.1-153
160 nnet /usr/lib/R/library 7.3-16
161 parallel /usr/lib/R/library 4.1.2
162 pillar /usr/lib/R/library 1.6.4
163 pingr /usr/lib/R/library 2.0.1
164 pkgbuild /usr/lib/R/library 1.2.1
165 pkgconfig /usr/lib/R/library 2.0.3
166 pkgload /usr/lib/R/library 1.2.4
167 praise /usr/lib/R/library 1.0.0
168 prettyunits /usr/lib/R/library 1.1.1
169 processx /usr/lib/R/library 3.5.2
170 promises /usr/lib/R/library 1.2.0.1
171 ps /usr/lib/R/library 1.6.0
172 R6 /usr/lib/R/library 2.5.1
173 Rcpp /usr/lib/R/library 1.0.7
174 rematch2 /usr/lib/R/library 2.1.2
175 rlang /usr/lib/R/library 0.4.12
176 rpart /usr/lib/R/library 4.1-15
177 rprojroot /usr/lib/R/library 2.0.2
178 rstudioapi /usr/lib/R/library 0.13
179 spatial /usr/lib/R/library 7.3-14
180 splines /usr/lib/R/library 4.1.2
181 stats /usr/lib/R/library 4.1.2
182 stats4 /usr/lib/R/library 4.1.2
183 survival /usr/lib/R/library 3.2-13
184 tcltk /usr/lib/R/library 4.1.2
185 testthat /usr/lib/R/library 3.1.0
186 tibble /usr/lib/R/library 3.1.6
187 tools /usr/lib/R/library 4.1.2
188 utf8 /usr/lib/R/library 1.2.2
189 utils /usr/lib/R/library 4.1.2
190 vctrs /usr/lib/R/library 0.3.8
191 waldo /usr/lib/R/library 0.3.1
192 webutils /usr/lib/R/library 1.1
193 withr /usr/lib/R/library 2.4.3
R System Profile: /usr/lib64/R/library/base/R/Rprofile
--------------------------------------------------
### This is the system Rprofile file. It is always run on startup.
### Additional commands can be placed in site or user Rprofile files
### (see ?Rprofile).
### Copyright (C) 1995-2020 The R Core Team
### Notice that it is a bad idea to use this file as a template for
### personal startup files, since things will be executed twice and in
### the wrong environment (user profiles are run in .GlobalEnv).
.GlobalEnv <- globalenv()
attach(NULL, name = "Autoloads")
.AutoloadEnv <- as.environment(2)
assign(".Autoloaded", NULL, envir = .AutoloadEnv)
T <- TRUE
F <- FALSE
R.version <- structure(R.Version(), class = "simple.list")
version <- R.version # for S compatibility
## for backwards compatibility only
R.version.string <- R.version$version.string
## NOTA BENE: options() for non-base package functionality are in places like
## --------- ../utils/R/zzz.R
options(keep.source = interactive())
options(warn = 0)
# options(repos = c(CRAN="@CRAN@"))
# options(BIOC = "http://www.bioconductor.org")
## setting from an env variable added in 4.0.2
local({to <- as.integer(Sys.getenv("R_DEFAULT_INTERNET_TIMEOUT", 60))
if (is.na(to) || to <= 0) to <- 60L
options(timeout = to)
})
options(encoding = "native.enc")
options(show.error.messages = TRUE)
## keep in sync with PrintDefaults() in ../../main/print.c :
options(scipen = 0)
options(max.print = 99999)# max. #{entries} in internal printMatrix()
options(add.smooth = TRUE)# currently only used in 'plot.lm'
if(isFALSE(as.logical(Sys.getenv("_R_OPTIONS_STRINGS_AS_FACTORS_",
"FALSE")))) {
options(stringsAsFactors = FALSE)
} else {
options(stringsAsFactors = TRUE)
}
if(!interactive() && is.null(getOption("showErrorCalls")))
options(showErrorCalls = TRUE)
local({dp <- Sys.getenv("R_DEFAULT_PACKAGES")
if(identical(dp, "")) ## it fact methods is done first
dp <- c("datasets", "utils", "grDevices", "graphics",
"stats", "methods")
else if(identical(dp, "NULL")) dp <- character(0)
else dp <- strsplit(dp, ",")[[1]]
dp <- sub("[[:blank:]]*([[:alnum:]]+)", "\\1", dp) # strip whitespace
options(defaultPackages = dp)
})
## Expand R_LIBS_* environment variables.
Sys.setenv(R_LIBS_SITE =
.expand_R_libs_env_var(Sys.getenv("R_LIBS_SITE")))
Sys.setenv(R_LIBS_USER =
.expand_R_libs_env_var(Sys.getenv("R_LIBS_USER")))
local({
if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_CPU")))
setSessionTimeLimit(cpu = tl)
if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_ELAPSED")))
setSessionTimeLimit(elapsed = tl)
})
.First.sys <- function()
{
for(pkg in getOption("defaultPackages")) {
res <- require(pkg, quietly = TRUE, warn.conflicts = FALSE,
character.only = TRUE)
if(!res)
warning(gettextf('package %s in options("defaultPackages") was not found', sQuote(pkg)),
call. = FALSE, domain = NA)
}
}
## called at C level in the startup process prior to .First.sys
.OptRequireMethods <- function()
{
pkg <- "methods" # done this way to avoid R CMD check warning
if(pkg %in% getOption("defaultPackages"))
if(!require(pkg, quietly = TRUE, warn.conflicts = FALSE,
character.only = TRUE))
warning('package "methods" in options("defaultPackages") was not found',
call. = FALSE)
}
if(nzchar(Sys.getenv("R_BATCH"))) {
.Last.sys <- function()
{
cat("> proc.time()\n")
print(proc.time())
}
## avoid passing on to spawned R processes
## A system has been reported without Sys.unsetenv, so try this
try(Sys.setenv(R_BATCH=""))
}
local({
if(nzchar(rv <- Sys.getenv("_R_RNG_VERSION_")))
suppressWarnings(RNGversion(rv))
})
.sys.timezone <- NA_character_
.First <- NULL
.Last <- NULL
###-*- R -*- Unix Specific ----
.Library <- file.path(R.home(), "library")
.Library.site <- Sys.getenv("R_LIBS_SITE")
.Library.site <- if(!nzchar(.Library.site)) file.path(R.home(), "site-library") else unlist(strsplit(.Library.site, ":"))
.Library.site <- .Library.site[file.exists(.Library.site)]
invisible(.libPaths(c(unlist(strsplit(Sys.getenv("R_LIBS"), ":")),
unlist(strsplit(Sys.getenv("R_LIBS_USER"), ":")
))))
local({
popath <- Sys.getenv("R_TRANSLATIONS", "")
if(!nzchar(popath)) {
paths <- file.path(.libPaths(), "translations", "DESCRIPTION")
popath <- dirname(paths[file.exists(paths)][1])
}
bindtextdomain("R", popath)
bindtextdomain("R-base", popath)
assign(".popath", popath, .BaseNamespaceEnv)
})
local({
## we distinguish between R_PAPERSIZE as set by the user and by configure
papersize <- Sys.getenv("R_PAPERSIZE_USER")
if(!nchar(papersize)) {
lcpaper <- Sys.getlocale("LC_PAPER") # might be null: OK as nchar is 0
papersize <- if(nchar(lcpaper))
if(length(grep("(_US|_CA)", lcpaper))) "letter" else "a4"
else Sys.getenv("R_PAPERSIZE")
}
options(papersize = papersize,
printcmd = Sys.getenv("R_PRINTCMD"),
dvipscmd = Sys.getenv("DVIPS", "dvips"),
texi2dvi = Sys.getenv("R_TEXI2DVICMD"),
browser = Sys.getenv("R_BROWSER"),
pager = file.path(R.home(), "bin", "pager"),
pdfviewer = Sys.getenv("R_PDFVIEWER"),
useFancyQuotes = TRUE)
})
## non standard settings for the R.app GUI of the macOS port
if(.Platform$GUI == "AQUA") {
## this is set to let RAqua use both X11 device and X11/TclTk
if (Sys.getenv("DISPLAY") == "")
Sys.setenv("DISPLAY" = ":0")
## this is to allow gfortran compiler to work
Sys.setenv("PATH" = paste(Sys.getenv("PATH"),":/usr/local/bin",sep = ""))
}## end "Aqua"
## de-dupe the environment on macOS (bug in Yosemite which affects things like PATH)
if (grepl("^darwin", R.version$os)) local({
## we have to de-dupe one at a time and re-check since the bug affects how
## environment modifications propagate
while(length(dupes <- names(Sys.getenv())[table(names(Sys.getenv())) > 1])) {
env <- dupes[1]
value <- Sys.getenv(env)
Sys.unsetenv(env) ## removes the dupes, good
.Internal(Sys.setenv(env, value)) ## wrapper requries named vector, a pain, hence internal
}
})
local({
tests_startup <- Sys.getenv("R_TESTS")
if(nzchar(tests_startup)) source(tests_startup)
})
R Site Profile: /usr/lib64/R/etc/Rprofile.site
--------------------------------------------------
(File does not exist)
R User Profile: /home/graham/.Rprofile
--------------------------------------------------
(File does not exist)
R Site Environ: /usr/lib64/R/etc/Renviron.site
--------------------------------------------------
(File does not exist)
R User Environ: /home/graham/.Renviron
--------------------------------------------------
(File does not exist)
R Temporary Directory
--------------------------------------------------
/tmp/RtmpmG9HrT
Files in R Temporary Directory
--------------------------------------------------
rs-graphics-66f4fd6d-6ab4-4d30-857b-facab64bc79b
Log file: /home/graham/.local/share/rstudio/log/rdesktop.log
--------------------------------------------------
(Not Found)
Log file: /home/graham/.local/share/rstudio/log/rsession-graham.log
--------------------------------------------------
2022-01-10T18:34:53.262144Z [rsession-graham] WARNING No memory control group found in /proc/self/cgroup; LOGGED FROM: std::__cxx11::string rstudio::core::system::{anonymous}::getMemoryCgroup() src/cpp/core/system/LinuxResources.cpp:335
...