got an error on installing lightgbm on linux

[franciszmy]

I have used lightgbm by using rstudio on centOS before, but for some reasons, yesterday I deleted my lightgbm package on rstudio server and when I tried to reinstall it later, it posted an error which I can't solve.

The error is

** testing if installed package can be loaded Error in UseMethod("conditionCall") : no applicable method for 'conditionCall' applied to an object of class "character" Calls: ... tryCatchList -> tryCatchOne -> -> conditionCall Execution halted ERROR: loading failed

• removing ‘/home/xxxx/R/x86_64-pc-linux-gnu-library/3.4/lightgbm’

this error seems a base function in R, but I don't know why something is wrong with this base function.

Anyone could help me? Thanks so much in advance!!!

[jameslamb]

Hi @franciszmy , we're here to help!

Can you please share the following?

1. The steps you used to remove lightgbm
2. The steps you used to reinstall it
3. The output for running sessionInfo()

[franciszmy]

thanks james, here are some information about what you mentioned above.

1.I just removed package from rstudio GUI. No other extra moves 2.I have lightgbm 2.0.1.0 package. I reinstalled it by using install.package in R

3. sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.10 (Final)

Matrix products: default BLAS: /opt/rinstall/R-3.4.4/lib/libRblas.so LAPACK: /opt/rinstall/R-3.4.4/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] R6_2.4.0 xgboost_0.6-4

loaded via a namespace (and not attached): [1] compiler_3.4.2 magrittr_1.5 Matrix_1.2-11 tools_3.4.2 stringi_1.1.6
[6] grid_3.4.2 data.table_1.10.4-3 lattice_0.20-35

Besides, the reason why I delete my lightgbm package is because I cannot use lightgbm package that I used to use successfully, the reason why I cannot use lightgbm is because I find later that the R is updated to 3.5 , so I reinstall R with 3.4 version.

below is the details of installation information:

Installing package into ‘/home/xxxx/R/x86_64-pc-linux-gnu-library/3.4’ (as ‘lib’ is unspecified)

• installing source package ‘lightgbm’ ... libs installing via 'install.libs.R' to /home/xxxx/R/x86_64-pc-linux-gnu-library/3.4/lightgbm -- The C compiler identification is GNU 4.4.7 -- The CXX compiler identification is GNU 4.8.5 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp
  -- Configuring done -- Generating done -- Build files have been written to: /tmp/Rtmpi544bM/R.INSTALL565976cfeab4/lightgbm/src/build Scanning dependencies of target _lightgbm [ 3%] [ 7%] [ 17%] [ 17%] [ 17%] [ 21%] [ 25%] [ 28%] [ 32%] [ 39%] [ 39%] [ 42%] [ 46%] [ 50%] [ 57%] [ 57%] Building CXX object CMakeFiles/_lightgbm.dir/src/c_api.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/application/application.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/boosting/gbdt_model_text.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/lightgbm_R.cpp.o [ 60%] Building CXX object CMakeFiles/_lightgbm.dir/src/boosting/boosting.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/boosting/prediction_early_stop.cpp.o [ 64%] [ 67%] Building CXX object CMakeFiles/_lightgbm.dir/src/io/dataset.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/io/metadata.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/boosting/gbdt.cpp.o [ 71%] Building CXX object CMakeFiles/_lightgbm.dir/src/io/dataset_loader.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/boosting/gbdt_prediction.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/io/bin.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/io/config.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/io/parser.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/io/tree.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/metric/dcg_calculator.cpp.o [ 75%] [ 78%] [ 82%] Building CXX object CMakeFiles/_lightgbm.dir/src/metric/metric.cpp.o [ 85%] [ 89%] Building CXX object CMakeFiles/_lightgbm.dir/src/objective/objective_function.cpp.o [ 92%] Building CXX object CMakeFiles/_lightgbm.dir/src/network/network.cpp.o [ 96%] Building CXX object CMakeFiles/_lightgbm.dir/src/network/linkers_socket.cpp.o [100%] Building CXX object CMakeFiles/_lightgbm.dir/src/network/linker_topo.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/network/linkers_mpi.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/treelearner/tree_learner.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/treelearner/data_parallel_tree_learner.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/treelearner/gpu_tree_learner.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/treelearner/serial_tree_learner.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/treelearner/voting_parallel_tree_learner.cpp.o Building CXX object CMakeFiles/_lightgbm.dir/src/treelearner/feature_parallel_tree_learner.cpp.o Linking CXX shared library ../lib_lightgbm.so [100%] Built target _lightgbm Found library file: /tmp/Rtmpi544bM/R.INSTALL565976cfeab4/lightgbm/src/lib_lightgbm.so to move to /home/xxxx/R/x86_64-pc-linux-gnu-library/3.4/lightgbm/libs R data demo preparing package for lazy loading help * installing help indices converting help for package ‘lightgbm’ finding HTML links ... done agaricus.test html
  agaricus.train html
  bank html
  dim html
  dimnames.lgb.Dataset html
  getinfo html
  lgb.Dataset html
  lgb.Dataset.construct html
  lgb.Dataset.create.valid html
  lgb.Dataset.save html
  lgb.Dataset.set.categorical html
  lgb.Dataset.set.reference html
  lgb.dump html
  lgb.get.eval.result html
  lgb.importance html
  lgb.interprete html
  lgb.load html
  lgb.model.dt.tree html
  lgb.plot.importance html
  lgb.plot.interpretation html
  lgb.prepare html
  lgb.prepare2 html
  lgb.prepare_rules html
  lgb.prepare_rules2 html
  lgb.save html
  lgb.train html
  lgb.unloader html
  predict.lgb.Booster html
  readRDS.lgb.Booster html
  saveRDS.lgb.Booster html
  setinfo html
  slice html
  building package indices ** testing if installed package can be loaded Error in UseMethod("conditionCall") : no applicable method for 'conditionCall' applied to an object of class "character" Calls: ... tryCatchList -> tryCatchOne -> -> conditionCall Execution halted ERROR: loading failed
• removing ‘/home/xxxx/R/x86_64-pc-linux-gnu-library/3.4/lightgbm’ Warning in install.packages : installation of package ‘/home/xxxx/lightgbm_2.0.10.tar.gz’ had non-zero exit status

thank you so much!

[jameslamb]

Hmmm I'm still trying to figure this one out.

That error message is a developer error somewhere in the code used to load packages. It indicates that some R code is relying on S3 dispatching but got a type of data with no registered method.

You're saying that you downgraded from R 3.5.x to R 3.4.x? Why did you have to do that? My best guess right now is that something was left behind on your system and that R or cmake thinks something is cached that actually needs to be recompiled.

R 3.5 was a significant departure from 3.4 (https://cran.r-project.org/doc/manuals/r-devel/NEWS.html) so it's possible for a package that worked on 3.5 to not be installable on 3.4.

The R side of our CI needs some work, so I cannot say with certainty what versions of R we support. I'll try to reproduce your environment and see if I can get the same error!

While I try to do that, could you manually remove /home/xxxx/R/x86_64-pc-linux-gnu-library/3.4/lightgbm and try re-installing?

One other thing...is there still a /home/xxxx/R/x86_64-pc-linux-gnu-library/3.5 left behind? When I've used RStudio Server with a shared file system in the past, sometimes I've needed to remove other R/ directories left behind when changing versions.

[StrikerRUS]

ping @franciszmy

[StrikerRUS]

@franciszmy Have you managed to try @jameslamb's advices about remaining folders?

[Laurae2]

@jameslamb @franciszmy Just had the same issue last week when switching to R 3.6 (except it's from R 3.5.3) on another package. RStudio Server is not fun to use when switching R versions.

In that case, it was better to nuke (delete) the hidden .rstudio folder to fully reset RStudio Server. Note that doing it will delete also all customizations done in RStudio Server (which have to be re-done manually).

You can find it in your home directory: ls ./.rstudio from your home directory.

[jameslamb]

😬 I feel that we have a set of strange R 3.6.0 issues coming our way 😬

@franciszmy could you try mine and @Laurae2 's suggestions and let us know if the issue gets resolved?

[StrikerRUS]

Closing due to inactivity.