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ecwheele/R-seurat env output

Created June 23, 2018 01:56
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R-seurat env output
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

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

  • installing source package 'tsne' ...
    ** 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
  • DONE (tsne)
    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)

devtools::install_version("pbdZMQ","0.3-3")
trying URL 'http://cran.stat.ucla.edu/src/contrib/pbdZMQ_0.3-3.tar.gz'
Content type 'application/x-tar' length 1052217 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

  • installing source package 'pbdZMQ' ...
    ** 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 *****************

GET_PKG_CONFIG = no
GET_SYSTEM_ZMQ = no
PKG_CONFIG =
SYSTEM_ZMQ_INCLUDEDIR =
SYSTEM_ZMQ_LIBDIR =
ENABLE_INTERNAL_ZMQ = no
INTERNAL_ZMQ_INCLUDEDIR = ./zmqsrc/include
INTERNAL_ZMQ_LIBDIR = ./
EXTERNAL_ZMQ_INCLUDE =
EXTERNAL_ZMQ_LDFLAGS =
ZMQ_INCLUDE = -I./zmqsrc/include
ZMQ_LDFLAGS = -L./ -lzmq
EXT_LIBS = $(R_ZMQ)
ZMQ_POLLER = select

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 details
make[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'

  • removing '/home/ucsd-train25/anaconda2/envs/R-Seurat/lib/R/library/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

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