r package installation error “unknown type name ‘R_CallMethodDef’”

0
votes

I'm trying to install r package "sparsesvd" using install.packages(), but got error during compilation. Any help is highly appreciated!

"unknown type name ‘R_CallMethodDef’"

I also tried conda install -c r r-sparsesvd; but got error.

Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  • r-sparsesvd

Current channels:

I tried

conda skeleton cran --recursive r-sparsesvd conda build r-sparsesvd.

While the 1st step was successful, the build failed.

Execution halted Tests failed for r-sparsesvd-0.1_4-r341h96ca727_0.tar.bz2

Here is the sessionInfo. Due to project reason, I have to use R3.3

R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

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] tools_3.3.2

1
rinstallationpackage
Have you tried the one archived: cran.r-project.org/src/contrib/Archive/sparsesvd – Stéphane Laurent
Thanks for the comment! But how would the archived one be different from the one chosen automatically by install.packages()? – blueskyddd
There is another post related to the error unknown type name ‘R_CallMethodDef But the author did not give details on how to solve the problem. Could anyone help, please? – blueskyddd

1 Answers

0
votes

This (once again) is not a problem with R, CRAN or its packages ...but apparently with Conda. On my system there is strictly no problem with this small package with very few dependencies:

R> install.packages("sparsesvd")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/sparsesvd_0.1-4.tar.gz'
Content type 'application/x-gzip' length 29729 bytes (29 KB)
==================================================
downloaded 29 KB

* installing *source* package ‘sparsesvd’ ...
** package ‘sparsesvd’ successfully unpacked and MD5 sums checked
** libs
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O3 -Wall -pipe   -std=gnu99 -march=native -c las2.c -o las2.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O3 -Wall -pipe   -std=gnu99 -march=native -c main.c -o main.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O3 -Wall -pipe   -std=gnu99 -march=native -c svdlib.c -o svdlib.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O3 -Wall -pipe   -std=gnu99 -march=native -c svdutil.c -o svdutil.o
svdutil.c: In function ‘svd_readBinFloat’:
svdutil.c:265:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     y = *((float *) &x);
     ^
svdutil.c: In function ‘svd_writeBinFloat’:
svdutil.c:290:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   int y = htonl(*((int *) &r));
   ^~~
gcc -Wl,-S -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o sparsesvd.so las2.o main.o svdlib.o svdutil.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/sparsesvd/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (sparsesvd)

The downloaded source packages are in
    ‘/tmp/RtmpI3TPWj/downloaded_packages’
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