https://bioinformaticsonline.com/snippets?offset=250 https://bioinformaticsonline.com/snippets/view/40976/update-conda Mon, 10 Feb 2020 04:06:25 -0600 https://bioinformaticsonline.com/snippets/view/40976/update-conda (my_GATK) [wsu29@bladeamd-2 testGATK]$ conda update -n base -c defaults conda Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/miniconda3 added / updated specs: - conda The following packages will be downloaded: package | build ---------------------------|----------------- asn1crypto-1.3.0 | py37_0 164 KB ca-certificates-2020.1.1 | 0 125 KB certifi-2019.11.28 | py37_0 153 KB cffi-1.13.2 | py37h2e261b9_0 224 KB conda-4.8.2 | py37_0 2.8 MB pip-20.0.2 | py37_1 1.7 MB pycosat-0.6.3 | py37h7b6447c_0 82 KB pyopenssl-19.1.0 | py37_0 87 KB requests-2.22.0 | py37_1 92 KB ruamel_yaml-0.15.87 | py37h7b6447c_0 256 KB setuptools-45.1.0 | py37_0 511 KB six-1.14.0 | py37_0 27 KB sqlite-3.31.1 | h7b6447c_0 1.1 MB tqdm-4.42.0 | py_0 55 KB urllib3-1.25.8 | py37_0 169 KB wheel-0.34.2 | py37_0 51 KB ------------------------------------------------------------ Total: 7.5 MB The following packages will be UPDATED: asn1crypto 1.2.0-py37_0 --> 1.3.0-py37_0 ca-certificates 2019.10.16-0 --> 2020.1.1-0 certifi 2019.9.11-py37_0 --> 2019.11.28-py37_0 cffi 1.13.0-py37h2e261b9_0 --> 1.13.2-py37h2e261b9_0 conda 4.7.12-py37_0 --> 4.8.2-py37_0 pip 19.3.1-py37_0 --> 20.0.2-py37_1 pyopenssl 19.0.0-py37_0 --> 19.1.0-py37_0 requests 2.22.0-py37_0 --> 2.22.0-py37_1 ruamel_yaml 0.15.46-py37h14c3975_0 --> 0.15.87-py37h7b6447c_0 setuptools 41.4.0-py37_0 --> 45.1.0-py37_0 six 1.12.0-py37_0 --> 1.14.0-py37_0 sqlite 3.30.0-h7b6447c_0 --> 3.31.1-h7b6447c_0 tqdm 4.36.1-py_0 --> 4.42.0-py_0 urllib3 1.24.2-py37_0 --> 1.25.8-py37_0 wheel 0.33.6-py37_0 --> 0.34.2-py37_0 The following packages will be DOWNGRADED: pycosat 0.6.3-py37h14c3975_0 --> 0.6.3-py37h7b6447c_0 Proceed ([y]/n)? Y Downloading and Extracting Packages six-1.14.0 | 27 KB | ####################################################################################################### | 100% ruamel_yaml-0.15.87 | 256 KB | ####################################################################################################### | 100% ca-certificates-2020 | 125 KB | ####################################################################################################### | 100% conda-4.8.2 | 2.8 MB | ####################################################################################################### | 100% sqlite-3.31.1 | 1.1 MB | ####################################################################################################### | 100% certifi-2019.11.28 | 153 KB | ####################################################################################################### | 100% urllib3-1.25.8 | 169 KB | ####################################################################################################### | 100% pyopenssl-19.1.0 | 87 KB | ####################################################################################################### | 100% asn1crypto-1.3.0 | 164 KB | ####################################################################################################### | 100% pip-20.0.2 | 1.7 MB | ####################################################################################################### | 100% wheel-0.34.2 | 51 KB | ####################################################################################################### | 100% setuptools-45.1.0 | 511 KB | ####################################################################################################### | 100% tqdm-4.42.0 | 55 KB | ####################################################################################################### | 100% pycosat-0.6.3 | 82 KB | ####################################################################################################### | 100% cffi-1.13.2 | 224 KB | ####################################################################################################### | 100% requests-2.22.0 | 92 KB | ####################################################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40932/installing-ggplot2-and-its-dependencies-on-ubuntu Thu, 06 Feb 2020 09:18:04 -0600 https://bioinformaticsonline.com/snippets/view/40932/installing-ggplot2-and-its-dependencies-on-ubuntu jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter/minidot/bin$ sudo R [sudo] password for jit: R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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. > install.packages("ggplot2") Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) also installing the dependencies ‘ellipsis’, ‘glue’, ‘magrittr’, ‘stringi’, ‘colorspace’, ‘assertthat’, ‘utf8’, ‘vctrs’, ‘plyr’, ‘Rcpp’, ‘stringr’, ‘farver’, ‘labeling’, ‘munsell’, ‘R6’, ‘RColorBrewer’, ‘lifecycle’, ‘cli’, ‘crayon’, ‘fansi’, ‘pillar’, ‘pkgconfig’, ‘digest’, ‘gtable’, ‘lazyeval’, ‘reshape2’, ‘rlang’, ‘scales’, ‘tibble’, ‘viridisLite’, ‘withr’ trying URL 'https://cloud.r-project.org/src/contrib/ellipsis_0.3.0.tar.gz' Content type 'application/x-gzip' length 7371 bytes ================================================== downloaded 7371 bytes trying URL 'https://cloud.r-project.org/src/contrib/glue_1.3.1.tar.gz' Content type 'application/x-gzip' length 122950 bytes (120 KB) ================================================== downloaded 120 KB trying URL 'https://cloud.r-project.org/src/contrib/magrittr_1.5.tar.gz' Content type 'application/x-gzip' length 200504 bytes (195 KB) ================================================== downloaded 195 KB trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.4.5.tar.gz' Content type 'application/x-gzip' length 7284255 bytes (6.9 MB) ================================================== downloaded 6.9 MB trying URL 'https://cloud.r-project.org/src/contrib/colorspace_1.4-1.tar.gz' Content type 'application/x-gzip' length 2152594 bytes (2.1 MB) ================================================== downloaded 2.1 MB trying URL 'https://cloud.r-project.org/src/contrib/assertthat_0.2.1.tar.gz' Content type 'application/x-gzip' length 12742 bytes (12 KB) ================================================== downloaded 12 KB trying URL 'https://cloud.r-project.org/src/contrib/utf8_1.1.4.tar.gz' Content type 'application/x-gzip' length 218882 bytes (213 KB) ================================================== downloaded 213 KB trying URL 'https://cloud.r-project.org/src/contrib/vctrs_0.2.2.tar.gz' Content type 'application/x-gzip' length 721926 bytes (705 KB) ================================================== downloaded 705 KB trying URL 'https://cloud.r-project.org/src/contrib/plyr_1.8.5.tar.gz' Content type 'application/x-gzip' length 394424 bytes (385 KB) ================================================== downloaded 385 KB trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.3.tar.gz' Content type 'application/x-gzip' length 2749025 bytes (2.6 MB) ================================================== downloaded 2.6 MB trying URL 'https://cloud.r-project.org/src/contrib/stringr_1.4.0.tar.gz' Content type 'application/x-gzip' length 135777 bytes (132 KB) ================================================== downloaded 132 KB trying URL 'https://cloud.r-project.org/src/contrib/farver_2.0.3.tar.gz' Content type 'application/x-gzip' length 1279579 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cloud.r-project.org/src/contrib/labeling_0.3.tar.gz' Content type 'application/x-gzip' length 10722 bytes (10 KB) ================================================== downloaded 10 KB trying URL 'https://cloud.r-project.org/src/contrib/munsell_0.5.0.tar.gz' Content type 'application/x-gzip' length 182653 bytes (178 KB) ================================================== downloaded 178 KB trying URL 'https://cloud.r-project.org/src/contrib/R6_2.4.1.tar.gz' Content type 'application/x-gzip' length 35536 bytes (34 KB) ================================================== downloaded 34 KB trying URL 'https://cloud.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz' Content type 'application/x-gzip' length 11532 bytes (11 KB) ================================================== downloaded 11 KB trying URL 'https://cloud.r-project.org/src/contrib/lifecycle_0.1.0.tar.gz' Content type 'application/x-gzip' length 150752 bytes (147 KB) ================================================== downloaded 147 KB trying URL 'https://cloud.r-project.org/src/contrib/cli_2.0.1.tar.gz' Content type 'application/x-gzip' length 111914 bytes (109 KB) ================================================== downloaded 109 KB trying URL 'https://cloud.r-project.org/src/contrib/crayon_1.3.4.tar.gz' Content type 'application/x-gzip' length 658694 bytes (643 KB) ================================================== downloaded 643 KB trying URL 'https://cloud.r-project.org/src/contrib/fansi_0.4.1.tar.gz' Content type 'application/x-gzip' length 270906 bytes (264 KB) ================================================== downloaded 264 KB trying URL 'https://cloud.r-project.org/src/contrib/pillar_1.4.3.tar.gz' Content type 'application/x-gzip' length 230874 bytes (225 KB) ================================================== downloaded 225 KB trying URL 'https://cloud.r-project.org/src/contrib/pkgconfig_2.0.3.tar.gz' Content type 'application/x-gzip' length 6080 bytes ================================================== downloaded 6080 bytes trying URL 'https://cloud.r-project.org/src/contrib/digest_0.6.23.tar.gz' Content type 'application/x-gzip' length 143316 bytes (139 KB) ================================================== downloaded 139 KB trying URL 'https://cloud.r-project.org/src/contrib/gtable_0.3.0.tar.gz' Content type 'application/x-gzip' length 368081 bytes (359 KB) ================================================== downloaded 359 KB trying URL 'https://cloud.r-project.org/src/contrib/lazyeval_0.2.2.tar.gz' Content type 'application/x-gzip' length 83482 bytes (81 KB) ================================================== downloaded 81 KB trying URL 'https://cloud.r-project.org/src/contrib/reshape2_1.4.3.tar.gz' Content type 'application/x-gzip' length 36405 bytes (35 KB) ================================================== downloaded 35 KB trying URL 'https://cloud.r-project.org/src/contrib/rlang_0.4.4.tar.gz' Content type 'application/x-gzip' length 813413 bytes (794 KB) ================================================== downloaded 794 KB trying URL 'https://cloud.r-project.org/src/contrib/scales_1.1.0.tar.gz' Content type 'application/x-gzip' length 510666 bytes (498 KB) ================================================== downloaded 498 KB trying URL 'https://cloud.r-project.org/src/contrib/tibble_2.1.3.tar.gz' Content type 'application/x-gzip' length 310774 bytes (303 KB) ================================================== downloaded 303 KB trying URL 'https://cloud.r-project.org/src/contrib/viridisLite_0.3.0.tar.gz' Content type 'application/x-gzip' length 44019 bytes (42 KB) ================================================== downloaded 42 KB trying URL 'https://cloud.r-project.org/src/contrib/withr_2.1.2.tar.gz' Content type 'application/x-gzip' length 53578 bytes (52 KB) ================================================== downloaded 52 KB trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_3.2.1.tar.gz' Content type 'application/x-gzip' length 3204655 bytes (3.1 MB) ================================================== downloaded 3.1 MB * installing *source* package ‘glue’ ... ** package ‘glue’ successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c glue.c -o glue.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c trim.c -o trim.o g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o glue.so glue.o init.o trim.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/glue/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (glue) * installing *source* package ‘magrittr’ ... ** package ‘magrittr’ successfully unpacked and MD5 sums checked ** 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 * DONE (magrittr) * installing *source* package ‘stringi’ ... ** package ‘stringi’ successfully unpacked and MD5 sums checked checking for R_HOME... /usr/lib/R checking for R... /usr/lib/R/bin/R checking for endianness... little checking for R >= 3.1.0 for C++11 use... yes checking for R < 3.4.0 for CXX1X flag use... no checking for cat... /bin/cat checking for local ICUDT_DIR... icu61/data checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking elf.h usability... yes checking elf.h presence... yes checking for elf.h... yes checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++11 accepts -g... yes checking whether the C++ compiler supports the long long type... yes checking whether the compiler implements namespaces... yes checking whether the compiler supports Standard Template Library... yes checking whether std::map is available... yes checking for pkg-config... /usr/bin/pkg-config checking with pkg-config for the system ICU4C... 60.2 checking for ICU4C >= 55... yes checking for additional required CPPFLAGS, LDFLAGS, and LIBS... done checking whether we may build an ICU4C-based project... yes checking programmatically for sufficient U_ICU_VERSION_MAJOR_NUM... yes checking programmatically if U_CHARSET_IS_UTF8 is defined and set... no checking for available ICU data library (ucnv, uloc, utrans)... yes checking for available ICU data library (ucol)... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/uconfig_local.h config.status: creating src/install.libs.R *** stringi configure summary: ICU_FOUND=1 STRINGI_CXXSTD=CXX_STD=CXX11 STRINGI_CFLAGS= -fpic STRINGI_CPPFLAGS=-I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H STRINGI_CXXFLAGS= -fpic STRINGI_LDFLAGS=-L/usr/lib/x86_64-linux-gnu STRINGI_LIBS=-licui18n -licuuc -licudata *** compiler settings used: CC=gcc -std=gnu99 LD=g++ CFLAGS=-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic CPPFLAGS= -UDEBUG -DNDEBUG CXX=g++ -std=gnu++11 CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic LDFLAGS= LIBS= ** libs g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_brkiter.cpp -o stri_brkiter.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_collator.cpp -o stri_collator.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_common.cpp -o stri_common.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_compare.cpp -o stri_compare.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_base.cpp -o stri_container_base.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_bytesearch.cpp -o stri_container_bytesearch.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_listint.cpp -o stri_container_listint.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_listraw.cpp -o stri_container_listraw.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_listutf8.cpp -o stri_container_listutf8.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_regex.cpp -o stri_container_regex.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_usearch.cpp -o stri_container_usearch.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_utf16.cpp -o stri_container_utf16.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_utf8.cpp -o stri_container_utf8.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_container_utf8_indexable.cpp -o stri_container_utf8_indexable.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_encoding_conversion.cpp -o stri_encoding_conversion.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_encoding_detection.cpp -o stri_encoding_detection.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_encoding_management.cpp -o stri_encoding_management.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_escape.cpp -o stri_escape.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_exception.cpp -o stri_exception.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_ICU_settings.cpp -o stri_ICU_settings.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_join.cpp -o stri_join.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_length.cpp -o stri_length.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_pad.cpp -o stri_pad.o g++ -std=gnu++11 -I/usr/share/R/include 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-fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_stats.cpp -o stri_stats.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_stringi.cpp -o stri_stringi.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_sub.cpp -o stri_sub.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_test.cpp -o stri_test.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_zone.cpp -o stri_time_zone.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_calendar.cpp -o stri_time_calendar.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_symbols.cpp -o stri_time_symbols.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_time_format.cpp -o stri_time_format.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_casemap.cpp -o stri_trans_casemap.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_other.cpp -o stri_trans_other.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_normalization.cpp -o stri_trans_normalization.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_trans_transliterate.cpp -o stri_trans_transliterate.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_ucnv.cpp -o stri_ucnv.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_uloc.cpp -o stri_uloc.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_utils.cpp -o stri_utils.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fpic -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stri_wrap.cpp -o stri_wrap.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o stringi.so stri_brkiter.o stri_collator.o stri_common.o stri_compare.o stri_container_base.o stri_container_bytesearch.o stri_container_listint.o stri_container_listraw.o stri_container_listutf8.o stri_container_regex.o stri_container_usearch.o stri_container_utf16.o stri_container_utf8.o stri_container_utf8_indexable.o stri_encoding_conversion.o stri_encoding_detection.o stri_encoding_management.o stri_escape.o stri_exception.o stri_ICU_settings.o stri_join.o stri_length.o stri_pad.o stri_prepare_arg.o stri_random.o stri_reverse.o stri_search_class_count.o stri_search_class_detect.o stri_search_class_extract.o stri_search_class_locate.o stri_search_class_replace.o stri_search_class_split.o stri_search_class_startsendswith.o stri_search_class_subset.o stri_search_class_trim.o stri_search_common.o stri_search_coll_count.o stri_search_coll_detect.o stri_search_coll_extract.o stri_search_coll_locate.o stri_search_coll_replace.o stri_search_coll_split.o stri_search_coll_startsendswith.o stri_search_coll_subset.o stri_search_boundaries_count.o stri_search_boundaries_extract.o stri_search_boundaries_locate.o stri_search_boundaries_split.o stri_search_fixed_count.o stri_search_fixed_detect.o stri_search_fixed_extract.o stri_search_fixed_locate.o stri_search_fixed_replace.o stri_search_fixed_split.o stri_search_fixed_subset.o stri_search_fixed_startsendswith.o stri_search_in.o stri_search_other_split.o stri_search_regex_count.o stri_search_regex_detect.o stri_search_regex_extract.o stri_search_regex_locate.o stri_search_regex_match.o stri_search_regex_replace.o stri_search_regex_split.o stri_search_regex_subset.o stri_sort.o stri_stats.o stri_stringi.o stri_sub.o stri_test.o stri_time_zone.o stri_time_calendar.o stri_time_symbols.o stri_time_format.o stri_trans_casemap.o stri_trans_other.o stri_trans_normalization.o stri_trans_transliterate.o stri_ucnv.o stri_uloc.o stri_utils.o stri_wrap.o -L/usr/lib/x86_64-linux-gnu -licui18n -licuuc -licudata -L/usr/lib/R/lib -lR installing via 'install.libs.R' to /usr/local/lib/R/site-library/stringi ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (stringi) * installing *source* package ‘colorspace’ ... ** package ‘colorspace’ successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c colorspace.c -o colorspace.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o colorspace.so colorspace.o init.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/colorspace/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (colorspace) * installing *source* package ‘assertthat’ ... ** package ‘assertthat’ 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 (assertthat) * installing *source* package ‘utf8’ ... ** package ‘utf8’ successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c as_utf8.c -o as_utf8.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bytes.c -o bytes.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c context.c -o context.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -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 -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c render.c -o render.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c render_table.c -o render_table.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c string.c -o string.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c text.c -o text.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8_encode.c -o utf8_encode.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8_format.c -o utf8_format.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8_normalize.c -o utf8_normalize.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8_valid.c -o utf8_valid.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8_width.c -o utf8_width.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/array.c -o utf8lite/src/array.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/char.c -o utf8lite/src/char.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/encode.c -o utf8lite/src/encode.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/error.c -o utf8lite/src/error.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/escape.c -o utf8lite/src/escape.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/graph.c -o utf8lite/src/graph.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/graphscan.c -o utf8lite/src/graphscan.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/normalize.c -o utf8lite/src/normalize.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/render.c -o utf8lite/src/render.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/text.c -o utf8lite/src/text.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/textassign.c -o utf8lite/src/textassign.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/textiter.c -o utf8lite/src/textiter.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iutf8lite/src -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8lite/src/textmap.c -o utf8lite/src/textmap.o ar rcs libcutf8lite.a utf8lite/src/array.o utf8lite/src/char.o utf8lite/src/encode.o utf8lite/src/error.o utf8lite/src/escape.o utf8lite/src/graph.o utf8lite/src/graphscan.o utf8lite/src/normalize.o utf8lite/src/render.o utf8lite/src/text.o utf8lite/src/textassign.o utf8lite/src/textiter.o utf8lite/src/textmap.o g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o utf8.so as_utf8.o bytes.o context.o init.o render.o render_table.o string.o text.o utf8_encode.o utf8_format.o utf8_normalize.o utf8_valid.o utf8_width.o util.o -L. -lcutf8lite -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/utf8/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (utf8) * installing *source* package ‘Rcpp’ ... ** package ‘Rcpp’ successfully unpacked and MD5 sums checked ** libs g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attributes.cpp -o attributes.o g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c barrier.cpp -o barrier.o g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c date.cpp -o date.o g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c module.cpp -o module.o g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rcpp_init.cpp -o rcpp_init.o g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/Rcpp/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Rcpp) * installing *source* package ‘farver’ ... ** package ‘farver’ successfully unpacked and MD5 sums checked ** libs g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ColorSpace.cpp -o ColorSpace.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Comparison.cpp -o Comparison.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Conversion.cpp -o Conversion.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c encode.cpp -o encode.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c farver.cpp -o farver.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.cpp -o init.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o farver.so ColorSpace.o Comparison.o Conversion.o encode.o farver.o init.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/farver/libs ** R ** preparing package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded * DONE (farver) * installing *source* package ‘labeling’ ... ** package ‘labeling’ 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 (labeling) * installing *source* package ‘R6’ ... ** package ‘R6’ 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 (R6) * installing *source* package ‘RColorBrewer’ ... ** package ‘RColorBrewer’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (RColorBrewer) * installing *source* package ‘crayon’ ... ** package ‘crayon’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (crayon) * installing *source* package ‘fansi’ ... ** package ‘fansi’ successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c assumptions.c -o assumptions.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c has.c -o has.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nchar.c -o nchar.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read.c -o read.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnchar.c -o rnchar.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c state.c -o state.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c strip.c -o strip.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c strsplit.c -o strsplit.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tabs.c -o tabs.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tohtml.c -o tohtml.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unhandled.c -o unhandled.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unique.c -o unique.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8.c -o utf8.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c wrap.c -o wrap.o g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o fansi.so assumptions.o has.o init.o nchar.o read.o rnchar.o state.o strip.o strsplit.o tabs.o tohtml.o unhandled.o unique.o utf8.o utils.o wrap.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/fansi/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (fansi) * installing *source* package ‘pkgconfig’ ... ** package ‘pkgconfig’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (pkgconfig) * installing *source* package ‘digest’ ... ** package ‘digest’ successfully unpacked and MD5 sums checked ** libs g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SpookyV2.cpp -o SpookyV2.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c crc32.c -o crc32.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c digest.c -o digest.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c digest2int.c -o digest2int.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pmurhash.c -o pmurhash.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c raes.c -o raes.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha1.c -o sha1.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha2.c -o sha2.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha256.c -o sha256.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spooky_serialize.cpp -o spooky_serialize.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xxhash.c -o xxhash.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o digest.so SpookyV2.o aes.o crc32.o digest.o digest2int.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o spooky_serialize.o xxhash.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/digest/libs ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (digest) * installing *source* package ‘gtable’ ... ** package ‘gtable’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (gtable) * installing *source* package ‘lazyeval’ ... ** package ‘lazyeval’ successf]]> Jit https://bioinformaticsonline.com/snippets/view/40927/install-miniasm-in-linux-ubuntu Thu, 06 Feb 2020 06:25:08 -0600 https://bioinformaticsonline.com/snippets/view/40927/install-miniasm-in-linux-ubuntu jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ sudo apt install miniasm Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: minimap The following NEW packages will be installed: miniasm minimap 0 upgraded, 2 newly installed, 0 to remove and 12 not upgraded. Need to get 55.8 kB of archives. After this operation, 136 kB of additional disk space will be used. Do you want to continue? [Y/n] Y Get:1 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 miniasm amd64 0.2+dfsg-2 [29.3 kB] Get:2 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 minimap amd64 0.2-3 [26.6 kB] Fetched 55.8 kB in 1s (40.7 kB/s) Selecting previously unselected package miniasm. (Reading database ... 187073 files and directories currently installed.) Preparing to unpack .../miniasm_0.2+dfsg-2_amd64.deb ... Unpacking miniasm (0.2+dfsg-2) ... Selecting previously unselected package minimap. Preparing to unpack .../minimap_0.2-3_amd64.deb ... Unpacking minimap (0.2-3) ... Setting up minimap (0.2-3) ... Setting up miniasm (0.2+dfsg-2) ... Processing triggers for man-db (2.8.3-2ubuntu0.1) ...]]> Jit https://bioinformaticsonline.com/snippets/view/40926/install-python-pip-and-numpy-on-linux-ubuntu Thu, 06 Feb 2020 06:00:57 -0600 https://bioinformaticsonline.com/snippets/view/40926/install-python-pip-and-numpy-on-linux-ubuntu jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ sudo apt install python-pip Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: libexpat1-dev libpython-all-dev libpython-dev libpython2.7-dev python-all python-all-dev python-crypto python-dbus python-dev python-gi python-keyring python-keyrings.alt python-pip-whl python-secretstorage python-setuptools python-wheel python-xdg python2.7-dev Suggested packages: python-crypto-doc python-dbus-dbg python-dbus-doc python-gi-cairo libkf5wallet-bin gir1.2-gnomekeyring-1.0 python-fs python-gdata python-keyczar python-secretstorage-doc python-setuptools-doc The following NEW packages will be installed: libexpat1-dev libpython-all-dev libpython-dev libpython2.7-dev python-all python-all-dev python-crypto python-dbus python-dev python-gi python-keyring python-keyrings.alt python-pip python-pip-whl python-secretstorage python-setuptools python-wheel python-xdg python2.7-dev 0 upgraded, 19 newly installed, 0 to remove and 12 not upgraded. Need to get 31.5 MB of archives. After this operation, 50.1 MB of additional disk space will be used. Do you want to continue? [Y/n] Y Get:1 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libexpat1-dev amd64 2.2.5-3ubuntu0.2 [122 kB] Get:2 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpython2.7-dev amd64 2.7.17-1~18.04 [28.3 MB] Get:3 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libpython-dev amd64 2.7.15~rc1-1 [7,684 B] Get:4 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libpython-all-dev amd64 2.7.15~rc1-1 [1,092 B] Get:5 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-all amd64 2.7.15~rc1-1 [1,076 B] Get:6 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python2.7-dev amd64 2.7.17-1~18.04 [277 kB] Get:7 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-dev amd64 2.7.15~rc1-1 [1,256 B] Get:8 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-all-dev amd64 2.7.15~rc1-1 [1,100 B] Get:9 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-crypto amd64 2.6.1-8ubuntu2 [244 kB] Get:10 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-dbus amd64 1.2.6-1 [90.2 kB] Get:11 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python-gi amd64 3.26.1-2ubuntu1 [197 kB] Get:12 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-secretstorage all 2.3.1-2 [11.8 kB] Get:13 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-keyring all 10.6.0-1 [30.6 kB] Get:14 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-keyrings.alt all 3.0-1 [16.7 kB] Get:15 http://in.archive.ubuntu.com/ubuntu bionic-updates/universe amd64 python-pip-whl all 9.0.1-2.3~ubuntu1.18.04.1 [1,653 kB] Get:16 http://in.archive.ubuntu.com/ubuntu bionic-updates/universe amd64 python-pip all 9.0.1-2.3~ubuntu1.18.04.1 [151 kB] Get:17 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-setuptools all 39.0.1-2 [329 kB] Get:18 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 python-wheel all 0.30.0-0.2 [36.4 kB] Get:19 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 python-xdg all 0.25-4ubuntu1 [31.3 kB] Fetched 31.5 MB in 15s (2,151 kB/s) Selecting previously unselected package libexpat1-dev:amd64. (Reading database ... 186309 files and directories currently installed.) Preparing to unpack .../00-libexpat1-dev_2.2.5-3ubuntu0.2_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.2.5-3ubuntu0.2) ... Selecting previously unselected package libpython2.7-dev:amd64. Preparing to unpack .../01-libpython2.7-dev_2.7.17-1~18.04_amd64.deb ... Unpacking libpython2.7-dev:amd64 (2.7.17-1~18.04) ... Selecting previously unselected package libpython-dev:amd64. Preparing to unpack .../02-libpython-dev_2.7.15~rc1-1_amd64.deb ... Unpacking libpython-dev:amd64 (2.7.15~rc1-1) ... Selecting previously unselected package libpython-all-dev:amd64. Preparing to unpack .../03-libpython-all-dev_2.7.15~rc1-1_amd64.deb ... Unpacking libpython-all-dev:amd64 (2.7.15~rc1-1) ... Selecting previously unselected package python-all. Preparing to unpack .../04-python-all_2.7.15~rc1-1_amd64.deb ... Unpacking python-all (2.7.15~rc1-1) ... Selecting previously unselected package python2.7-dev. Preparing to unpack .../05-python2.7-dev_2.7.17-1~18.04_amd64.deb ... Unpacking python2.7-dev (2.7.17-1~18.04) ... Selecting previously unselected package python-dev. Preparing to unpack .../06-python-dev_2.7.15~rc1-1_amd64.deb ... Unpacking python-dev (2.7.15~rc1-1) ... Selecting previously unselected package python-all-dev. Preparing to unpack .../07-python-all-dev_2.7.15~rc1-1_amd64.deb ... Unpacking python-all-dev (2.7.15~rc1-1) ... Selecting previously unselected package python-crypto. Preparing to unpack .../08-python-crypto_2.6.1-8ubuntu2_amd64.deb ... Unpacking python-crypto (2.6.1-8ubuntu2) ... Selecting previously unselected package python-dbus. Preparing to unpack .../09-python-dbus_1.2.6-1_amd64.deb ... Unpacking python-dbus (1.2.6-1) ... Selecting previously unselected package python-gi. Preparing to unpack .../10-python-gi_3.26.1-2ubuntu1_amd64.deb ... Unpacking python-gi (3.26.1-2ubuntu1) ... Selecting previously unselected package python-secretstorage. Preparing to unpack .../11-python-secretstorage_2.3.1-2_all.deb ... Unpacking python-secretstorage (2.3.1-2) ... Selecting previously unselected package python-keyring. Preparing to unpack .../12-python-keyring_10.6.0-1_all.deb ... Unpacking python-keyring (10.6.0-1) ... Selecting previously unselected package python-keyrings.alt. Preparing to unpack .../13-python-keyrings.alt_3.0-1_all.deb ... Unpacking python-keyrings.alt (3.0-1) ... Selecting previously unselected package python-pip-whl. Preparing to unpack .../14-python-pip-whl_9.0.1-2.3~ubuntu1.18.04.1_all.deb ... Unpacking python-pip-whl (9.0.1-2.3~ubuntu1.18.04.1) ... Selecting previously unselected package python-pip. Preparing to unpack .../15-python-pip_9.0.1-2.3~ubuntu1.18.04.1_all.deb ... Unpacking python-pip (9.0.1-2.3~ubuntu1.18.04.1) ... Selecting previously unselected package python-setuptools. Preparing to unpack .../16-python-setuptools_39.0.1-2_all.deb ... Unpacking python-setuptools (39.0.1-2) ... Selecting previously unselected package python-wheel. Preparing to unpack .../17-python-wheel_0.30.0-0.2_all.deb ... Unpacking python-wheel (0.30.0-0.2) ... Selecting previously unselected package python-xdg. Preparing to unpack .../18-python-xdg_0.25-4ubuntu1_all.deb ... Unpacking python-xdg (0.25-4ubuntu1) ... Setting up python-pip-whl (9.0.1-2.3~ubuntu1.18.04.1) ... Setting up python-setuptools (39.0.1-2) ... Setting up python-crypto (2.6.1-8ubuntu2) ... Setting up python-wheel (0.30.0-0.2) ... Setting up python-keyrings.alt (3.0-1) ... Setting up python-gi (3.26.1-2ubuntu1) ... Setting up libexpat1-dev:amd64 (2.2.5-3ubuntu0.2) ... Setting up libpython2.7-dev:amd64 (2.7.17-1~18.04) ... Setting up python-dbus (1.2.6-1) ... Setting up python-pip (9.0.1-2.3~ubuntu1.18.04.1) ... Setting up python2.7-dev (2.7.17-1~18.04) ... Setting up python-all (2.7.15~rc1-1) ... Setting up python-xdg (0.25-4ubuntu1) ... Setting up python-secretstorage (2.3.1-2) ... Setting up libpython-dev:amd64 (2.7.15~rc1-1) ... Setting up python-keyring (10.6.0-1) ... Setting up python-dev (2.7.15~rc1-1) ... Setting up libpython-all-dev:amd64 (2.7.15~rc1-1) ... Setting up python-all-dev (2.7.15~rc1-1) ... Processing triggers for man-db (2.8.3-2ubuntu0.1) ... jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ pip install numpy Collecting numpy Downloading https://files.pythonhosted.org/packages/3a/5f/47e578b3ae79e2624e205445ab77a1848acdaa2929a00eeef6b16eaaeb20/numpy-1.16.6-cp27-cp27mu-manylinux1_x86_64.whl (17.0MB) 100% |████████████████████████████████| 17.0MB 30kB/s Installing collected packages: numpy Successfully installed numpy-1.16.6]]> Jit https://bioinformaticsonline.com/snippets/view/40925/install-nucmer-on-linux-ubuntu Thu, 06 Feb 2020 05:56:32 -0600 https://bioinformaticsonline.com/snippets/view/40925/install-nucmer-on-linux-ubuntu jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ sudo apt install mummer [sudo] password for jit: Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: gawk Suggested packages: gawk-doc The following NEW packages will be installed: gawk mummer 0 upgraded, 2 newly installed, 0 to remove and 12 not upgraded. Need to get 1,213 kB of archives. After this operation, 3,521 kB of additional disk space will be used. Do you want to continue? [Y/n] Y Get:1 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 gawk amd64 1:4.1.4+dfsg-1build1 [401 kB] Get:2 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 mummer amd64 3.23+dfsg-3 [811 kB] Fetched 1,213 kB in 2s (672 kB/s) Selecting previously unselected package gawk. (Reading database ... 186076 files and directories currently installed.)............] Preparing to unpack .../gawk_1%3a4.1.4+dfsg-1build1_amd64.deb ... Unpacking gawk (1:4.1.4+dfsg-1build1) ... Selecting previously unselected package mummer. Preparing to unpack .../mummer_3.23+dfsg-3_amd64.deb ... Unpacking mummer (3.23+dfsg-3) ... Setting up gawk (1:4.1.4+dfsg-1build1) ... Setting up mummer (3.23+dfsg-3) ... Processing triggers for man-db (2.8.3-2ubuntu0.1) ...]]> Jit https://bioinformaticsonline.com/snippets/view/40910/perl-script-to-delete-the-adjacent-repeats Wed, 05 Feb 2020 23:09:15 -0600 https://bioinformaticsonline.com/snippets/view/40910/perl-script-to-delete-the-adjacent-repeats /usr/bin/perl #Mostly the interview question for bioinfomatician ! #Write a code to delete the adjacent repeated character .... $string='ATTTTTTGGC'; # This should be converted to ATGC $string =~ s/(\w)\1/$1/g; print $string; #For more helps ... check out this #This bit of code will do the job: $string =~ s/(.)\1/$1/g #Alternatively, if you want to ignore case when comparing, you could use: $string =~ s/(.)\1/$1/gi #And finally, if you wanted to trim any number of duplicates down to a single letter, this would work: $string =~ s/(.)\1+/$1/gi]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40905/install-zef-for-raku Wed, 05 Feb 2020 06:59:48 -0600 https://bioinformaticsonline.com/snippets/view/40905/install-zef-for-raku jit@jit-HP-Pro-3335-MT:~/Downloads$ git clone https://github.com/ugexe/zef.git Cloning into 'zef'... remote: Enumerating objects: 218, done. remote: Counting objects: 100% (218/218), done. remote: Compressing objects: 100% (136/136), done. remote: Total 10255 (delta 115), reused 153 (delta 81), pack-reused 10037 Receiving objects: 100% (10255/10255), 1.92 MiB | 1.53 MiB/s, done. Resolving deltas: 100% (6290/6290), done. jit@jit-HP-Pro-3335-MT:~/Downloads$ cd zef jit@jit-HP-Pro-3335-MT:~/Downloads/zef$ perl6 -I. bin/zef install . ===> Testing: zef:ver<0.8.2>:auth<github:ugexe>:api<0> ===> Testing [OK] for zef:ver<0.8.2>:auth<github:ugexe>:api<0> ===> Installing: zef:ver<0.8.2>:auth<github:ugexe>:api<0> 1 bin/ script [zef] installed to: /home/jit/.perl6/bin #Now ready to roll jit@jit-HP-Pro-3335-MT:~/Downloads/zef$ /home/jit/.perl6/bin/zef install String::FuzzyIndex ===> Searching for: String::FuzzyIndex ===> Updating cpan mirror: https://raw.githubusercontent.com/ugexe/Perl6-ecosystems/master/cpan1.json ===> Updated cpan mirror: https://raw.githubusercontent.com/ugexe/Perl6-ecosystems/master/cpan1.json ===> Updating p6c mirror: https://raw.githubusercontent.com/ugexe/Perl6-ecosystems/master/p6c1.json ===> Updated p6c mirror: https://raw.githubusercontent.com/ugexe/Perl6-ecosystems/master/p6c1.json ===> Testing: String::FuzzyIndex:ver<0.2>:auth<github:threadless-screw> ===> Testing [OK] for String::FuzzyIndex:ver<0.2>:auth<github:threadless-screw> ===> Installing: String::FuzzyIndex:ver<0.2>:auth<github:threadless-screw>]]> Jit https://bioinformaticsonline.com/snippets/view/40904/install-raku-on-ubuntu Wed, 05 Feb 2020 06:45:12 -0600 https://bioinformaticsonline.com/snippets/view/40904/install-raku-on-ubuntu $ sudo apt-get install rakudo [sudo] password for jit: Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: libjs-angularjs libtommath1 moarvm nqp Suggested packages: valgrind The following NEW packages will be installed: libjs-angularjs libtommath1 moarvm nqp rakudo 0 upgraded, 5 newly installed, 0 to remove and 3 not upgraded. Need to get 5,316 kB of archives. After this operation, 36.8 MB of additional disk space will be used. Do you want to continue? [Y/n] Y Get:1 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libjs-angularjs all 1.5.10-1 [506 kB] Get:2 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libtommath1 amd64 1.0.1-1 [43.9 kB] Get:3 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 moarvm amd64 2018.03+dfsg-1 [981 kB] Get:4 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 nqp amd64 2018.03+dfsg-2 [539 kB] Get:5 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 rakudo amd64 2018.03-1 [3,246 kB] Fetched 5,316 kB in 12s (458 kB/s) Selecting previously unselected package libjs-angularjs. (Reading database ... 185114 files and directories currently installed.) Preparing to unpack .../libjs-angularjs_1.5.10-1_all.deb ... Unpacking libjs-angularjs (1.5.10-1) ... Selecting previously unselected package libtommath1:amd64. Preparing to unpack .../libtommath1_1.0.1-1_amd64.deb ... Unpacking libtommath1:amd64 (1.0.1-1) ... Selecting previously unselected package moarvm. Preparing to unpack .../moarvm_2018.03+dfsg-1_amd64.deb ... Unpacking moarvm (2018.03+dfsg-1) ... Selecting previously unselected package nqp. Preparing to unpack .../nqp_2018.03+dfsg-2_amd64.deb ... Unpacking nqp (2018.03+dfsg-2) ... Selecting previously unselected package rakudo. Preparing to unpack .../rakudo_2018.03-1_amd64.deb ... Unpacking rakudo (2018.03-1) ... Setting up libtommath1:amd64 (1.0.1-1) ... Setting up libjs-angularjs (1.5.10-1) ... Setting up moarvm (2018.03+dfsg-1) ... Setting up nqp (2018.03+dfsg-2) ... Setting up rakudo (2018.03-1) ... Processing triggers for man-db (2.8.3-2ubuntu0.1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... $ perl6 -v This is Rakudo version 2018.03 built on MoarVM version 2018.03 implementing Perl 6.c.]]> Jit https://bioinformaticsonline.com/snippets/view/40879/install-npm Mon, 03 Feb 2020 07:02:07 -0600 https://bioinformaticsonline.com/snippets/view/40879/install-npm $ sudo apt install npm Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: gyp javascript-common libjs-async libjs-inherits libjs-jquery libjs-node-uuid libjs-underscore libssl1.0-dev libuv1-dev node-abbrev node-ansi node-ansi-color-table node-archy node-async node-balanced-match node-block-stream node-brace-expansion node-builtin-modules node-combined-stream node-concat-map node-cookie-jar node-delayed-stream node-forever-agent node-form-data node-fs.realpath node-fstream node-fstream-ignore node-github-url-from-git node-glob node-graceful-fs node-gyp node-hosted-git-info node-inflight node-inherits node-ini node-is-builtin-module node-isexe node-json-stringify-safe node-lockfile node-lru-cache node-mime node-minimatch node-mkdirp node-mute-stream node-node-uuid node-nopt node-normalize-package-data node-npmlog node-once node-osenv node-path-is-absolute node-pseudomap node-qs node-read node-read-package-json node-request node-retry node-rimraf node-semver node-sha node-slide node-spdx-correct node-spdx-expression-parse node-spdx-license-ids node-tar node-tunnel-agent node-underscore node-validate-npm-package-license node-which node-wrappy node-yallist nodejs-dev Suggested packages: apache2 | lighttpd | httpd node-hawk node-aws-sign node-oauth-sign node-http-signature The following NEW packages will be installed: gyp javascript-common libjs-async libjs-inherits libjs-jquery libjs-node-uuid libjs-underscore libssl1.0-dev libuv1-dev node-abbrev node-ansi node-ansi-color-table node-archy node-async node-balanced-match node-block-stream node-brace-expansion node-builtin-modules node-combined-stream node-concat-map node-cookie-jar node-delayed-stream node-forever-agent node-form-data node-fs.realpath node-fstream node-fstream-ignore node-github-url-from-git node-glob node-graceful-fs node-gyp node-hosted-git-info node-inflight node-inherits node-ini node-is-builtin-module node-isexe node-json-stringify-safe node-lockfile node-lru-cache node-mime node-minimatch node-mkdirp node-mute-stream node-node-uuid node-nopt node-normalize-package-data node-npmlog node-once node-osenv node-path-is-absolute node-pseudomap node-qs node-read node-read-package-json node-request node-retry node-rimraf node-semver node-sha node-slide node-spdx-correct node-spdx-expression-parse node-spdx-license-ids node-tar node-tunnel-agent node-underscore node-validate-npm-package-license node-which node-wrappy node-yallist nodejs-dev npm 0 upgraded, 73 newly installed, 0 to remove and 387 not upgraded. Need to get 4,335 kB of archives. After this operation, 24.2 MB of additional disk space will be used. Do you want to continue? [Y/n] Y Get:1 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 gyp all 0.1+20150913git1f374df9-1ubuntu1 [265 kB] Get:2 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 javascript-common all 11 [6,066 B] Get:3 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-async all 0.8.0-3 [25.4 kB] Get:4 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libjs-jquery all 3.2.1-1 [152 kB] Get:5 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-node-uuid all 1.4.7-5 [11.5 kB] Get:6 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libjs-underscore all 1.8.3~dfsg-1 [59.9 kB] Get:7 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libssl1.0-dev amd64 1.0.2n-1ubuntu5.3 [1,365 kB] Get:8 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libuv1-dev amd64 1.18.0-3 [82.0 kB] Get:9 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-async all 0.8.0-3 [2,840 B] Get:10 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-builtin-modules all 1.1.1-1 [3,338 B] Get:11 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-fs.realpath all 1.0.0-1 [5,572 B] Get:12 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-hosted-git-info all 2.5.0-1 [6,756 B] Get:13 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-wrappy all 1.0.2-1 [3,162 B] Get:14 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-once all 1.4.0-2ubuntu1 [3,588 B] Get:15 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-inflight all 1.0.6-1 [3,382 B] Get:16 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-is-builtin-module all 1.0.0-1 [2,906 B] Get:17 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-isexe all 2.0.0-3 [4,376 B] Get:18 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-node-uuid all 1.4.7-5 [2,844 B] Get:19 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-path-is-absolute all 1.0.0-1 [3,310 B] Get:20 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-pseudomap all 1.0.2-1 [3,534 B] Get:21 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-spdx-license-ids all 1.2.2-1 [4,792 B] Get:22 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-spdx-correct all 1.0.2-1 [3,718 B] Get:23 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-spdx-expression-parse all 1.0.4-1 [12.1 kB] Get:24 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-underscore all 1.8.3~dfsg-1 [3,790 B] Get:25 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-validate-npm-package-license all 3.0.1-1 [3,488 B] Get:26 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-yallist all 2.0.0-1 [5,398 B] Get:27 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-inherits all 2.0.3-1 [2,792 B] Get:28 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-abbrev all 1.0.9-1 [3,708 B] Get:29 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-ansi all 0.3.0-2ubuntu1 [8,720 B] Get:30 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-ansi-color-table all 1.0.0-1 [4,478 B] Get:31 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-archy all 1.0.0-1ubuntu1 [4,264 B] Get:32 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-balanced-match all 0.4.2-1 [4,030 B] Get:33 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-inherits all 2.0.3-1 [3,092 B] Get:34 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-block-stream all 0.0.9-1ubuntu1 [4,736 B] Get:35 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-concat-map all 0.0.1-1 [3,502 B] Get:36 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-brace-expansion all 1.1.8-1 [5,840 B] Get:37 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-delayed-stream all 0.0.5-1 [4,750 B] Get:38 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-combined-stream all 0.0.5-1 [4,958 B] Get:39 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-cookie-jar all 0.3.1-1 [3,746 B] Get:40 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-forever-agent all 0.5.1-1 [3,194 B] Get:41 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-mime all 1.3.4-1 [11.9 kB] Get:42 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-form-data all 0.1.0-1 [6,412 B] Get:43 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-minimatch all 3.0.4-3 [13.5 kB] Get:44 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-glob all 7.1.2-4 [17.7 kB] Get:45 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-rimraf all 2.6.2-1 [8,152 B] Get:46 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-mkdirp all 0.5.1-1 [4,848 B] Get:47 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-graceful-fs all 4.1.11-1 [10.8 kB] Get:48 http://in.archive.ubuntu.com/ubuntu bionic-updates/universe amd64 node-fstream all 1.0.10-1ubuntu0.18.04.1 [18.4 kB] Get:49 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-fstream-ignore all 0.0.6-2 [5,586 B] Get:50 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-github-url-from-git all 1.4.0-1 [3,782 B] Get:51 http://in.archive.ubuntu.com/ubuntu bionic-updates/universe amd64 nodejs-dev amd64 8.10.0~dfsg-2ubuntu0.4 [351 kB] Get:52 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-nopt all 3.0.6-3 [9,572 B] Get:53 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-npmlog all 0.0.4-1 [5,844 B] Get:54 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-osenv all 0.1.4-1 [4,212 B] Get:55 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-tunnel-agent all 0.3.1-1 [4,018 B] Get:56 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-json-stringify-safe all 5.0.0-1 [3,544 B] Get:57 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-qs all 2.2.4-1ubuntu1 [7,680 B] Get:58 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-request all 2.26.1-1 [14.5 kB] Get:59 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-semver all 5.4.1-1 [22.6 kB] Get:60 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-tar all 2.2.1-1 [17.7 kB] Get:61 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-which all 1.3.0-1 [4,504 B] Get:62 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-gyp all 3.6.2-1ubuntu1 [29.4 kB] Get:63 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-ini all 1.3.4-1 [5,588 B] Get:64 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-lockfile all 0.4.1-1 [5,450 B] Get:65 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-lru-cache all 4.1.1-1 [8,228 B] Get:66 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-mute-stream all 0.0.7-1 [4,372 B] Get:67 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-normalize-package-data all 2.3.5-2 [10.6 kB] Get:68 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-read all 1.0.7-1 [4,572 B] Get:69 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-read-package-json all 1.2.4-1 [7,780 B] Get:70 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-retry all 0.10.1-1 [8,016 B] Get:71 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-sha all 1.2.3-1 [4,272 B] Get:72 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-slide all 1.1.6-1 [6,212 B] Get:73 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 npm all 3.5.2-0ubuntu4 [1,586 kB] Fetched 4,335 kB in 15s (297 kB/s) Extracting templates from packages: 100% Selecting previously unselected package gyp. (Reading database ... 180389 files and directories currently installed.) Preparing to unpack .../00-gyp_0.1+20150913git1f374df9-1ubuntu1_all.deb ... Unpacking gyp (0.1+20150913git1f374df9-1ubuntu1) ... Selecting previously unselected package javascript-common. Preparing to unpack .../01-javascript-common_11_all.deb ... Unpacking javascript-common (11) ... Selecting previously unselected package libjs-async. Preparing to unpack .../02-libjs-async_0.8.0-3_all.deb ... Unpacking libjs-async (0.8.0-3) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../03-libjs-jquery_3.2.1-1_all.deb ... Unpacking libjs-jquery (3.2.1-1) ... Selecting previously unselected package libjs-node-uuid. Preparing to unpack .../04-libjs-node-uuid_1.4.7-5_all.deb ... Unpacking libjs-node-uuid (1.4.7-5) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../05-libjs-underscore_1.8.3~dfsg-1_all.deb ... Unpacking libjs-underscore (1.8.3~dfsg-1) ... 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Setting up npm (3.5.2-0ubuntu4) ...]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40876/cuda-toolkit-102-download Mon, 03 Feb 2020 04:12:32 -0600 https://bioinformaticsonline.com/snippets/view/40876/cuda-toolkit-102-download #More at https://developer.nvidia.com/cuda-downloads?target_os=Linux&target_arch=x86_64&target_distro=Ubuntu&target_version=1804&target_type=deblocal $ wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin --2020-02-03 15:15:56-- https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin Resolving developer.download.nvidia.com (developer.download.nvidia.com)... 192.229.232.112, 2606:2800:247:2063:46e:21d:825:102e Connecting to developer.download.nvidia.com (developer.download.nvidia.com)|192.229.232.112|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 56 [application/octet-stream] Saving to: ‘cuda-ubuntu1804.pin’ cuda-ubuntu1804.pin 100%[===========================================================>] 56 --.-KB/s in 0s 2020-02-03 15:15:56 (1.48 MB/s) - ‘cuda-ubuntu1804.pin’ saved [56/56] $ sudo mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600 $ wget http://developer.download.nvidia.com/compute/cuda/10.2/Prod/local_installers/cuda-repo-ubuntu1804-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb --2020-02-03 15:19:22-- http://developer.download.nvidia.com/compute/cuda/10.2/Prod/local_installers/cuda-repo-ubuntu1804-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb Resolving developer.download.nvidia.com (developer.download.nvidia.com)... 192.229.232.112, 2606:2800:247:2063:46e:21d:825:102e Connecting to developer.download.nvidia.com (developer.download.nvidia.com)|192.229.232.112|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 1896270068 (1.8G) [application/x-deb] Saving to: ‘cuda-repo-ubuntu1804-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb’ cuda-repo-ubuntu1804-10-2-local-1 100%[===========================================================>] 1.77G 4.90MB/s in 6m 27s 2020-02-03 15:25:50 (4.67 MB/s) - ‘cuda-repo-ubuntu1804-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb’ saved [1896270068/1896270068] $ sudo dpkg -i cuda-repo-ubuntu1804-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb $ sudo apt-key add /var/cuda-repo-10-2-local-10.2.89-440.33.01/7fa2af80.pub $ sudo apt-get update $ apt-get -y install cuda]]> Rahul Nayak