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June 23, 2018 01:56
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SafetyError: The package for r-base located at /home/ucsd-train25/anaconda2/pkgs/r-base-3.4.1-1 | |
appears to be corrupted. The path 'lib/R/doc/html/packages.html' | |
has a sha256 mismatch. | |
reported sha256: 7d66db1bf6965741f31d52ee0085f61fac29983b5ba6d5372785531af39c0299 | |
actual sha256: 627828310cd1356817837e6c3197b8bd6d854ee437587c85247bac62c51a6a65 | |
ClobberError: The package 'defaults::libgcc-7.2.0-h69d50b8_2' cannot be installed due to a | |
path collision for 'lib/libgfortran.so.3'. | |
This path already exists in the target prefix, and it won't be removed by | |
an uninstall action in this transaction. The path appears to be coming from | |
the package 'defaults::gcc-4.8.5-7', which is already installed in the prefix. | |
ClobberError: The package 'defaults::libgcc-7.2.0-h69d50b8_2' cannot be installed due to a | |
path collision for 'lib/libgfortran.so.3.0.0'. | |
This path already exists in the target prefix, and it won't be removed by | |
an uninstall action in this transaction. The path appears to be coming from | |
the package 'defaults::gcc-4.8.5-7', which is already installed in the prefix. | |
done | |
Executing transaction: | dbus post-link :: /etc/machine-id not found .. | |
dbus post-link :: .. using /proc/sys/kernel/random/boot_id | |
done |
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** R
** data
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
trying URL 'http://cran.stat.ucla.edu/src/contrib/tsne_0.1-3.tar.gz'
Content type 'application/x-tar' length 4553 bytes
==================================================
downloaded 4553 bytes
Installing tsne
'/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/bin/R' --no-site-file
--no-environ --no-save --no-restore --quiet CMD INSTALL
'/tmp/Rtmp8pnXB5/devtools3f583478425b/tsne'
--library='/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library'
--install-tests
** package 'tsne' successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
trying URL 'http://cran.stat.ucla.edu/src/contrib/VGAM_1.0-5.tar.gz'
Content type 'application/x-tar' length 2552397 bytes (2.4 MB)
==================================================
downloaded 2.4 MB
Installing VGAM
'/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/bin/R' --no-site-file
--no-environ --no-save --no-restore --quiet CMD INSTALL
'/tmp/Rtmp8pnXB5/devtools3f5828d476cd/VGAM'
--library='/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library'
--install-tests
installing source package 'VGAM' ...
** package 'VGAM' successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c VGAM_init.c -o VGAM_init.o
gcc -std=gnu99 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c caqo3.c -o caqo3.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c cqof.f -o cqof.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c ei.f -o ei.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c fgam.f -o fgam.o
gcc -std=gnu99 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c gautr.c -o gautr.o
gcc -std=gnu99 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c lerchphi.c -o lerchphi.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c lms.f -o lms.o
gcc -std=gnu99 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c muxr3.c -o muxr3.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c rgam.f -o rgam.o
gcc -std=gnu99 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c rgam3.c -o rgam3.o
gcc -std=gnu99 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c specfun3.c -o specfun3.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c tyeepolygamma.f -o tyeepolygamma.o
gcc -std=gnu99 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c tyeepolygamma3.c -o tyeepolygamma3.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c vcall2.f -o vcall2.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c vdigami.f -o vdigami.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c veigen.f -o veigen.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c vgam.f -o vgam.o
gcc -std=gnu99 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c vgam3.c -o vgam3.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c vlinpack1.f -o vlinpack1.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c vlinpack2.f -o vlinpack2.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c vlinpack3.f -o vlinpack3.o
gfortran -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -c vmux.f -o vmux.o
gcc -std=gnu99 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c vmux3.c -o vmux3.o
gcc -std=gnu99 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c zeta3.c -o zeta3.o
gcc -std=gnu99 -shared -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/lib -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -lgfortran -o VGAM.so VGAM_init.o caqo3.o cqof.o ei.o fgam.o gautr.o lerchphi.o lms.o muxr3.o rgam.o rgam3.o specfun3.o tyeepolygamma.o tyeepolygamma3.o vcall2.o vdigami.o veigen.o vgam.o vgam3.o vlinpack1.o vlinpack2.o vlinpack3.o vmux.o vmux3.o zeta3.o -lgfortran -lm -lquadmath -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/lib -lR
installing to /home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library/VGAM/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Creating a new generic function for 'Rank' in package 'VGAM'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
DONE (VGAM)
'/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/bin/R' --no-site-file
--no-environ --no-save --no-restore --quiet CMD INSTALL
'/tmp/Rtmp8pnXB5/devtools3f58635c0e37/Seurat'
--library='/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library'
--install-tests
installing source package 'Seurat' ...
** package 'Seurat' successfully unpacked and MD5 sums checked
** libs
g++ -std=gnu++11 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I"/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library/Rcpp/include" -I"/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library/RcppEigen/include" -I"/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library/RcppProgress/include" -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -I../inst/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I"/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library/Rcpp/include" -I"/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library/RcppEigen/include" -I"/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library/RcppProgress/include" -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -I../inst/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c data_manipulation.cpp -o data_manipulation.o
g++ -std=gnu++11 -I/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/include -DNDEBUG -I"/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library/Rcpp/include" -I"/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library/RcppEigen/include" -I"/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library/RcppProgress/include" -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -I../inst/include -fpic -I/home/ucsd-train25/anaconda2/envs/R-Seurat/include -c snn.cpp -o snn.o
g++ -std=gnu++11 -shared -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/lib -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib -lgfortran -o Seurat.so RcppExports.o data_manipulation.o snn.o -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/lib -lRlapack -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/lib -lR
installing to /home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library/Seurat/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
DONE (Seurat)
** package 'pbdZMQ' successfully unpacked and MD5 sums checked
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.25... no
****************** Results of pbdZMQ package configure *****************
configure: creating ./config.status
config.status: creating src/Makevars
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/build_zmq
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/build_zmq
config.status: creating R/zzz.r
** libs
( sh ./chmod_zmq.inc; cd zmqsrc; sh ../build_zmq )
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '508656' is supported by ustar format... yes
checking whether GID '8075' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in
/tmp/Rtmp6H8uQL/R.INSTALL6588618acef0/pbdZMQ/src/zmqsrc': configure: error: C compiler cannot create executables See
config.log' for more detailsmake[1]: Entering directory
/tmp/Rtmp6H8uQL/R.INSTALL6588618acef0/pbdZMQ/src/zmqsrc' make[1]: *** No targets specified and no makefile found. Stop. make[1]: Leaving directory
/tmp/Rtmp6H8uQL/R.INSTALL6588618acef0/pbdZMQ/src/zmqsrc'make[1]: Entering directory
/tmp/Rtmp6H8uQL/R.INSTALL6588618acef0/pbdZMQ/src/zmqsrc' make[1]: *** No rule to make target
install'. Stop.make[1]: Leaving directory `/tmp/Rtmp6H8uQL/R.INSTALL6588618acef0/pbdZMQ/src/zmqsrc'
make: *** [libzmq] Error 2
ERROR: compilation failed for package 'pbdZMQ'
The downloaded source packages are in
'/tmp/Rtmp8pnXB5/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(package, repos = repos, contriburl = contriburl, :
installation of package 'pbdZMQ' had non-zero exit status