Your message dated Sun, 7 Jun 2020 12:52:44 -0500 with message-id <[email protected]> and subject line Re: Bug#962379: r-cran-rmysql: crash of R from within RStudio has caused the Debian Bug report #962379, regarding r-cran-rmysql: crash of R from within RStudio to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 962379: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962379 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: r-cran-rmysql Version: 0.10.20-1+b1 Severity: important Dear Maintainer, *** Reporter, please consider answering these questions, where appropriate *** * What led up to the situation? * What exactly did you do (or not do) that was effective (or ineffective)? * What was the outcome of this action? * What outcome did you expect instead? I run exactly the same script on two different machines, both running Debian. The itself script is quite old and stable. I run it weekly from RStudio. Since the Debian updates last week (or week before) as soon as I run the script in RStudio I get a R crash. If I run it a few more times the crashes disappear. Below the essential part of the script. I do not know how to debug it. The crash occurs likely in the dbConnect() call. I would not have reported it if it would occur on one of my machines, but is it now occurs on a very different machine, I think it is something structural and needs to be reported. library(RMySQL) library(tidyverse) library(lubridate) con <- dbConnect(RMySQL::MySQL(), username = xx, password = yy, host = bla, dbname = 'blabla) rs <- dbSendQuery(con, "SQL Query;"); df_raw <- dbFetch(rs, n = -1) *** End of the template - remove these template lines *** -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (990, 'testing'), (500, 'experimental'), (500, 'unstable') Architecture: amd64 (x86_64) Kernel: Linux 5.5.0-1-amd64 (SMP w/4 CPU cores) Kernel taint flags: TAINT_UNSIGNED_MODULE Locale: LANG=nl_NL.UTF-8, LC_CTYPE=nl_NL.UTF-8 (charmap=UTF-8), LANGUAGE=nl (charmap=UTF-8) Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages r-cran-rmysql depends on: ii libc6 2.31-0experimental2 ii libmariadb3 1:10.3.22-1 ii r-base-core [r-api-4.0] 4.0.1-1 ii r-cran-dbi 1.1.0-3 r-cran-rmysql recommends no packages. r-cran-rmysql suggests no packages. -- no debconf information
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--- Begin Message ---On 7 June 2020 at 11:25, Luc Castermans wrote: | On Sun, 07 Jun 2020 10:10:50 +0200 Luc Castermans <[email protected]> | wrote: | > Package: r-cran-rmysql | > Version: 0.10.20-1+b1 | > Severity: important | > | > Dear Maintainer, | > | > *** Reporter, please consider answering these questions, where | appropriate *** | > | > * What led up to the situation? | > * What exactly did you do (or not do) that was effective (or | > ineffective)? | > * What was the outcome of this action? | > * What outcome did you expect instead? | > | > I run exactly the same script on two different machines, both running | Debian. | > The itself script is quite old and stable. I run it weekly from | RStudio. Since the Debian updates | > last week (or week before) as soon as I run the script in RStudio I | get a R crash. If I run it | > a few more times the crashes disappear. | > | > Below the essential part of the script. I do not know how to debug | it. The crash occurs likely in the dbConnect() call. | > | > I would not have reported it if it would occur on one of my machines, | but is it now occurs on a very different machine, | > I think it is something structural and needs to be reported. | > | > | > library(RMySQL) | > library(tidyverse) | > library(lubridate) | > | > | > con <- dbConnect(RMySQL::MySQL(), | > username = xx, | > password = yy, | > host = bla, | > dbname = 'blabla) | > | > rs <- dbSendQuery(con, "SQL Query;"); | > df_raw <- dbFetch(rs, n = -1) | > | > | > | > | > *** End of the template - remove these template lines *** | > | > | > -- System Information: | > Debian Release: bullseye/sid | > APT prefers testing | > APT policy: (990, 'testing'), (500, 'experimental'), (500, 'unstable') | > Architecture: amd64 (x86_64) | > | > Kernel: Linux 5.5.0-1-amd64 (SMP w/4 CPU cores) | > Kernel taint flags: TAINT_UNSIGNED_MODULE | > Locale: LANG=nl_NL.UTF-8, LC_CTYPE=nl_NL.UTF-8 (charmap=UTF-8), | LANGUAGE=nl (charmap=UTF-8) | > Shell: /bin/sh linked to /usr/bin/dash | > Init: systemd (via /run/systemd/system) | > LSM: AppArmor: enabled | > | > Versions of packages r-cran-rmysql depends on: | | > ii libc6 2.31-0experimental2 | | | Hi, | | After upgrading RStudio from 1.25033 to 1.3.959 the bug is solved. Good to know. Also, in case you need to file another one, doing > library(RMySQL) > library(tidyverse) > library(lubridate) is pretty bad as too many moving parts are involving. _Minimal_ examples are always best. Dirk | | Luc | | | | -- | | m.vr.gr. | | Luc Castermans | mailto:[email protected] -- http://dirk.eddelbuettel.com | @eddelbuettel | [email protected]
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