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| RE: Unable to install Matrix on R 3.1.2 (RedHat) --- only inside 'screen' [ Reply ] By: Martin Maechler on 2015-02-16 08:27 | [forum:41906] |
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Thank you, Scott. I think the issue can be considered "closed" - even though we remain puzzled why this did behave differently in 'screen'. -- it is still good to keep "the solution" here in public. Martin |
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| RE: Unable to install Matrix on R 3.1.2 (RedHat) [ Reply ] By: Scott Norton on 2015-02-10 19:06 | [forum:41905] |
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The CHOLMOD directory is present in the Matrix/src directory, and the size represented in the traceback agrees with the size of the tarball on CRAN. The issue occurs when Matrix 1.1.5 is downloaded from four separate mirrors. "cd" was not redefined in the "PATH", as evidenced by the successful installation of several other R packages. The problem was that I was in a "SCREEN" environment. I installed the package outside of "SCREEN" successfully. |
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| RE: Unable to install Matrix on R 3.1.2 (RedHat) [ Reply ] By: Martin Maechler on 2015-02-10 17:45 | [forum:41888] |
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Pretty strange,... CHOLMOD is a subdirectory of Matrix/src/ and the compilations before that *do* happen in directory Matrix/src .. so how could 'cd CHOLMOD' not work? Have you redefined 'cd' in your PATH by a super-duper smart version that does not work here, or was there a download problem with the Matrix "tar ball" (the file Matrix_1.1.5.tar.gz). Some CRAN mirrors are said to not always be reliable... Did you try more than once? Try to download the Matrix tar ball yourself, look at it -- first its size -- and see if it has the same size as on CRAN... |
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| Unable to install Matrix on R 3.1.2 (RedHat) [ Reply ] By: Scott Norton on 2015-02-09 06:19 | [forum:41884] |
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I attempted to update my locally-installed version of Matrix. The traceback is below. > install.packages('Matrix') Installing package into ‘/home/scnorton/R/x86_64-redhat-linux-gnu-library/3.1’ (as ‘lib’ is unspecified) trying URL 'http://cran.mirrors.hoobly.com/src/contrib/Matrix_1.1-5.tar.gz' Content type 'application/x-gzip' length 1718840 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb * installing *source* package ‘Matrix’ ... ** package ‘Matrix’ successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c CHMfactor.c -o CHMfactor.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c Csparse.c -o Csparse.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c TMatrix_as.c -o TMatrix_as.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c Tsparse.c -o Tsparse.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c init.c -o init.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c Mutils.c -o Mutils.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c chm_common.c -o chm_common.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c cs.c -o cs.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c cs_utils.c -o cs_utils.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c dense.c -o dense.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c dgCMatrix.c -o dgCMatrix.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c dgTMatrix.c -o dgTMatrix.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c dgeMatrix.c -o dgeMatrix.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c dpoMatrix.c -o dpoMatrix.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c dppMatrix.c -o dppMatrix.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c dsCMatrix.c -o dsCMatrix.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c dsyMatrix.c -o dsyMatrix.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c dspMatrix.c -o dspMatrix.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c dtCMatrix.c -o dtCMatrix.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c dtTMatrix.c -o dtTMatrix.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c dtrMatrix.c -o dtrMatrix.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c dtpMatrix.c -o dtpMatrix.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c factorizations.c -o factorizations.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c ldense.c -o ldense.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c lgCMatrix.c -o lgCMatrix.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c sparseQR.c -o sparseQR.o gcc -std=gnu99 -I/opt/software/R/3.1.2/lib64/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -c abIndex.c -o abIndex.o /bin/sh: line 1: cd: CHOLMOD: No such file or directory make: *** [subclean] Error 1 ERROR: compilation failed for package ‘Matrix’ * removing ‘/home/scnorton/R/x86_64-redhat-linux-gnu-library/3.1/Matrix’ Warning message: In install.packages("Matrix_1.1-5.tar.gz", repos = NULL) : installation of package ‘Matrix_1.1-5.tar.gz’ had non-zero exit status |
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