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Installing DropletUtils in Docker
Raw
DropletUtils_install.log
> install("DropletUtils")
Bioconductor version 3.10 (BiocManager 1.30.7), R 3.6.1 (2019-07-05)
Installing package(s) 'DropletUtils'
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DropletUtils_1.5.10.tar.gz'
Content type 'application/x-gzip' length 446056 bytes (435 KB)
==================================================
downloaded 435 KB
* installing *source* package ‘DropletUtils’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/beachmat/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/dqrng/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c compute_multinom.cpp -o compute_multinom.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/beachmat/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/dqrng/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c downsample_counts.cpp -o downsample_counts.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/beachmat/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/dqrng/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c encode_sequences.cpp -o encode_sequences.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/beachmat/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/dqrng/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c find_swapped.cpp -o find_swapped.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/beachmat/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/dqrng/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c get_cell_barcodes.cpp -o get_cell_barcodes.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/beachmat/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/dqrng/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c group_cells.cpp -o group_cells.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/beachmat/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/dqrng/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.cpp -o init.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/beachmat/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/dqrng/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c montecarlo_pval.cpp -o montecarlo_pval.o
In file included from /usr/local/lib/R/site-library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /usr/local/lib/R/site-library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from /usr/local/lib/R/site-library/BH/include/boost/random/detail/const_mod.hpp:23,
from /usr/local/lib/R/site-library/BH/include/boost/random/linear_congruential.hpp:30,
from /usr/local/lib/R/site-library/BH/include/boost/random/additive_combine.hpp:27,
from /usr/local/lib/R/site-library/BH/include/boost/random.hpp:36,
from montecarlo_pval.cpp:3:
/usr/local/lib/R/site-library/BH/include/boost/pending/integer_log2.hpp:7:59: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/beachmat/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/dqrng/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rand_custom.cpp -o rand_custom.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/beachmat/include" -I"/usr/local/lib/R/site-library/Rhdf5lib/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/dqrng/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o DropletUtils.so compute_multinom.o downsample_counts.o encode_sequences.o find_swapped.o get_cell_barcodes.o group_cells.o init.o montecarlo_pval.o rand_custom.o utils.o "/usr/local/lib/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a" "/usr/local/lib/R/site-library/Rhdf5lib/lib/libhdf5.a" "/usr/local/lib/R/site-library/Rhdf5lib/lib/libsz.a" -lz -L/usr/local/lib/R/lib -lR
g++: error: "/usr/local/lib/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a": No such file or directory
g++: error: "/usr/local/lib/R/site-library/Rhdf5lib/lib/libhdf5.a": No such file or directory
g++: error: "/usr/local/lib/R/site-library/Rhdf5lib/lib/libsz.a": No such file or directory
/usr/local/lib/R/share/make/shlib.mk:6: recipe for target 'DropletUtils.so' failed
make: *** [DropletUtils.so] Error 1
ERROR: compilation failed for package ‘DropletUtils’
* removing ‘/usr/local/lib/R/site-library/DropletUtils’
The downloaded source packages are in
‘/tmp/RtmpW7Tbaq/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package ‘DropletUtils’ had non-zero exit status
Raw
sessioninfo
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.7
loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1
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