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envmetagen / metabinkit

Set of programs to perform taxonomic binning.
GNU General Public License v3.0
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new error #5

Closed bastianegeter closed 4 years ago

bastianegeter commented 4 years ago

Hi installed ok now, but got this:

tutorial@tutorial-VirtualBox:~$ metabin -h
metabinkit v0.0.1
Error in library(optparse) : there is no package called ‘optparse’
Execution halted
nunofonseca commented 4 years ago

:) It seems that you did not finish the installation[1]:

source $HOME/metabinkit_env.sh

or add the above line to the $HOME/.bash_profile file.

[1] https://github.com/envmetagen/metabinkit#installing-metabinkit-and-some-dependencies :-)

bastianegeter commented 4 years ago

here is the full output from three commands (install, source, metabin -h)

tutorial@tutorial-VirtualBox:~/TOOLS/metabinkit$ sudo ./install.sh $HOME
[sudo] password for tutorial: 
[INFO] Checking dependencies...
[INFO] Checking dependencies...done.
[INFO] Installing taxonkit..
--2020-05-25 08:45:39--  https://github.com/shenwei356/taxonkit/releases/download/v0.6.0/taxonkit_linux_amd64.tar.gz
Resolving github.com (github.com)... 140.82.112.4
Connecting to github.com (github.com)|140.82.112.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/72552525/e55cc100-8a1c-11ea-94aa-32079f116820?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20200525%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20200525T074541Z&X-Amz-Expires=300&X-Amz-Signature=6e8e6abdff1ff089c9b0abfdca618f3404f6f07e5eae64193dc8b92664afb1a2&X-Amz-SignedHeaders=host&actor_id=0&repo_id=72552525&response-content-disposition=attachment%3B%20filename%3Dtaxonkit_linux_amd64.tar.gz&response-content-type=application%2Foctet-stream [following]
--2020-05-25 08:45:40--  https://github-production-release-asset-2e65be.s3.amazonaws.com/72552525/e55cc100-8a1c-11ea-94aa-32079f116820?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20200525%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20200525T074541Z&X-Amz-Expires=300&X-Amz-Signature=6e8e6abdff1ff089c9b0abfdca618f3404f6f07e5eae64193dc8b92664afb1a2&X-Amz-SignedHeaders=host&actor_id=0&repo_id=72552525&response-content-disposition=attachment%3B%20filename%3Dtaxonkit_linux_amd64.tar.gz&response-content-type=application%2Foctet-stream
Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 52.216.145.235
Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|52.216.145.235|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3239347 (3,1M) [application/octet-stream]
Saving to: ‘tmp.tar.gz’

tmp.tar.gz          100%[===================>]   3,09M  2,65MB/s    in 1,2s    

2020-05-25 08:45:42 (2,65 MB/s) - ‘tmp.tar.gz’ saved [3239347/3239347]

taxonkit
[INFO] Installing taxonkit..done.
[INFO] Installing blast to /opt/blast/2.10.0...
/tmp/tmp.YZkb6hz3gs ~/TOOLS/metabinkit
--2020-05-25 08:45:42--  ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.10.0+-x64-linux.tar.gz
           => ‘tmp.tar.gz’
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.7, 2607:f220:41e:250::11
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.7|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /blast/executables/blast+/LATEST ... done.
==> SIZE ncbi-blast-2.10.0+-x64-linux.tar.gz ... 233258021
==> PASV ... done.    ==> RETR ncbi-blast-2.10.0+-x64-linux.tar.gz ... done.
Length: 233258021 (222M) (unauthoritative)

ncbi-blast-2.10.0+- 100%[===================>] 222,45M  4,55MB/s    in 1m 40s  

2020-05-25 08:47:24 (2,24 MB/s) - ‘tmp.tar.gz’ saved [233258021]

ncbi-blast-2.10.0+/
ncbi-blast-2.10.0+/ChangeLog
ncbi-blast-2.10.0+/LICENSE
ncbi-blast-2.10.0+/README
ncbi-blast-2.10.0+/bin/
ncbi-blast-2.10.0+/bin/blast_formatter
ncbi-blast-2.10.0+/bin/blastdb_aliastool
ncbi-blast-2.10.0+/bin/blastdbcheck
ncbi-blast-2.10.0+/bin/blastdbcmd
ncbi-blast-2.10.0+/bin/blastn
ncbi-blast-2.10.0+/bin/blastp
ncbi-blast-2.10.0+/bin/blastx
ncbi-blast-2.10.0+/bin/cleanup-blastdb-volumes.py
ncbi-blast-2.10.0+/bin/convert2blastmask
ncbi-blast-2.10.0+/bin/deltablast
ncbi-blast-2.10.0+/bin/dustmasker
ncbi-blast-2.10.0+/bin/get_species_taxids.sh
ncbi-blast-2.10.0+/bin/legacy_blast.pl
ncbi-blast-2.10.0+/bin/makeblastdb
ncbi-blast-2.10.0+/bin/makembindex
ncbi-blast-2.10.0+/bin/makeprofiledb
ncbi-blast-2.10.0+/bin/psiblast
ncbi-blast-2.10.0+/bin/rpsblast
ncbi-blast-2.10.0+/bin/rpstblastn
ncbi-blast-2.10.0+/bin/segmasker
ncbi-blast-2.10.0+/bin/tblastn
ncbi-blast-2.10.0+/bin/tblastx
ncbi-blast-2.10.0+/bin/update_blastdb.pl
ncbi-blast-2.10.0+/bin/windowmasker
ncbi-blast-2.10.0+/doc/
ncbi-blast-2.10.0+/doc/README.txt
ncbi-blast-2.10.0+/ncbi_package_info
--2020-05-25 08:47:36--  ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
           => ‘taxdb.tar.gz’
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.13, 2607:f220:41e:250::12
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.13|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /blast/db ... done.
==> SIZE taxdb.tar.gz ... 30602006
==> PASV ... done.    ==> RETR taxdb.tar.gz ... done.
Length: 30602006 (29M) (unauthoritative)

taxdb.tar.gz        100%[===================>]  29,18M  4,51MB/s    in 6,9s    

2020-05-25 08:47:44 (4,21 MB/s) - ‘taxdb.tar.gz’ saved [30602006]

/opt/blast/2.10.0/db /tmp/tmp.YZkb6hz3gs ~/TOOLS/metabinkit
taxdb.btd
taxdb.bti
/tmp/tmp.YZkb6hz3gs ~/TOOLS/metabinkit
~/TOOLS/metabinkit
READ: To enable blast version 2.10.0 run in the terminal or add the following line to the end of your .bashrc file
PATH=/opt/blast/2.10.0/bin:$PATH
[INFO] Installing blast...done.
[INFO] Installing metabinkit...
[INFO] Creating /opt/metabinkit_env.sh...
You may want to consider adding the following line to your .bash_profile file.

source /opt/metabinkit_env.sh
[INFO] Creating /opt/metabinkit_env.sh...done.
[INFO] Installing metabinkit...done.
[INFO] Installing R packages to /opt/Rlibs ...

R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> repo<-"http://www.stats.bris.ac.uk/R/"
> 
> ########################
> # Check if version is ok
> version <- getRversion()
> currentVersion <- sprintf("%d.%d", version$major, version$minor)
> message("R version:",version)
R version:3.6.0
> usebiocmanager<-TRUE
> if ( version$major < 3 || (version$major>=3 && version$minor<5) ) {
+   cat("ERROR: R version should be 3.5 or above\n")
+   q(status=1)
+ }
> 
> ########################
> # Where to install the packages
> assign(".lib.loc",.libPaths()[1],envir=environment(.libPaths))
> 
> message("Using library: ", .libPaths()[1])
Using library: /opt/Rlibs
> ##print(.libPaths())
> 
> message("_____________________________________________________")
_____________________________________________________
> 
> if (version$major > 3 || (version$major == 3 && version$minor>5)) {
+    if (!requireNamespace("BiocManager", quietly = TRUE))
+        install.packages("BiocManager",repo=repo)
+    BiocManager::install()
+ } else {
+    usebiocmanager<-FALSE
+    source("http://bioconductor.org/biocLite.R")
+ } 
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.0 (2019-04-26)
> 
> message("_____________________________________________________")
_____________________________________________________
> 
> message("Installing packages")
Installing packages
> packages2install<-c("Matrix","data.table","optparse")
> 
> for (p in packages2install ) {
+   message("PACKAGE:",p,"\n")
+   if ( usebiocmanager ) BiocManager::install(p,ask=FALSE)
+   else  biocLite(p,ask=FALSE)
+ }
PACKAGE:Matrix

Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.0 (2019-04-26)
Installing package(s) 'Matrix'
Warning: dependencies ‘methods’, ‘graphics’, ‘grid’, ‘stats’, ‘utils’ are not available
trying URL 'https://cran.rstudio.com/src/contrib/Matrix_1.2-18.tar.gz'
Content type 'application/x-gzip' length 1871705 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

* installing *source* package ‘Matrix’ ...
** package ‘Matrix’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c CHMfactor.c -o CHMfactor.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Csparse.c -o Csparse.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c TMatrix_as.c -o TMatrix_as.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Tsparse.c -o Tsparse.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Mutils.c -o Mutils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c chm_common.c -o chm_common.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cs.c -o cs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cs_utils.c -o cs_utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dense.c -o dense.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dgCMatrix.c -o dgCMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dgTMatrix.c -o dgTMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dgeMatrix.c -o dgeMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dpoMatrix.c -o dpoMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dppMatrix.c -o dppMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dsCMatrix.c -o dsCMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dsyMatrix.c -o dsyMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dspMatrix.c -o dspMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dtCMatrix.c -o dtCMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dtTMatrix.c -o dtTMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dtrMatrix.c -o dtrMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dtpMatrix.c -o dtpMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c factorizations.c -o factorizations.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ldense.c -o ldense.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lgCMatrix.c -o lgCMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sparseQR.c -o sparseQR.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c abIndex.c -o abIndex.o
make[1]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/CHOLMOD'
( cd Lib ; make clean )
make[2]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/CHOLMOD/Lib'
make[2]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/CHOLMOD/Lib'
make[1]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/CHOLMOD'
make[1]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/COLAMD'
( cd Source ; make clean )
make[2]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/COLAMD/Source'
make[2]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/COLAMD/Source'
make[1]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/COLAMD'
make[1]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/AMD'
( cd Source ; make clean )
make[2]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/AMD/Source'
make[2]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/AMD/Source'
make[1]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/AMD'
make[1]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/SuiteSparse_config'
make[1]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/SuiteSparse_config'
make[1]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/CHOLMOD'
( cd Lib ; make -f "/usr/lib/R/etc/Makeconf" -f Makefile )
make[2]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/CHOLMOD/Lib'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_aat.c -o cholmod_aat.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_add.c -o cholmod_add.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_band.c -o cholmod_band.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_common.c -o cholmod_common.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_complex.c -o cholmod_complex.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_copy.c -o cholmod_copy.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_dense.c -o cholmod_dense.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_error.c -o cholmod_error.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_factor.c -o cholmod_factor.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_memory.c -o cholmod_memory.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_sparse.c -o cholmod_sparse.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Core/cholmod_version.c -o cholmod_version.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Check/cholmod_check.c -o cholmod_check.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Check/cholmod_read.c -o cholmod_read.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Check/cholmod_write.c -o cholmod_write.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Modify/cholmod_updown.c -o cholmod_updown.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_aat.c -o cholmod_l_aat.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_add.c -o cholmod_l_add.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_band.c -o cholmod_l_band.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_common.c -o cholmod_l_common.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_complex.c -o cholmod_l_complex.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_copy.c -o cholmod_l_copy.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_dense.c -o cholmod_l_dense.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_error.c -o cholmod_l_error.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_factor.c -o cholmod_l_factor.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_memory.c -o cholmod_l_memory.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_sparse.c -o cholmod_l_sparse.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Core/cholmod_version.c -o cholmod_l_version.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Check/cholmod_check.c -o cholmod_l_check.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Check/cholmod_read.c -o cholmod_l_read.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Check/cholmod_write.c -o cholmod_l_write.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Modify/cholmod_updown.c -o cholmod_l_updown.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DDLONG -c  ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o
ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o  cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o 
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/CHOLMOD/Lib'
make[1]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/CHOLMOD'
make[1]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/COLAMD'
( cd Source ; make -f "/usr/lib/R/etc/Makeconf" -f Makefile lib )
make[2]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/COLAMD/Source'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c colamd_global.c -o colamd_global.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c colamd.c -o colamd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c colamd.c -o colamd_l.o
ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/COLAMD/Source'
make[1]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/COLAMD'
make[1]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/AMD'
( cd Source ; make -f "/usr/lib/R/etc/Makeconf" -f Makefile lib )
make[2]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/AMD/Source'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_1.c -o amd_i_1.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_2.c -o amd_i_2.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_order.c -o amd_i_order.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_control.c -o amd_i_control.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_info.c -o amd_i_info.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDINT -c amd_global.c -o amd_i_global.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I../Include -DDLONG -c amd_global.c -o amd_l_global.o
ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o 
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/AMD/Source'
make[1]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/AMD'
make[1]: Entering directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[1]: Leaving directory '/tmp/RtmpIwyY2U/R.INSTALLb9f493e4203/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /opt/Rlibs/00LOCK-Matrix/00new/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘chol2inv’ from ‘base’ in package ‘Matrix’
    (from the saved implicit definition)
Creating a generic function for ‘chol2inv’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘diag’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘drop’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘cov2cor’ from package ‘stats’ in package ‘Matrix’
Creating a generic function for ‘unname’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘norm’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘rcond’ from ‘base’ in package ‘Matrix’
    (from the saved implicit definition)
Creating a generic function for ‘rcond’ from package ‘base’ in package ‘Matrix’
in method for ‘coerce’ with signature ‘"matrix.csr","dgRMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"dgRMatrix","matrix.csr"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.csc","dgCMatrix"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"dgCMatrix","matrix.csc"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.coo","dgTMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"dgTMatrix","matrix.coo"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"dsparseMatrix","matrix.csr"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.csr","dgCMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.coo","dgCMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.csr","RsparseMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.csc","CsparseMatrix"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.coo","TsparseMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.csr","CsparseMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.coo","CsparseMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.csc","TsparseMatrix"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.csr","TsparseMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"CsparseMatrix","matrix.csr"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"CsparseMatrix","matrix.coo"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"CsparseMatrix","matrix.csc"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.csr","Matrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.coo","Matrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.csc","Matrix"’: no definition for class “matrix.csc”
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘colMeans’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘rowMeans’ from package ‘base’ in package ‘Matrix’
in method for ‘colSums’ with signature ‘x="igCMatrix"’: no definition for class “igCMatrix”
in method for ‘rowSums’ with signature ‘x="igCMatrix"’: no definition for class “igCMatrix”
in method for ‘colMeans’ with signature ‘x="igCMatrix"’: no definition for class “igCMatrix”
in method for ‘rowMeans’ with signature ‘x="igCMatrix"’: no definition for class “igCMatrix”
Creating a generic function for ‘zapsmall’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘diag<-’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘crossprod’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘tcrossprod’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘which’ from package ‘base’ in package ‘Matrix’
in method for ‘coerce’ with signature ‘"graphAM","sparseMatrix"’: no definition for class “graphAM”
in method for ‘coerce’ with signature ‘"graph","CsparseMatrix"’: no definition for class “graph”
in method for ‘coerce’ with signature ‘"graph","Matrix"’: no definition for class “graph”
in method for ‘coerce’ with signature ‘"graphNEL","CsparseMatrix"’: no definition for class “graphNEL”
in method for ‘coerce’ with signature ‘"graphNEL","TsparseMatrix"’: no definition for class “graphNEL”
in method for ‘coerce’ with signature ‘"sparseMatrix","graph"’: no definition for class “graph”
in method for ‘coerce’ with signature ‘"sparseMatrix","graphNEL"’: no definition for class “graphNEL”
in method for ‘coerce’ with signature ‘"TsparseMatrix","graphNEL"’: no definition for class “graphNEL”
Creating a generic function for ‘qr.R’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.Q’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.qy’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.qty’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.coef’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.resid’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.fitted’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘toeplitz’ from package ‘stats’ in package ‘Matrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Matrix)

The downloaded source packages are in
    ‘/tmp/RtmpdqbxRO/downloaded_packages’
PACKAGE:data.table

Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.0 (2019-04-26)
Installing package(s) 'data.table'
Warning: dependency ‘methods’ is not available
trying URL 'https://cran.rstudio.com/src/contrib/data.table_1.12.8.tar.gz'
Content type 'application/x-gzip' length 4948391 bytes (4.7 MB)
==================================================
downloaded 4.7 MB

* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
zlib 1.2.11 is available ok
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c assign.c -o assign.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c between.c -o between.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bmerge.c -o bmerge.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c chmatch.c -o chmatch.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cj.c -o cj.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c coalesce.c -o coalesce.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dogroups.c -o dogroups.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastmean.c -o fastmean.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fcast.c -o fcast.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fifelse.c -o fifelse.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fmelt.c -o fmelt.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c forder.c -o forder.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c frank.c -o frank.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fread.c -o fread.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c freadR.c -o freadR.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c froll.c -o froll.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c frollR.c -o frollR.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c frolladaptive.c -o frolladaptive.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fsort.c -o fsort.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fwrite.c -o fwrite.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fwriteR.c -o fwriteR.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gsumm.c -o gsumm.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ijoin.c -o ijoin.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c inrange.c -o inrange.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nafill.c -o nafill.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nqrecreateindices.c -o nqrecreateindices.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c openmp-utils.c -o openmp-utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c quickselect.c -o quickselect.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rbindlist.c -o rbindlist.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c reorder.c -o reorder.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c shift.c -o shift.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c subset.c -o subset.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c transpose.c -o transpose.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c types.c -o types.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c uniqlist.c -o uniqlist.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vecseq.c -o vecseq.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c wrappers.c -o wrappers.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nafill.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -lz -L/usr/lib/R/lib -lR
mv data.table.so datatable.so
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id datatable.so datatable.so; fi
installing to /opt/Rlibs/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)

The downloaded source packages are in
    ‘/tmp/RtmpdqbxRO/downloaded_packages’
PACKAGE:optparse

Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.0 (2019-04-26)
Installing package(s) 'optparse'
Warning: dependency ‘methods’ is not available
trying URL 'https://cran.rstudio.com/src/contrib/optparse_1.6.6.tar.gz'
Content type 'application/x-gzip' length 37896 bytes (37 KB)
==================================================
downloaded 37 KB

* installing *source* package ‘optparse’ ...
** package ‘optparse’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (optparse)

The downloaded source packages are in
    ‘/tmp/RtmpdqbxRO/downloaded_packages’
> 
> 
> 
[INFO] Installing R packages to /opt/Rlibs ...done.
[INFO] Installing taxonomy database...
--2020-05-25 08:50:50--  ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
           => ‘taxdump.tar.gz’
Resolving ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)... 130.14.250.10, 2607:f220:41e:250::10
Connecting to ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)|130.14.250.10|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/taxonomy ... done.
==> SIZE taxdump.tar.gz ... 52140949
==> PASV ... done.    ==> RETR taxdump.tar.gz ... done.
Length: 52140949 (50M) (unauthoritative)

taxdump.tar.gz      100%[===================>]  49,72M  4,73MB/s    in 14s     

2020-05-25 08:51:06 (3,60 MB/s) - ‘taxdump.tar.gz’ saved [52140949]

citations.dmp
delnodes.dmp
division.dmp
gencode.dmp
merged.dmp
names.dmp
nodes.dmp
gc.prt
readme.txt
[INFO] Installing taxonomy database...done
---------------------------------------------------
All done.
tutorial@tutorial-VirtualBox:~/TOOLS/metabinkit$ source $HOME/metabinkit_env.sh
tutorial@tutorial-VirtualBox:~/TOOLS/metabinkit$ metabin -h
metabinkit v0.0.1
Error in library(optparse) : there is no package called ‘optparse’
Execution halted
tutorial@tutorial-VirtualBox:~/TOOLS/metabinkit$
nunofonseca commented 4 years ago

Did you manage to install it...and run it?

bastianegeter commented 4 years ago

installed and tested briefly.