Problem with starting R since latest update

English Applications
1

Dear all,

I am using openSUSE 13.2 (Harlequin) (x86_64) and
R - patched
repository: http://download.opensuse.org/repositories/devel:/languages:/R:/patched/openSUSE_13.2/

Since the latest update to version 3.3.2 R does not start properly.

I get the following error:

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-suse-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.

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/lib64/R/library/utils/libs/utils.so':
  /usr/lib64/R/library/utils/libs/utils.so: undefined symbol: csduplicated
In addition: Warning messages:
1: package "methods" in options("defaultPackages") was not found 
2: S3 methods ‘.getAnywhere’, ‘.roman’, ‘as.character.person’, ‘as.character.roman’, ‘as.person.default’, ‘as.personList.default’, ‘as.personList.person’, ‘close.txtProgressBar’, ‘edit.data.frame’, ‘edit.default’, ‘edit.matrix’, ‘edit.vignette’, ‘format.news_db’, ‘format.object_size’, ‘format.roman’, ‘head.data.frame’, ‘head.default’, ‘head.function’, ‘head.matrix’, ‘head.ftable’, ‘head.table’, ‘print.aspell’, ‘print.aspell_inspect_context’, ‘print.Bibtex’, ‘print.changedFiles’, ‘print.fileSnapshot’, ‘print.findLineNumResult’, ‘print.getAnywhere’, ‘print.hsearch’, ‘print.help_files_with_topic’, ‘print.Latex’, ‘print.ls_str’, ‘print.MethodsFunction’, ‘print.news_db’, ‘print.object_size’, ‘print.packageDescription’, ‘print.packageIQR’, ‘print.packageStatus’, ‘print.roman’, ‘print.sessionInfo’, ‘print.socket’, ‘print.summary.p ... truncated] 
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/lib64/R/library/grDevices/libs/grDevices.so':
  /usr/lib64/R/library/grDevices/libs/grDevices.so: undefined symbol: mbcsToUcs2
In addition: Warning messages:
1: package ‘utils’ in options("defaultPackages") was not found 
2: S3 methods ‘print.recordedplot’, ‘print.colorConverter’, ‘print.RGBcolorConverter’, ‘checkFont.default’, ‘checkFont.Type1Font’, ‘checkFont.CIDFont’, ‘matchEncoding.Type1Font’, ‘matchEncoding.CIDFont’, ‘as.raster.raster’, ‘as.raster.logical’, ‘as.raster.numeric’, ‘as.raster.character’, ‘as.raster.matrix’, ‘as.raster.array’, ‘as.matrix.raster’, ‘is.na.raster’, ‘anyNA.raster’, ‘.raster’, ‘<-.raster’, ‘Ops.raster’, ‘print.raster’, ‘pretty.Date’, ‘pretty.POSIXt’ were declared in NAMESPACE but not found 
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/lib64/R/library/grDevices/libs/grDevices.so':
  /usr/lib64/R/library/grDevices/libs/grDevices.so: undefined symbol: mbcsToUcs2
In addition: Warning messages:
1: package ‘grDevices’ in options("defaultPackages") was not found 
2: S3 methods ‘print.recordedplot’, ‘print.colorConverter’, ‘print.RGBcolorConverter’, ‘checkFont.default’, ‘checkFont.Type1Font’, ‘checkFont.CIDFont’, ‘matchEncoding.Type1Font’, ‘matchEncoding.CIDFont’, ‘as.raster.raster’, ‘as.raster.logical’, ‘as.raster.numeric’, ‘as.raster.character’, ‘as.raster.matrix’, ‘as.raster.array’, ‘as.matrix.raster’, ‘is.na.raster’, ‘anyNA.raster’, ‘.raster’, ‘<-.raster’, ‘Ops.raster’, ‘print.raster’, ‘pretty.Date’, ‘pretty.POSIXt’ were declared in NAMESPACE but not found 
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/lib64/R/library/grDevices/libs/grDevices.so':
  /usr/lib64/R/library/grDevices/libs/grDevices.so: undefined symbol: mbcsToUcs2
In addition: Warning messages:
1: package ‘graphics’ in options("defaultPackages") was not found 
2: S3 methods ‘print.recordedplot’, ‘print.colorConverter’, ‘print.RGBcolorConverter’, ‘checkFont.default’, ‘checkFont.Type1Font’, ‘checkFont.CIDFont’, ‘matchEncoding.Type1Font’, ‘matchEncoding.CIDFont’, ‘as.raster.raster’, ‘as.raster.logical’, ‘as.raster.numeric’, ‘as.raster.character’, ‘as.raster.matrix’, ‘as.raster.array’, ‘as.matrix.raster’, ‘is.na.raster’, ‘anyNA.raster’, ‘.raster’, ‘<-.raster’, ‘Ops.raster’, ‘print.raster’, ‘pretty.Date’, ‘pretty.POSIXt’ were declared in NAMESPACE but not found 
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/lib64/R/library/utils/libs/utils.so':
  /usr/lib64/R/library/utils/libs/utils.so: undefined symbol: csduplicated
In addition: Warning messages:
1: package ‘stats’ in options("defaultPackages") was not found 
2: S3 methods ‘.getAnywhere’, ‘.roman’, ‘as.character.person’, ‘as.character.roman’, ‘as.person.default’, ‘as.personList.default’, ‘as.personList.person’, ‘close.txtProgressBar’, ‘edit.data.frame’, ‘edit.default’, ‘edit.matrix’, ‘edit.vignette’, ‘format.news_db’, ‘format.object_size’, ‘format.roman’, ‘head.data.frame’, ‘head.default’, ‘head.function’, ‘head.matrix’, ‘head.ftable’, ‘head.table’, ‘print.aspell’, ‘print.aspell_inspect_context’, ‘print.Bibtex’, ‘print.changedFiles’, ‘print.fileSnapshot’, ‘print.findLineNumResult’, ‘print.getAnywhere’, ‘print.hsearch’, ‘print.help_files_with_topic’, ‘print.Latex’, ‘print.ls_str’, ‘print.MethodsFunction’, ‘print.news_db’, ‘print.object_size’, ‘print.packageDescription’, ‘print.packageIQR’, ‘print.packageStatus’, ‘print.roman’, ‘print.sessionInfo’, ‘print.socket’, ‘print.summary.p ... truncated] 
During startup - Warning message:
package ‘methods’ in options("defaultPackages") was not found

I tried uninstalling and re-installing in YaST, but that did not help.

Any suggestions, why this happens and how to fix it?

2

(Sorry I personally don’t have R installed on one of my machines)

Need…

  • Name of the RPM package containing the R you’re using
    I’d recommend on general principles using the packages from the “release” repository instead of the “patched” repository.
    Try the following that adds the repo I’d recommend.
    First, disable the repo you’re currently using, I think the following should work although I don’t usually try to reference a repo by its URI. If the following doesn’t work, you can reference the repo by number or label (You can display those by listing your repos) or using YAST repo management.
zypper mr --disable http://download.opensuse.org/repositories/devel:/languages:/R:/patched/openSUSE_13.2/

Then add

zypper ar -f http://download.opensuse.org/repositories/devel:/languages:/R:/released/openSUSE_13.2/ openSUSE_13.2_devel:language_R

If you aren’t already configured to do so, you can add the above repository, then update your system to pull in any new R packages

zypper up

From what you posted,
To me, it looks like you don’t have installed or properly updated with a “devel” package for your R package.
If your R was working earlier, then it’s probably a package availability or mistake problem.
But, IMO getting your R from the release repo should be recommended in any case.

HTH,
TSU

3

Hi Tsu,
Thanks for your reply. I am going to proceed as you suggest.
I was actually using R-patched, because this was suggested at https://cran.r-project.org/bin/linux/suse/README.html