segfault with readDCF on R 3.1.2 on AIX 6.1 when using install.packages
Here's an update: I checked the ChangeLog for R, and it seems like readDCF was changed in 3.0.2. I went on a whim and copied src/main/dcf.c from R 2.15.3 over to 3.2.2, and R compiled fine and install.packages now work for me. This is probably not ideal, but it at least makes R usable on AIX for me. Would definitely like to help figure out what's wrong with the new dcf.c on AIX. Thanks. -- Vinh
On Mon, Sep 21, 2015 at 10:01 AM, Vinh Nguyen <vinhdizzo at gmail.com> wrote:
Hi there, I just wanted to follow up on this readDCF issue with install.packages on AIX on R 3.*. I'm happy to help try potential solutions or debug if anyone could point me in the right direction. To re-cap, it appears readDCF is segfault'ing since R 3.* on AIX. This was not the case up until R 2.15.3. This makes install.packages not usable. Thanks. -- Vinh On Tue, Nov 11, 2014 at 10:23 AM, Vinh Nguyen <vinhdizzo at gmail.com> wrote:
Dear list (re-posting from r-help as r-devel is probably more appropriate), I was able to successfully compile R on our AIX box at work using the GNU compilers following the instructions on the R Administration guide. The output can be seen at here (https://gist.github.com/nguyenvinh/504321ea9c89d8919bef) and yields no errors . However, I get a segfault whenever I try to use the install.packages function to install packages. Using debug, I was able to trace it to the readDCF function: Browse[2]> debug: if (!all) return(.Internal(readDCF(file, fields, keep.white))) Browse[2]> debug: return(.Internal(readDCF(file, fields, keep.white))) Browse[2]> *** caught segfault *** address 4, cause 'invalid permissions' Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: Was curious if anyone has a clue on why such error exists or what I could do to fix it? I'm able to install packages via R CMD INSTALL, but I would hate to have to manually determine dependencies, download the source for each package, and install them "by hand" via R CMD INSTALL. I went back and compiled older versions of R to see if this error exists. On R 3.0.3, I get: debug(available.packages) install.packages('ggplot2', dep=TRUE, repo='http://cran.stat.ucla.edu') ... Browse[2]> debug: z <- res0 <- tryCatch(read.dcf(file = tmpf), error = identity) Browse[2]> Error: segfault from C stack overflow On R 2.15.3, I do not see the error. Would be great to get this resolved. Thank you for your help. -- Vinh