scDblFinder and xgboost
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Entering edit mode
Bogdan ▴ 640
@bogdan-2367
Last seen 5 weeks ago
Palo Alto, CA, USA

Hi everyone,

I am encountering the error below related to xgboost when I am installing

make: *** [amalgamation/xgboost-all0.o] Error 1
ERROR: compilation failed for package ‘xgboost’
* removing ‘/home/btanasa/R-4.1.2/R-4.1.2/library/xgboost’
ERROR: dependency ‘xgboost’ is not available for package ‘scDblFinder’
* removing ‘/home/btanasa/R-4.1.2/R-4.1.2/library/scDblFinder

When I do install.packages("xgboost"), I am getting the error below. Any suggestions please ?

amalgamation/../src/tree/updater_histmaker.cc:221:6:   required from here
amalgamation/../src/tree/updater_histmaker.cc:218:9: error: cannot call member function ‘void xgboost::tree::HistMaker::EnumerateSplit(const xgboost::tree::HistMaker::HistUnit&, const xgboost::tree::GradStats&, xgboost::bst_uint, xgboost::tree::SplitEntry*, xgboost::tree::GradStats*) const’ without object
         EnumerateSplit(this->wspace_.hset[0][i + wid * (num_feature + 1)], node_sum, feature_set[i],
         ^~~~~~~~~~~~~~
/home/btanasa/R-4.1.2/R-4.1.2/etc/Makeconf:175: recipe for target 'amalgamation/xgboost-all0.o' failed
make: *** [amalgamation/xgboost-all0.o] Error 1
ERROR: compilation failed for package ‘xgboost’
* removing ‘/home/btanasa/R-4.1.2/R-4.1.2/library/xgboost’

The downloaded source packages are in
        ‘/tmp/RtmpPrLWTj/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("xgboost") :
  installation of package ‘xgboost’ had non-zero exit status


> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS:   /home/btanasa/R-4.1.2/R-4.1.2/lib/libRblas.so
LAPACK: /home/btanasa/R-4.1.2/R-4.1.2/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] 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
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.17 compiler_4.1.2      tools_4.1.2
[4] tcltk_4.1.2
scDblFinder xgboost • 125 views
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Entering edit mode

Hi,

there was a similar issue in the xgboost github

Could it be that your compiler is not sufficiently up-to-date to compile the latest xgboost version? (maybe check your GCC version)

plger

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