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#1 2020-07-11 05:03:26

zekebsatx
Member
Registered: 2016-01-29
Posts: 72

[SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

I don't really know how to explain this problem. I updated R to v4.0 and had to reinstall all of the external packages I use. After doing so, R runs perfectly well in Konsole.  Here is the startup text:

 ~]$ R

R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]

>

But when I run R in the Kate terminal window I get this:

~]$ R

R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Warning: namespace ‘lme4’ is not available and has been replaced
by .GlobalEnv when processing object ‘lmtl’
Warning: namespace ‘stats’ is not available and has been replaced
by .GlobalEnv when processing object ‘glmcat’
Warning: namespace ‘ggplot2’ is not available and has been replaced
by .GlobalEnv when processing object ‘gp’
Warning: namespace ‘scales’ is not available and has been replaced
by .GlobalEnv when processing object ‘gp’
[Previously saved workspace restored]

Error: package or namespace load failed for ‘utils’:
 .onLoad failed in loadNamespace() for 'utils', details:
  call: options(op.utils[toset])
  error: invalid value for 'editor'
Error: package or namespace load failed for ‘stats’:
 .onLoad failed in loadNamespace() for 'utils', details:
  call: options(op.utils[toset])
  error: invalid value for 'editor'
During startup - Warning messages:
1: package ‘utils’ in options("defaultPackages") was not found 
2: package ‘stats’ in options("defaultPackages") was not found 
>

It worked fine in Kate before the update. It is annoying because running R in Kate (terminal window) was the only way I could drag and drop code from Kate.  Kate has a persistent bug that doesn't allow drag and drop to Konsole or other shell windows.
Any help resolving this is appreciated.

Last edited by zekebsatx (2020-07-19 23:45:11)

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#2 2020-07-11 10:37:49

Lone_Wolf
Administrator
From: Netherlands, Europe
Registered: 2005-10-04
Posts: 15,388

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

Archlinux Kate package was recently (47 hours ago ) updated, which version of kate are you running ?

Disliking systemd intensely, but not satisfied with alternatives so focusing on taming systemd.

clean chroot building not flexible enough ?
Try clean chroot manager by graysky

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#3 2020-07-12 05:56:15

zekebsatx
Member
Registered: 2016-01-29
Posts: 72

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

I was on
Kate
Version 20.04.2

Konsole
Version 20.04.2

Dolphin
Version 20.04.2

I forgot to mention that R works with no issues in the Dolphin terminal pane as well as in Konsole.

I updated to Kate v20.04.3 and the problem persists.

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#4 2020-07-12 06:18:07

seth
Member
From: Won't reply 2 private help req
Registered: 2012-09-03
Posts: 77,689

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

I'd compare the shell environments in the various terminals. Notably for https://wiki.archlinux.org/index.php/R#Environment

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#5 2020-07-13 19:17:17

zekebsatx
Member
Registered: 2016-01-29
Posts: 72

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

I did not have a local Renviron file, so I created a generic ~/.Renviron file as described in the wiki.  This broke R in Konsole, but not quite the same as it is broken in Kate.

$ R

R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Warning: namespace ‘lme4’ is not available and has been replaced
by .GlobalEnv when processing object ‘lmtl’
Warning: namespace ‘ggplot2’ is not available and has been replaced
by .GlobalEnv when processing object ‘gp’
Warning: namespace ‘scales’ is not available and has been replaced
by .GlobalEnv when processing object ‘gp’
[Previously saved workspace restored]

>

Then, I replaced the local .Renviron file with the master from /etc/R/Renviron and
I confirmed that R ran as expected in Konsole.  However Kate still threw the same errors as described in my OP
So this doesn't appear to the be exact problem.

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#6 2020-07-13 19:24:07

seth
Member
From: Won't reply 2 private help req
Registered: 2012-09-03
Posts: 77,689

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

Did you compare/diff the outputs of "env" in either terminal?

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#7 2020-07-13 22:31:56

zekebsatx
Member
Registered: 2016-01-29
Posts: 72

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

I don't see anything jump out at me.
The differences are::
A window id number in Konsole, windowID=0 in Kate
the line "EDITOR=" in Kate
A different KONSOLE_DBUS_SERVICE=:1.xxx .vs. yyy in Kate
The line "KATE_PID=21733" in Kate
The line "KONSOLE_DBUS_WINDOW=/Windows/1" in Kosole, not in Kate
and an OLDPWD pointer in Konsole, not in Kate.

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#8 2020-07-14 06:52:47

seth
Member
From: Won't reply 2 private help req
Registered: 2012-09-03
Posts: 77,689

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

Yeah, no that's all irrelevant. So should be the VTE, the difference would be in the calling shell (and kate really just embeds a konsolepart just as konsole does)

=> strace the "R" call into files

strace -f -o ~/konsole.strace R
strace -f -o ~/kate.strace R

and diff them to see where things run apart.

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#9 2020-07-14 22:23:56

zekebsatx
Member
Registered: 2016-01-29
Posts: 72

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

Thanks,
Here is output Kate throws that Konsole does not:

4121  stat("/home/[MYUSER]", {st_mode=S_IFDIR|0700, st_size=12288, ...}) = 0
4121  getpid()                          = 4121
4121  getppid()                         = 4118
4121  getpid()                          = 4121
4121  getpgrp()                         = 4118
4121  ioctl(2, TIOCGPGRP, [4118])       = 0
4121  rt_sigaction(SIGCHLD, {sa_handler=0x5610279a35a0, sa_mask=[], sa_flags=SA_RESTORER|SA_RESTART, sa_restorer=0x7fc33cf383e0}, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER|SA_RESTART, sa_restorer=0x7fc33cf383e0}, 8) = 0
4121  prlimit64(0, RLIMIT_NPROC, NULL, {rlim_cur=31252, rlim_max=31252}) = 0
4121  rt_sigprocmask(SIG_BLOCK, NULL, [], 8) = 0
4121  openat(AT_FDCWD, "/usr/bin/R", O_RDONLY) = 3
4121  stat("/usr/bin/R", {st_mode=S_IFREG|0755, st_size=8953, ...}) = 0
4121  ioctl(3, TCGETS, 0x7ffd1b4d5fc0)  = -1 ENOTTY (Inappropriate ioctl for device)
4121  lseek(3, 0, SEEK_CUR)             = 0
4121  read(3, "#!/bin/sh\n# Shell wrapper for R "..., 80) = 80
4121  lseek(3, 0, SEEK_SET)             = 0
4121  prlimit64(0, RLIMIT_NOFILE, NULL, {rlim_cur=1024, rlim_max=512*1024}) = 0
4121  fcntl(255, F_GETFD)               = -1 EBADF (Bad file descriptor)
4121  dup2(3, 255)                      = 255
4121  close(3)                          = 0
4121  fcntl(255, F_SETFD, FD_CLOEXEC)   = 0
4121  fcntl(255, F_GETFL)               = 0x8000 (flags O_RDONLY|O_LARGEFILE)
4121  fstat(255, {st_mode=S_IFREG|0755

4121  fstat(255, {st_mode=S_IFREG|0755, st_size=8953, ...}) = 0
4121  lseek(255, 0, SEEK_CUR)           = 0
4121  read(255, "#!/bin/sh\n# Shell wrapper for R "..., 8192) = 8192
4121  pipe([3, 4]
4122  <... close resumed>)              = 0
4121  <... rt_sigaction resumed>{sa_handler=0x5610279a35a0, sa_mask=[], sa_flags=SA_RESTORER|SA_RESTART, sa_restorer=0x7fc33cf383e0}, 8) = 0
4122  rt_sigprocmask(SIG_SETMASK, [],  <unfinished ...>
4121  close(4 <unfinished ...>
4122  <... rt_sigprocmask resumed>NULL, 8) = 0
4121  <... close resumed>)              = 0
4122  rt_sigaction(SIGTSTP, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0},  <unfinished ...>
4121  read(3,  <unfinished ...>
4122  <... rt_sigaction resumed>{sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, 8) = 0
4122  rt_sigaction(SIGTTIN, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, 8) = 0
4122  rt_sigaction(SIGTTOU, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, 8) = 0
4122  rt_sigaction(SIGINT, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, 8) = 0
4122  rt_sigaction(SIGQUIT, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, {sa_handler=SIG_IGN, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, 8) = 0
4122  rt_sigaction(SIGCHLD, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER|SA_RESTART, sa_restorer=0x7fc33cf383e0}, {sa_handler=0x5610279a35a0, sa_mask=[], sa_flags=SA_RESTORER|SA_RESTART, sa_restorer=0x7fc33cf383e0}, 8) = 0
4122  rt_sigaction(SIGCHLD, {sa_handler=0x5610279a35a0, sa_mask=[], sa_flags=SA_RESTORER|SA_RESTART, sa_restorer=0x7fc33cf383e0}, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER|SA_RESTART, sa_restorer=0x7fc33cf383e0}, 8) = 0
4122  rt_sigaction(SIGINT, {sa_handler=0x5610279c1cf0, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, 8) = 0
4122  dup2(4, 1)                        = 1
4122  close(4)                          = 0
4122  close(3)                          = 0
4122  rt_sigprocmask(SIG_BLOCK, NULL, [], 8) = 0
4122  stat(".", {st_mode=S_IFDIR|0700, st_size=12288, ...}) = 0
4122  stat("/usr/local/sbin/uname", 0x7ffd1b4d51c0) = -1 ENOENT (No such file or directory)
4122  stat("/usr/local/bin/uname", 0x7ffd1b4d51c0) = -1 ENOENT (No such file or directory)
4122  stat("/usr/bin/uname", {st_mode=S_IFREG|0755, st_size=39080, ...}) = 0
4122  stat("/usr/bin/uname", {st_mode=S_IFREG|0755, st_size=39080, ...}) = 0
4122  geteuid()                         = 1000
4122  getegid()                         = 1000
4122  getuid()                          = 1000
4122  getgid()                          = 1000
4122  getegid()                         = 1000
4122  getuid()                          = 1000
4122  getgid()                          = 1000
4122  access("/usr/bin/uname", R_OK)    = 0
4122  stat("/usr/bin/uname", {st_mode=S_IFREG|0755, st_size=39080, ...}) = 0
4122  stat("/usr/bin/uname", {st_mode=S_IFREG|0755, st_size=39080, ...}) = 0
4122  geteuid()                         = 1000
4122  getegid()                         = 1000
4122  getuid()                          = 1000
4122  getgid()                          = 1000
4122  access("/usr/bin/uname", X_OK)    = 0
4122  stat("/usr/bin/uname", {st_mode=S_IFREG|0755, st_size=39080, ...}) = 0
4122  geteuid()                         = 1000
4122  getegid()                         = 1000
4122  getuid()                          = 1000
4122  getgid()                          = 1000
4122  access("/usr/bin/uname", R_OK)    = 0
4122  rt_sigaction(SIGINT, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, {sa_handler=0x5610279c1cf0, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, 8) = 0
4122  rt_sigaction(SIGQUIT, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fc33cf383e0}, 8) = 0
4122  rt_sigaction(SIGCHLD, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER|SA_RESTART, sa_restorer=0x7fc33cf383e0}, {sa_handler=0x5610279a35a0, sa_mask=[], sa_flags=SA_RESTORER|SA_RESTART, sa_restorer=0x7fc33cf383e0}, 8) = 0
4122  execve("/usr/bin/uname", ["uname", "-m"], 0x561027e63e10 /* 54 vars */) = 0
4122  brk(NULL)                         = 0x55b69dc0d000
4122  arch_prctl(0x3001 /* ARCH_??? */, 0x7ffebf385190) = -1 EINVAL (Invalid argument)
4122  access("/etc/ld.so.preload", R_OK) = -1 ENOENT (No such file or directory)

This goes on, and then 

4121  openat(AT_FDCWD, "/usr/lib64/R/lib/tls/libR.so", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
4121  stat("/usr/lib64/R/lib/tls", 0x7fffbedfbb30) = -1 ENOENT (No such file or directory)
4121  openat(AT_FDCWD, "/usr/lib64/R/lib/haswell/x86_64/libR.so", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
4121  stat("/usr/lib64/R/lib/haswell/x86_64", 0x7fffbedfbb30) = -1 ENOENT (No such file or directory)
4121  openat(AT_FDCWD, "/usr/lib64/R/lib/haswell/libR.so", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
4121  stat("/usr/lib64/R/lib/haswell", 0x7fffbedfbb30) = -1 ENOENT (No such file or directory)
4121  openat(AT_FDCWD, "/usr/lib64/R/lib/x86_64/libR.so", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
4121  stat("/usr/lib64/R/lib/x86_64", 0x7fffbedfbb30) = -1 ENOENT (No such file or directory)

This appears to be where I start seeing error messages as the base-level libraries are not loading.
But I have no idea what to do to prevent this behavior by Kate.

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#10 2020-07-15 07:19:04

seth
Member
From: Won't reply 2 private help req
Registered: 2012-09-03
Posts: 77,689

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

Why would konsole not run the R wrapper script?
Compare "type R" in either context.

Also 

stat /usr/lib64/R

The wrapper script will make this the default R_HOME_DIR if it exists, but that's not where arch installs stuff.
Ultimately it should™ resolve and open /usr/lib/R/lib/libR.so

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#11 2020-07-15 18:20:43

zekebsatx
Member
Registered: 2016-01-29
Posts: 72

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

type R is the same in both Konsole and Kate panel:

R is /usr/bin/R

I am afraid I don't understand the other part of your reply.

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#12 2020-07-15 18:51:04

seth
Member
From: Won't reply 2 private help req
Registered: 2012-09-03
Posts: 77,689

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

What's the output of "stat /usr/lib64/R"? R should™ not look there unless that path exists and it should™ not exist - at least the R package doesn't create it.

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#13 2020-07-16 14:19:55

zekebsatx
Member
Registered: 2016-01-29
Posts: 72

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

From Konsole:

$ stat /usr/lib64/R
  File: /usr/lib64/R
  Size: 4096            Blocks: 8          IO Block: 4096   directory
Device: 802h/2050d      Inode: 1074684     Links: 7
Access: (0755/drwxr-xr-x)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2020-07-12 00:46:36.803854468 -0500
Modify: 2020-07-03 13:29:16.026708178 -0500
Change: 2020-07-03 13:29:16.026708178 -0500
 Birth: 2016-08-11 23:12:18.797168659 -0500

From Kate:

$ stat /usr/lib64/R
  File: /usr/lib64/R
  Size: 4096            Blocks: 8          IO Block: 4096   directory
Device: 802h/2050d      Inode: 1074684     Links: 7
Access: (0755/drwxr-xr-x)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2020-07-12 00:46:36.803854468 -0500
Modify: 2020-07-03 13:29:16.026708178 -0500
Change: 2020-07-03 13:29:16.026708178 -0500
 Birth: 2016-08-11 23:12:18.797168659 -0500

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#14 2020-07-16 14:36:45

seth
Member
From: Won't reply 2 private help req
Registered: 2012-09-03
Posts: 77,689

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

This at least explains why R starts looking in that path… (not the difference, though)

ls /usr/lib64/R
pacman -Qo /usr/lib64/R

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#15 2020-07-16 14:46:37

zekebsatx
Member
Registered: 2016-01-29
Posts: 72

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

$ ls /usr/lib64/R
bin  COPYING  etc  lib  library  modules  SVN-REVISION
$ pacman -Qo /usr/lib64/R
/usr/lib/R/ is owned by r 4.0.1-1

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#16 2020-07-16 14:51:32

seth
Member
From: Won't reply 2 private help req
Registered: 2012-09-03
Posts: 77,689

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

Yeahno. /usr/lib64 is just a symlink to /usr/lib, the "failures" in the strace are early attempts before the library is most likely resolved from /usr/lib/R/lib/libR.so

Please just post/upload both straces.

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#17 2020-07-17 14:10:13

zekebsatx
Member
Registered: 2016-01-29
Posts: 72

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

Kate strace
Konsole strace

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#18 2020-07-17 14:42:30

seth
Member
From: Won't reply 2 private help req
Registered: 2012-09-03
Posts: 77,689

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

4121  write(1, "Type 'demo()' for some demos, 'h"..., 137) = 137
4121  openat(AT_FDCWD, "/usr/lib64/R/etc//Rprofile.site", O_RDONLY) = -1 ENOENT (No such file or directory)
4121  openat(AT_FDCWD, "/usr/lib64/R/etc/Rprofile.site", O_RDONLY) = -1 ENOENT (No such file or directory)
4121  openat(AT_FDCWD, ".Rprofile", O_RDONLY) = -1 ENOENT (No such file or directory)
4121  openat(AT_FDCWD, "/home/brett/.Rprofile", O_RDONLY) = -1 ENOENT (No such file or directory)
4121  stat(".RData", {st_mode=S_IFREG|0644, st_size=244963, ...}) = 0
4121  openat(AT_FDCWD, ".RData", O_RDONLY) = 3
4121  fstat(3, {st_mode=S_IFREG|0644, st_size=244963, ...}) = 0
4121  read(3, "\37\213\10\0\0\0\0\0\0\3\354=\7x\34\305\325\263\222,\311r\223\v\6c\214\317\306\306\22\330"..., 4096) = 4096
4121  close(3)                          = 0
4121  stat(".RData", {st_mode=S_IFREG|0644, st_size=244963, ...}) = 0
4121  openat(AT_FDCWD, ".RData", O_RDONLY) = 3
4121  fstat(3, {st_mode=S_IFREG|0644, st_size=244963, ...}) = 0
4121  read(3, "\37\213\10\0\0\0\0\0\0\3\354=\7x\34\305\325\263\222,\311r\223\v\6c\214\317\306\306\22\330"..., 16384) = 16384
4121  lseek(3, 0, SEEK_CUR)             = 16384
4121  close(3)                          = 0
4121  stat(".RData", {st_mode=S_IFREG|0644, st_size=244963, ...}) = 0
4121  openat(AT_FDCWD, ".RData", O_RDONLY) = 3
4121  fstat(3, {st_mode=S_IFREG|0644, st_size=244963, ...}) = 0
4121  read(3, "\37\213\10\0\0\0\0\0\0\3\354=\7x\34\305\325\263\222,\311r\223\v\6c\214\317\306\306\22\330"..., 16384) = 16384
4121  lseek(3, 0, SEEK_CUR)             = 16384
4121  brk(0x5572a39dd000)               = 0x5572a39dd000
4121  stat("/home/brett/R/x86_64-pc-linux-gnu-library/4.0/lme4/DESCRIPTION", {st_mode=S_IFREG|0644, st_size=2747, ...}) = 0
4237  write(1, "Type 'demo()' for some demos, 'h"..., 137) = 137
4237  openat(AT_FDCWD, "/usr/lib64/R/etc//Rprofile.site", O_RDONLY) = -1 ENOENT (No such file or directory)
4237  openat(AT_FDCWD, "/usr/lib64/R/etc/Rprofile.site", O_RDONLY) = -1 ENOENT (No such file or directory)
4237  openat(AT_FDCWD, ".Rprofile", O_RDONLY) = -1 ENOENT (No such file or directory)
4237  openat(AT_FDCWD, "/home/brett/.Rprofile", O_RDONLY) = -1 ENOENT (No such file or directory)
4237  stat(".RData", 0x7fff1247e5a0)    = -1 ENOENT (No such file or directory)
4237  stat("/home/brett/R/x86_64-pc-linux-gnu-library/4.0", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0

It's the .Rdata file in $PWD - exists in the konsole case, doesn't in kate case. After reading that, the konsole call checks and loads the /home/brett/R/x86_64-pc-linux-gnu-library/4.0/lme4/ stuff which doesn't happen in the kate case.

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#19 2020-07-19 00:23:49

zekebsatx
Member
Registered: 2016-01-29
Posts: 72

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

I don't know why, I get the same errors if I make sure I am starting R in the home dir in the Kate terminal.
Still, I think there is another issue as well. Both may be related.
Look at this from inside the R console in the Kate terminal pane:

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Warning: namespace ‘lme4’ is not available and has been replaced
by .GlobalEnv when processing object ‘lmtl’
Warning: namespace ‘stats’ is not available and has been replaced
by .GlobalEnv when processing object ‘glmcat’
Warning: namespace ‘ggplot2’ is not available and has been replaced
by .GlobalEnv when processing object ‘gp’
Warning: namespace ‘scales’ is not available and has been replaced
by .GlobalEnv when processing object ‘gp’
[Previously saved workspace restored]

Error: package or namespace load failed for ‘utils’:
 .onLoad failed in loadNamespace() for 'utils', details:
  call: options(op.utils[toset])
  error: invalid value for 'editor'
Error: package or namespace load failed for ‘stats’:
 .onLoad failed in loadNamespace() for 'utils', details:
  call: options(op.utils[toset])
  error: invalid value for 'editor'
During startup - Warning messages:
1: package ‘utils’ in options("defaultPackages") was not found 
2: package ‘stats’ in options("defaultPackages") was not found 
> load("~/.RData")
Warning: namespace ‘lme4’ is not available and has been replaced
by .GlobalEnv when processing object ‘lmtl’
Warning: namespace ‘stats’ is not available and has been replaced
by .GlobalEnv when processing object ‘glmcat’
Warning: namespace ‘ggplot2’ is not available and has been replaced
by .GlobalEnv when processing object ‘gp’
Warning: namespace ‘scales’ is not available and has been replaced
by .GlobalEnv when processing object ‘gp’
>

So when I load the .RData file contained in the home dir, which does exist, I get the advanced module package load error messages (lme4, ggplot2, etc). Those are modules I installed beyond the base packages.  But then at boot, I also get error messages for the base packages 'utils' and 'stats' which are part of any default install of R.
Why would the Kate terminal not see the .RData file which is certainly present where it is looking for it?  I can see it in the Kate terminal, and the uid and home directories are both correct in the Kate panel.

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#20 2020-07-19 14:41:38

seth
Member
From: Won't reply 2 private help req
Registered: 2012-09-03
Posts: 77,689

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

error: invalid value for 'editor'

the line "EDITOR=" in Kate

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#21 2020-07-19 23:44:04

zekebsatx
Member
Registered: 2016-01-29
Posts: 72

Re: [SOLVED] Kate console not in sync with Konsole (KDE Plasma DE)

Thank you!!!  Solved now.
This link helped:
I added my preferred editor to my /etc/profile file and it now works as expected in Kate.

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