Initialization script fails

> source("DifferentialExpressionFunctions.R") Installing packages into ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6’ (as ‘lib’ is unspecified) Warning in install.packages : dependency ‘FactoMineR’ is not available also installing the dependencies ‘nloptr’, ‘pbkrtest’, ‘lme4’, ‘car’, ‘rstatix’, ‘gargle’, ‘curl’, ‘ggpubr’, ‘googledrive’, ‘googlesheets4’, ‘httr’, ‘rvest’ trying URL 'https://cloud.r-project.org/src/contrib/nloptr_2.0.3.tar.gz' Content type 'application/x-gzip' length 2219877 bytes (2.1 MB) ================================================== downloaded 2.1 MB trying URL 'https://cloud.r-project.org/src/contrib/pbkrtest_0.5.1.tar.gz' Content type 'application/x-gzip' length 246327 bytes (240 KB) ================================================== downloaded 240 KB trying URL 'https://cloud.r-project.org/src/contrib/lme4_1.1-30.tar.gz' Content type 'application/x-gzip' length 3307884 bytes (3.2 MB) ================================================== downloaded 3.2 MB trying URL 'https://cloud.r-project.org/src/contrib/car_3.1-0.tar.gz' Content type 'application/x-gzip' length 569914 bytes (556 KB) ================================================== downloaded 556 KB trying URL 'https://cloud.r-project.org/src/contrib/rstatix_0.7.0.tar.gz' Content type 'application/x-gzip' length 402481 bytes (393 KB) ================================================== downloaded 393 KB trying URL 'https://cloud.r-project.org/src/contrib/gargle_1.2.1.tar.gz' Content type 'application/x-gzip' length 312943 bytes (305 KB) ================================================== downloaded 305 KB trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz' Content type 'application/x-gzip' length 670416 bytes (654 KB) ================================================== downloaded 654 KB trying URL 'https://cloud.r-project.org/src/contrib/ggpubr_0.4.0.tar.gz' Content type 'application/x-gzip' length 2689307 bytes (2.6 MB) ================================================== downloaded 2.6 MB trying URL 'https://cloud.r-project.org/src/contrib/googledrive_2.0.0.tar.gz' Content type 'application/x-gzip' length 1593656 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://cloud.r-project.org/src/contrib/googlesheets4_1.0.1.tar.gz' Content type 'application/x-gzip' length 223314 bytes (218 KB) ================================================== downloaded 218 KB trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.4.tar.gz' Content type 'application/x-gzip' length 161140 bytes (157 KB) ================================================== downloaded 157 KB trying URL 'https://cloud.r-project.org/src/contrib/rvest_1.0.3.tar.gz' Content type 'application/x-gzip' length 94659 bytes (92 KB) ================================================== downloaded 92 KB trying URL 'https://cloud.r-project.org/src/contrib/factoextra_1.0.7.tar.gz' Content type 'application/x-gzip' length 1386480 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.3.2.tar.gz' Content type 'application/x-gzip' length 702514 bytes (686 KB) ================================================== downloaded 686 KB * installing *source* package ‘nloptr’ ... ** package ‘nloptr’ successfully unpacked and MD5 sums checked ** using staged installation 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 the compiler supports GNU C++... yes checking whether g++ -std=gnu++11 accepts -g... yes checking for g++ -std=gnu++11 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -std=gnu++11 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++11 accepts -g... (cached) yes checking for g++ -std=gnu++11 option to enable C++11 features... (cached) none needed checking for pkg-config... /usr/bin/pkg-config checking if pkg-config knows NLopt... no checking for cmake... no ------------------ CMAKE NOT FOUND -------------------- CMake was not found on the PATH. Please install CMake: - sudo yum install cmake (Fedora/CentOS; inside a terminal) - sudo apt install cmake (Debian/Ubuntu; inside a terminal). - sudo pacman -S cmake (Arch Linux; inside a terminal). - sudo brew install cmake (MacOS; inside a terminal with Homebrew) - sudo port install cmake (MacOS; inside a terminal with MacPorts) Alternatively install CMake from: <https://cmake.org/> ------------------------------------------------------- ERROR: configuration failed for package ‘nloptr’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/nloptr’ Warning in install.packages : installation of package ‘nloptr’ had non-zero exit status * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Using PKG_CFLAGS= Using PKG_LIBS=-lcurl ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libcurl was not found. Try installing: * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc) * rpm: libcurl-devel (Fedora, CentOS, RHEL) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------------------------------------------------- ERROR: configuration failed for package ‘curl’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/curl’ Warning in install.packages : installation of package ‘curl’ had non-zero exit status ERROR: dependency ‘nloptr’ is not available for package ‘lme4’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/lme4’ Warning in install.packages : installation of package ‘lme4’ had non-zero exit status ERROR: dependency ‘curl’ is not available for package ‘httr’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/httr’ Warning in install.packages : installation of package ‘httr’ had non-zero exit status ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/pbkrtest’ Warning in install.packages : installation of package ‘pbkrtest’ had non-zero exit status ERROR: dependency ‘httr’ is not available for package ‘gargle’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/gargle’ Warning in install.packages : installation of package ‘gargle’ had non-zero exit status ERROR: dependency ‘httr’ is not available for package ‘rvest’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/rvest’ Warning in install.packages : installation of package ‘rvest’ had non-zero exit status ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/car’ Warning in install.packages : installation of package ‘car’ had non-zero exit status ERROR: dependencies ‘gargle’, ‘httr’ are not available for package ‘googledrive’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/googledrive’ Warning in install.packages : installation of package ‘googledrive’ had non-zero exit status ERROR: dependency ‘car’ is not available for package ‘rstatix’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/rstatix’ Warning in install.packages : installation of package ‘rstatix’ had non-zero exit status ERROR: dependencies ‘curl’, ‘gargle’, ‘googledrive’, ‘httr’ are not available for package ‘googlesheets4’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/googlesheets4’ Warning in install.packages : installation of package ‘googlesheets4’ had non-zero exit status ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/ggpubr’ Warning in install.packages : installation of package ‘ggpubr’ had non-zero exit status ERROR: dependencies ‘googledrive’, ‘googlesheets4’, ‘httr’, ‘rvest’ are not available for package ‘tidyverse’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/tidyverse’ Warning in install.packages : installation of package ‘tidyverse’ had non-zero exit status ERROR: dependencies ‘FactoMineR’, ‘ggpubr’ are not available for package ‘factoextra’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/factoextra’ Warning in install.packages : installation of package ‘factoextra’ had non-zero exit status The downloaded source packages are in ‘/tmp/Rtmpdhd6vt/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.10 (BiocManager 1.30.18), R 3.6.3 (2020-02-29) Installing package(s) 'DESeq2' Warning: dependency ‘locfit’ is not available also installing the dependencies ‘RCurl’, ‘GenomeInfoDb’, ‘annotate’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.9.tar.gz' Content type 'application/x-gzip' length 731611 bytes (714 KB) ================================================== downloaded 714 KB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomeInfoDb_1.22.1.tar.gz' Content type 'application/octet-stream' length 3409252 bytes (3.3 MB) ================================================== downloaded 3.3 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/annotate_1.64.0.tar.gz' Content type 'application/octet-stream' length 1873132 bytes (1.8 MB) ================================================== downloaded 1.8 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomicRanges_1.38.0.tar.gz' Content type 'application/octet-stream' length 1169872 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/SummarizedExperiment_1.16.1.tar.gz' Content type 'application/octet-stream' length 1518022 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/genefilter_1.68.0.tar.gz' Content type 'application/octet-stream' length 1421076 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/geneplotter_1.64.0.tar.gz' Content type 'application/octet-stream' length 1431450 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DESeq2_1.26.0.tar.gz' Content type 'application/octet-stream' length 2060061 bytes (2.0 MB) ================================================== downloaded 2.0 MB * installing *source* package ‘RCurl’ ... ** package ‘RCurl’ successfully unpacked and MD5 sums checked ** using staged installation checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ‘RCurl’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/RCurl’ ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/GenomeInfoDb’ ERROR: dependency ‘RCurl’ is not available for package ‘annotate’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/annotate’ ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/GenomicRanges’ ERROR: dependency ‘annotate’ is not available for package ‘genefilter’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/genefilter’ ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’ ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/SummarizedExperiment’ ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘locfit’, ‘geneplotter’ are not available for package ‘DESeq2’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’ The downloaded source packages are in ‘/tmp/Rtmpdhd6vt/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: boot, class, cluster, codetools, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival path: /usr/lib/R/site-library packages: littler 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.10 (BiocManager 1.30.18), R 3.6.3 (2020-02-29) Installing package(s) 'DEGreport' Warning: dependencies ‘lasso2’, ‘locfit’, ‘rjson’ are not available also installing the dependencies ‘annotate’, ‘RCurl’, ‘GetoptLong’, ‘GenomicRanges’, ‘genefilter’, ‘geneplotter’, ‘GenomeInfoDb’, ‘ComplexHeatmap’, ‘DESeq2’, ‘edgeR’, ‘SummarizedExperiment’ trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/annotate_1.64.0.tar.gz' Content type 'application/octet-stream' length 1873132 bytes (1.8 MB) ================================================== downloaded 1.8 MB trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.9.tar.gz' Content type 'application/x-gzip' length 731611 bytes (714 KB) ================================================== downloaded 714 KB trying URL 'https://cloud.r-project.org/src/contrib/GetoptLong_1.0.5.tar.gz' Content type 'application/x-gzip' length 767681 bytes (749 KB) ================================================== downloaded 749 KB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomicRanges_1.38.0.tar.gz' Content type 'application/octet-stream' length 1169872 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/genefilter_1.68.0.tar.gz' Content type 'application/octet-stream' length 1421076 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/geneplotter_1.64.0.tar.gz' Content type 'application/octet-stream' length 1431450 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomeInfoDb_1.22.1.tar.gz' Content type 'application/octet-stream' length 3409252 bytes (3.3 MB) ================================================== downloaded 3.3 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/ComplexHeatmap_2.2.0.tar.gz' Content type 'application/octet-stream' length 1371868 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DESeq2_1.26.0.tar.gz' Content type 'application/octet-stream' length 2060061 bytes (2.0 MB) ================================================== downloaded 2.0 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/edgeR_3.28.1.tar.gz' Content type 'application/octet-stream' length 1481788 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/SummarizedExperiment_1.16.1.tar.gz' Content type 'application/octet-stream' length 1518022 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DEGreport_1.22.0.tar.gz' Content type 'application/octet-stream' length 20151878 bytes (19.2 MB) ================================================== downloaded 19.2 MB * installing *source* package ‘RCurl’ ... ** package ‘RCurl’ successfully unpacked and MD5 sums checked ** using staged installation checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ‘RCurl’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/RCurl’ ERROR: dependency ‘rjson’ is not available for package ‘GetoptLong’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/GetoptLong’ ERROR: dependency ‘locfit’ is not available for package ‘edgeR’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/edgeR’ ERROR: dependency ‘RCurl’ is not available for package ‘annotate’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/annotate’ ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/GenomeInfoDb’ ERROR: dependency ‘GetoptLong’ is not available for package ‘ComplexHeatmap’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/ComplexHeatmap’ ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/GenomicRanges’ ERROR: dependency ‘annotate’ is not available for package ‘genefilter’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/genefilter’ ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’ ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/SummarizedExperiment’ ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘locfit’, ‘geneplotter’ are not available for package ‘DESeq2’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’ ERROR: dependencies ‘ComplexHeatmap’, ‘DESeq2’, ‘edgeR’, ‘lasso2’, ‘SummarizedExperiment’ are not available for package ‘DEGreport’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/DEGreport’ The downloaded source packages are in ‘/tmp/Rtmpdhd6vt/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: boot, class, cluster, codetools, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival path: /usr/lib/R/site-library packages: littler 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.10 (BiocManager 1.30.18), R 3.6.3 (2020-02-29) Installing package(s) 'pathview' also installing the dependencies ‘curl’, ‘RCurl’, ‘httr’, ‘KEGGgraph’, ‘KEGGREST’ trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz' Content type 'application/x-gzip' length 670416 bytes (654 KB) ================================================== downloaded 654 KB trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.9.tar.gz' Content type 'application/x-gzip' length 731611 bytes (714 KB) ================================================== downloaded 714 KB trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.4.tar.gz' Content type 'application/x-gzip' length 161140 bytes (157 KB) ================================================== downloaded 157 KB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/KEGGgraph_1.46.0.tar.gz' Content type 'application/octet-stream' length 1482115 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/KEGGREST_1.26.1.tar.gz' Content type 'application/octet-stream' length 25020 bytes (24 KB) ================================================== downloaded 24 KB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/pathview_1.26.0.tar.gz' Content type 'application/octet-stream' length 2194351 bytes (2.1 MB) ================================================== downloaded 2.1 MB * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Using PKG_CFLAGS= Using PKG_LIBS=-lcurl ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libcurl was not found. Try installing: * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc) * rpm: libcurl-devel (Fedora, CentOS, RHEL) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------------------------------------------------- ERROR: configuration failed for package ‘curl’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/curl’ * installing *source* package ‘RCurl’ ... ** package ‘RCurl’ successfully unpacked and MD5 sums checked ** using staged installation checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ‘RCurl’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/RCurl’ ERROR: dependency ‘curl’ is not available for package ‘httr’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/httr’ ERROR: dependency ‘RCurl’ is not available for package ‘KEGGgraph’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/KEGGgraph’ ERROR: dependency ‘httr’ is not available for package ‘KEGGREST’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/KEGGREST’ ERROR: dependencies ‘KEGGgraph’, ‘KEGGREST’ are not available for package ‘pathview’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/pathview’ The downloaded source packages are in ‘/tmp/Rtmpdhd6vt/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: boot, class, cluster, codetools, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival path: /usr/lib/R/site-library packages: littler Loading required package: ggplot2 Attaching package: ‘gplots’ The following object is masked from ‘package:stats’: lowess Error in library(package, character.only = TRUE) : there is no package called ‘factoextra’ In addition: There were 26 warnings (use warnings() to see them)

Installing package into ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘FactoMineR’ is not available (for R version 3.6.3)

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.10 (BiocManager 1.30.18), R 3.6.3 (2020-02-29) Installing package(s) 'FactoMineR' Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: boot, class, cluster, codetools, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival path: /usr/lib/R/site-library packages: littler Warning message: package ‘FactoMineR’ is not available (for R version 3.6.3)

ERROR: configuration failed for package ‘nloptr’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/nloptr’ Warning in install.packages : installation of package ‘nloptr’ had non-zero exit status * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Using PKG_CFLAGS= Using PKG_LIBS=-lcurl

> install.packages('nloptr', dependencies=TRUE) Installing package into ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6’ (as ‘lib’ is unspecified) trying URL 'https://cloud.r-project.org/src/contrib/nloptr_2.0.3.tar.gz' Content type 'application/x-gzip' length 2219877 bytes (2.1 MB) ================================================== downloaded 2.1 MB * installing *source* package ‘nloptr’ ... ** package ‘nloptr’ successfully unpacked and MD5 sums checked ** using staged installation 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 the compiler supports GNU C++... yes checking whether g++ -std=gnu++11 accepts -g... yes checking for g++ -std=gnu++11 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -std=gnu++11 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++11 accepts -g... (cached) yes checking for g++ -std=gnu++11 option to enable C++11 features... (cached) none needed checking for pkg-config... /usr/bin/pkg-config checking if pkg-config knows NLopt... no checking for cmake... /usr/bin/cmake using NLopt via local cmake build on x86_64 set CMAKE_BIN=/usr/bin/cmake set CC=gcc -std=gnu99 set CFLAGS= -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g set CXX=g++ set CXXFLAGS=-std=gnu++11 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g set LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro -- The C compiler identification is GNU 9.4.0 -- The CXX compiler identification is GNU 9.4.0 -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/g++ -- Check for working CXX compiler: /usr/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- NLopt version 2.7.1 -- Looking for getopt.h -- Looking for getopt.h - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for time.h -- Looking for time.h - found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for getpid -- Looking for getpid - found -- Looking for syscall -- Looking for syscall - found -- Looking for isinf -- Looking for isinf - found -- Looking for isnan -- Looking for isnan - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for qsort_r -- Looking for qsort_r - found -- Looking for time -- Looking for time - found -- Looking for copysign -- Looking for copysign - found -- Looking for getopt -- Looking for getopt - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of uint32_t -- Check size of uint32_t - done -- Check size of unsigned int -- Check size of unsigned int - done -- Check size of unsigned long -- Check size of unsigned long - done -- Looking for sqrt in m -- Looking for sqrt in m - found -- Looking for fpclassify -- Looking for fpclassify - TRUE -- Performing Test HAVE_THREAD_LOCAL_STORAGE -- Performing Test HAVE_THREAD_LOCAL_STORAGE - Success -- Performing Test HAVE_THREAD_LOCAL_STORAGE -- Performing Test HAVE_THREAD_LOCAL_STORAGE - Failed -- Looking for __cplusplus -- Looking for __cplusplus - found -- Performing Test SUPPORTS_STDCXX11 -- Performing Test SUPPORTS_STDCXX11 - Success -- Performing Test HAS_FPIC -- Performing Test HAS_FPIC - Success -- Configuring done -- Generating done -- Build files have been written to: /tmp/RtmpPXV2Sl/R.INSTALL69e9773c4681/nloptr/src/nlopt-build Scanning dependencies of target generate-cpp Scanning dependencies of target generate-fortran [ 3%] Generating nlopt.hpp [ 3%] Generating nlopt.f [ 3%] Built target generate-fortran [ 3%] Built target generate-cpp Scanning dependencies of target nlopt [ 7%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/direct_wrap.c.o [ 7%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/DIRect.c.o [ 9%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/DIRserial.c.o [ 11%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/DIRsubrout.c.o [ 13%] Building C object CMakeFiles/nlopt.dir/src/algs/cdirect/cdirect.c.o [ 15%] Building C object CMakeFiles/nlopt.dir/src/algs/cdirect/hybrid.c.o [ 17%] Building C object CMakeFiles/nlopt.dir/src/algs/praxis/praxis.c.o [ 19%] Building C object CMakeFiles/nlopt.dir/src/algs/luksan/plis.c.o [ 21%] Building C object CMakeFiles/nlopt.dir/src/algs/luksan/plip.c.o [ 23%] Building C 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50%] Building C object CMakeFiles/nlopt.dir/src/algs/slsqp/slsqp.c.o [ 52%] Building C object CMakeFiles/nlopt.dir/src/algs/esch/esch.c.o [ 54%] Building C object CMakeFiles/nlopt.dir/src/api/general.c.o [ 56%] Building C object CMakeFiles/nlopt.dir/src/api/options.c.o [ 58%] Building C object CMakeFiles/nlopt.dir/src/api/optimize.c.o [ 60%] Building C object CMakeFiles/nlopt.dir/src/api/deprecated.c.o [ 62%] Building C object CMakeFiles/nlopt.dir/src/api/f77api.c.o [ 64%] Building C object CMakeFiles/nlopt.dir/src/util/mt19937ar.c.o [ 66%] Building C object CMakeFiles/nlopt.dir/src/util/sobolseq.c.o [ 68%] Building C object CMakeFiles/nlopt.dir/src/util/timer.c.o [ 70%] Building C object CMakeFiles/nlopt.dir/src/util/stop.c.o [ 72%] Building C object CMakeFiles/nlopt.dir/src/util/redblack.c.o [ 74%] Building C object CMakeFiles/nlopt.dir/src/util/qsort_r.c.o [ 76%] Building C object CMakeFiles/nlopt.dir/src/util/rescale.c.o [ 78%] Building CXX object CMakeFiles/nlopt.dir/src/algs/stogo/global.cc.o [ 80%] Building CXX object CMakeFiles/nlopt.dir/src/algs/stogo/linalg.cc.o [ 82%] Building CXX object CMakeFiles/nlopt.dir/src/algs/stogo/local.cc.o [ 84%] Building CXX object CMakeFiles/nlopt.dir/src/algs/stogo/stogo.cc.o [ 86%] Building CXX object CMakeFiles/nlopt.dir/src/algs/stogo/tools.cc.o [ 88%] Building CXX object CMakeFiles/nlopt.dir/src/algs/ags/evolvent.cc.o [ 90%] Building CXX object CMakeFiles/nlopt.dir/src/algs/ags/solver.cc.o [ 92%] Building CXX object CMakeFiles/nlopt.dir/src/algs/ags/local_optimizer.cc.o [ 94%] Building CXX object CMakeFiles/nlopt.dir/src/algs/ags/ags.cc.o [ 96%] Linking CXX static library libnlopt.a [100%] Built target nlopt [ 1%] Built target generate-cpp [ 98%] Built target nlopt [100%] Built target generate-fortran Install the project... -- Install configuration: "Release" -- Installing: /tmp/RtmpPXV2Sl/R.INSTALL69e9773c4681/nloptr/src/nlopt/lib/pkgconfig/nlopt.pc -- Installing: /tmp/RtmpPXV2Sl/R.INSTALL69e9773c4681/nloptr/src/nlopt/include/nlopt.h -- Installing: /tmp/RtmpPXV2Sl/R.INSTALL69e9773c4681/nloptr/src/nlopt/include/nlopt.hpp -- Installing: /tmp/RtmpPXV2Sl/R.INSTALL69e9773c4681/nloptr/src/nlopt/include/nlopt.f -- Installing: /tmp/RtmpPXV2Sl/R.INSTALL69e9773c4681/nloptr/src/nlopt/lib/libnlopt.a -- Installing: /tmp/RtmpPXV2Sl/R.INSTALL69e9773c4681/nloptr/src/nlopt/lib/cmake/nlopt/NLoptLibraryDepends.cmake -- Installing: /tmp/RtmpPXV2Sl/R.INSTALL69e9773c4681/nloptr/src/nlopt/lib/cmake/nlopt/NLoptLibraryDepends-release.cmake -- Installing: /tmp/RtmpPXV2Sl/R.INSTALL69e9773c4681/nloptr/src/nlopt/lib/cmake/nlopt/NLoptConfig.cmake -- Installing: /tmp/RtmpPXV2Sl/R.INSTALL69e9773c4681/nloptr/src/nlopt/lib/cmake/nlopt/NLoptConfigVersion.cmake -- Installing: /tmp/RtmpPXV2Sl/R.INSTALL69e9773c4681/nloptr/src/nlopt/share/man/man3/nlopt.3 -- Installing: /tmp/RtmpPXV2Sl/R.INSTALL69e9773c4681/nloptr/src/nlopt/share/man/man3/nlopt_minimize.3 -- Installing: /tmp/RtmpPXV2Sl/R.INSTALL69e9773c4681/nloptr/src/nlopt/share/man/man3/nlopt_minimize_constrained.3 mv: cannot move 'nlopt/lib' to a subdirectory of itself, 'nlopt/lib/lib' configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/testthat/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init_nloptr.c -o init_nloptr.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/testthat/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nloptr.c -o nloptr.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/testthat/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c test-C-API.cpp -o test-C-API.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/testthat/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c test-runner.cpp -o test-runner.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o nloptr.so init_nloptr.o nloptr.o test-C-API.o test-runner.o -llapack -lblas -lgfortran -lm -lquadmath nlopt/lib/libnlopt.a -L/usr/lib/R/lib -lR installing to /home/galen/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-nloptr/00new/nloptr/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (nloptr) The downloaded source packages are in ‘/tmp/Rtmphl3PDx/downloaded_packages’

------------------ CMAKE NOT FOUND -------------------- CMake was not found on the PATH. Please install CMake: - sudo yum install cmake (Fedora/CentOS; inside a terminal) - sudo apt install cmake (Debian/Ubuntu; inside a terminal). - sudo pacman -S cmake (Arch Linux; inside a terminal). - sudo brew install cmake (MacOS; inside a terminal with Homebrew) - sudo port install cmake (MacOS; inside a terminal with MacPorts) Alternatively install CMake from: <https://cmake.org/>

------------------------- ANTICONF ERROR --------------------------- Configuration failed because libcurl was not found. Try installing: * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc) * rpm: libcurl-devel (Fedora, CentOS, RHEL) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

> install.packages('curl') Installing package into ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6’ (as ‘lib’ is unspecified) trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz' Content type 'application/x-gzip' length 670416 bytes (654 KB) ================================================== downloaded 654 KB * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu Using PKG_LIBS=-lcurl ** libs rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c callbacks.c -o callbacks.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c curl.c -o curl.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c download.c -o download.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c escape.c -o escape.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fetch.c -o fetch.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c form.c -o form.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getdate.c -o getdate.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c handle.c -o handle.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ieproxy.c -o ieproxy.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -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 -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c interrupt.c -o interrupt.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c multi.c -o multi.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nslookup.c -o nslookup.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reflist.c -o reflist.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c split.c -o split.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ssl.c -o ssl.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c typechecking.c -o typechecking.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -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 -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c version.c -o version.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c winidn.c -o winidn.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c writer.c -o writer.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl -L/usr/lib/R/lib -lR installing to /home/galen/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-curl/00new/curl/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (curl) The downloaded source packages are in ‘/tmp/Rtmphl3PDx/downloaded_packages’

> install.packages('lme4') Installing package into ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6’ (as ‘lib’ is unspecified) trying URL 'https://cloud.r-project.org/src/contrib/lme4_1.1-30.tar.gz' Content type 'application/x-gzip' length 3307884 bytes (3.2 MB) ================================================== downloaded 3.2 MB * installing *source* package ‘lme4’ ... ** package ‘lme4’ successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include" -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c external.cpp -o external.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include" -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c glmFamily.cpp -o glmFamily.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include" -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optimizer.cpp -o optimizer.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include" -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c predModule.cpp -o predModule.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include" -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c respModule.cpp -o respModule.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o lme4.so external.o glmFamily.o optimizer.o predModule.o respModule.o -L/usr/lib/R/lib -lR installing to /home/galen/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-lme4/00new/lme4/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (lme4) The downloaded source packages are in ‘/tmp/Rtmphl3PDx/downloaded_packages’

> library('lme4') Loading required package: Matrix Attaching package: ‘Matrix’ The following objects are masked from ‘package:tidyr’: expand, pack, unpack > library('Matrix') > library('lme4')

> install.packages("httr") Installing package into ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6’ (as ‘lib’ is unspecified) trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.4.tar.gz' Content type 'application/x-gzip' length 161140 bytes (157 KB) ================================================== downloaded 157 KB * installing *source* package ‘httr’ ... ** package ‘httr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (httr) The downloaded source packages are in ‘/tmp/RtmpW7Z30M/downloaded_packages’

> source("DifferentialExpressionFunctions.R") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.10 (BiocManager 1.30.18), R 3.6.3 (2020-02-29) Installing package(s) 'DESeq2' Warning: dependency ‘locfit’ is not available trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DESeq2_1.26.0.tar.gz' Content type 'application/octet-stream' length 2060061 bytes (2.0 MB) ================================================== downloaded 2.0 MB ERROR: dependency ‘locfit’ is not available for package ‘DESeq2’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’ The downloaded source packages are in ‘/tmp/RtmpW7Z30M/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: boot, class, cluster, codetools, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival path: /usr/lib/R/site-library packages: backports, BH, bit, bit64, bitops, blob, brew, callr, car, carData, cli, cliapp, clipr, colorspace, commonmark, covr, crayon, crosstalk, curl, data.table, DBI, DBItest, desc, devtools, diffobj, digest, doMC, dplyr, DT, ellipse, ellipsis, evaluate, fansi, farver, fastmap, filehash, forcats, foreach, fs, future, gdtools, generics, ggplot2, ggrepel, gh, git2r, globals, glue, gtable, haven, hexbin, highr, hms, htmltools, htmlwidgets, httpuv, httr, iterators, jsonlite, knitr, labeling, later, lifecycle, littler, lme4, lubridate, magrittr, mapproj, maps, maptools, MatrixModels, memoise, mime, mockery, mockr, nloptr, openssl, openxlsx, pbkrtest, pillar, pkgbuild, pkgKitten, pkgload, plyr, processx, promises, ps, purrr, quantreg, R.methodsS3, R.oo, R6, rcmdcheck, RColorBrewer, Rcpp, RcppEigen, readr, readxl, remotes, reshape2, rex, rio, rlang, rmarkdown, roxygen2, rprojroot, RSQLite, rstudioapi, rversions, scales, scatterplot3d, sessioninfo, shiny, sodium, sp, SparseM, stringi, stringr, sys, systemfonts, testit, testthat, tibble, tidyselect, tikzDevice, tinytex, usethis, utf8, vctrs, vdiffr, viridisLite, webutils, withr, xfun, xml2, yaml, zip 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.10 (BiocManager 1.30.18), R 3.6.3 (2020-02-29) Installing package(s) 'DEGreport' Warning: dependencies ‘lasso2’, ‘locfit’, ‘rjson’ are not available also installing the dependencies ‘GetoptLong’, ‘ComplexHeatmap’, ‘DESeq2’, ‘edgeR’ trying URL 'https://cloud.r-project.org/src/contrib/GetoptLong_1.0.5.tar.gz' Content type 'application/x-gzip' length 767681 bytes (749 KB) ================================================== downloaded 749 KB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/ComplexHeatmap_2.2.0.tar.gz' Content type 'application/octet-stream' length 1371868 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DESeq2_1.26.0.tar.gz' Content type 'application/octet-stream' length 2060061 bytes (2.0 MB) ================================================== downloaded 2.0 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/edgeR_3.28.1.tar.gz' Content type 'application/octet-stream' length 1481788 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DEGreport_1.22.0.tar.gz' Content type 'application/octet-stream' length 20151878 bytes (19.2 MB) ================================================== downloaded 19.2 MB ERROR: dependency ‘rjson’ is not available for package ‘GetoptLong’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/GetoptLong’ ERROR: dependency ‘locfit’ is not available for package ‘DESeq2’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’ ERROR: dependency ‘locfit’ is not available for package ‘edgeR’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/edgeR’ ERROR: dependency ‘GetoptLong’ is not available for package ‘ComplexHeatmap’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/ComplexHeatmap’ ERROR: dependencies ‘ComplexHeatmap’, ‘DESeq2’, ‘edgeR’, ‘lasso2’ are not available for package ‘DEGreport’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.6/DEGreport’ The downloaded source packages are in ‘/tmp/RtmpW7Z30M/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: boot, class, cluster, codetools, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival path: /usr/lib/R/site-library packages: backports, BH, bit, bit64, bitops, blob, brew, callr, car, carData, cli, cliapp, clipr, colorspace, commonmark, covr, crayon, crosstalk, curl, data.table, DBI, DBItest, desc, devtools, diffobj, digest, doMC, dplyr, DT, ellipse, ellipsis, evaluate, fansi, farver, fastmap, filehash, forcats, foreach, fs, future, gdtools, generics, ggplot2, ggrepel, gh, git2r, globals, glue, gtable, haven, hexbin, highr, hms, htmltools, htmlwidgets, httpuv, httr, iterators, jsonlite, knitr, labeling, later, lifecycle, littler, lme4, lubridate, magrittr, mapproj, maps, maptools, MatrixModels, memoise, mime, mockery, mockr, nloptr, openssl, openxlsx, pbkrtest, pillar, pkgbuild, pkgKitten, pkgload, plyr, processx, promises, ps, purrr, quantreg, R.methodsS3, R.oo, R6, rcmdcheck, RColorBrewer, Rcpp, RcppEigen, readr, readxl, remotes, reshape2, rex, rio, rlang, rmarkdown, roxygen2, rprojroot, RSQLite, rstudioapi, rversions, scales, scatterplot3d, sessioninfo, shiny, sodium, sp, SparseM, stringi, stringr, sys, systemfonts, testit, testthat, tibble, tidyselect, tikzDevice, tinytex, usethis, utf8, vctrs, vdiffr, viridisLite, webutils, withr, xfun, xml2, yaml, zip Loading required package: ggplot2 Attaching package: ‘gplots’ The following object is masked from ‘package:stats’: lowess Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa ── Attaching packages ──────────────────────────── tidyverse 1.3.2 ── ✔ tibble 3.1.8 ✔ dplyr 1.0.10 ✔ tidyr 1.2.1 ✔ stringr 1.4.1 ✔ readr 2.1.3 ✔ forcats 0.5.2 ✔ purrr 0.3.5 ── Conflicts ─────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() Error in library(package, character.only = TRUE) : there is no package called ‘DESeq2’ In addition: Warning messages: 1: In install.packages(...) : installation of package ‘DESeq2’ had non-zero exit status 2: In install.packages(...) : installation of package ‘GetoptLong’ had non-zero exit status 3: In install.packages(...) : installation of package ‘DESeq2’ had non-zero exit status 4: In install.packages(...) : installation of package ‘edgeR’ had non-zero exit status 5: In install.packages(...) : installation of package ‘ComplexHeatmap’ had non-zero exit status 6: In install.packages(...) : installation of package ‘DEGreport’ had non-zero exit status

> source("DifferentialExpressionFunctions.R") Installing packages into ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1’ (as ‘lib’ is unspecified) also installing the dependencies ‘nloptr’, ‘pbkrtest’, ‘lme4’, ‘car’, ‘rstatix’, ‘gargle’, ‘curl’, ‘FactoMineR’, ‘ggpubr’, ‘googledrive’, ‘googlesheets4’, ‘httr’, ‘rvest’, ‘xml2’ trying URL 'https://cloud.r-project.org/src/contrib/nloptr_2.0.3.tar.gz' Content type 'application/x-gzip' length 2219877 bytes (2.1 MB) ================================================== downloaded 2.1 MB trying URL 'https://cloud.r-project.org/src/contrib/pbkrtest_0.5.1.tar.gz' Content type 'application/x-gzip' length 246327 bytes (240 KB) ================================================== downloaded 240 KB trying URL 'https://cloud.r-project.org/src/contrib/lme4_1.1-30.tar.gz' Content type 'application/x-gzip' length 3307884 bytes (3.2 MB) ================================================== downloaded 3.2 MB trying URL 'https://cloud.r-project.org/src/contrib/car_3.1-0.tar.gz' Content type 'application/x-gzip' length 569914 bytes (556 KB) ================================================== downloaded 556 KB trying URL 'https://cloud.r-project.org/src/contrib/rstatix_0.7.0.tar.gz' Content type 'application/x-gzip' length 402481 bytes (393 KB) ================================================== downloaded 393 KB trying URL 'https://cloud.r-project.org/src/contrib/gargle_1.2.1.tar.gz' Content type 'application/x-gzip' length 312943 bytes (305 KB) ================================================== downloaded 305 KB trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz' Content type 'application/x-gzip' length 670416 bytes (654 KB) ================================================== downloaded 654 KB trying URL 'https://cloud.r-project.org/src/contrib/FactoMineR_2.6.tar.gz' Content type 'application/x-gzip' length 2831505 bytes (2.7 MB) ================================================== downloaded 2.7 MB trying URL 'https://cloud.r-project.org/src/contrib/ggpubr_0.4.0.tar.gz' Content type 'application/x-gzip' length 2689307 bytes (2.6 MB) ================================================== downloaded 2.6 MB trying URL 'https://cloud.r-project.org/src/contrib/googledrive_2.0.0.tar.gz' Content type 'application/x-gzip' length 1593656 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://cloud.r-project.org/src/contrib/googlesheets4_1.0.1.tar.gz' Content type 'application/x-gzip' length 223314 bytes (218 KB) ================================================== downloaded 218 KB trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.4.tar.gz' Content type 'application/x-gzip' length 161140 bytes (157 KB) ================================================== downloaded 157 KB trying URL 'https://cloud.r-project.org/src/contrib/rvest_1.0.3.tar.gz' Content type 'application/x-gzip' length 94659 bytes (92 KB) ================================================== downloaded 92 KB trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.3.3.tar.gz' Content type 'application/x-gzip' length 283965 bytes (277 KB) ================================================== downloaded 277 KB trying URL 'https://cloud.r-project.org/src/contrib/factoextra_1.0.7.tar.gz' Content type 'application/x-gzip' length 1386480 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.3.2.tar.gz' Content type 'application/x-gzip' length 702514 bytes (686 KB) ================================================== downloaded 686 KB * installing *source* package ‘nloptr’ ... ** package ‘nloptr’ successfully unpacked and MD5 sums checked ** using staged installation 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 the compiler supports GNU C++... yes checking whether g++ -std=gnu++14 accepts -g... yes checking for g++ -std=gnu++14 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -std=gnu++14 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++14 accepts -g... (cached) yes checking for g++ -std=gnu++14 option to enable C++11 features... (cached) none needed checking for pkg-config... /usr/bin/pkg-config checking if pkg-config knows NLopt... no checking for cmake... no ------------------ CMAKE NOT FOUND -------------------- CMake was not found on the PATH. Please install CMake: - sudo yum install cmake (Fedora/CentOS; inside a terminal) - sudo apt install cmake (Debian/Ubuntu; inside a terminal). - sudo pacman -S cmake (Arch Linux; inside a terminal). - sudo brew install cmake (MacOS; inside a terminal with Homebrew) - sudo port install cmake (MacOS; inside a terminal with MacPorts) Alternatively install CMake from: <https://cmake.org/> ------------------------------------------------------- ERROR: configuration failed for package ‘nloptr’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/nloptr’ Warning in install.packages : installation of package ‘nloptr’ had non-zero exit status * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Using PKG_CFLAGS= Using PKG_LIBS=-lcurl ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libcurl was not found. Try installing: * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc) * rpm: libcurl-devel (Fedora, CentOS, RHEL) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------------------------------------------------- ERROR: configuration failed for package ‘curl’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/curl’ Warning in install.packages : installation of package ‘curl’ had non-zero exit status * installing *source* package ‘xml2’ ... ** package ‘xml2’ successfully unpacked and MD5 sums checked ** using staged installation Package libxml-2.0 was not found in the pkg-config search path. Perhaps you should add the directory containing `libxml-2.0.pc' to the PKG_CONFIG_PATH environment variable No package 'libxml-2.0' found Package libxml-2.0 was not found in the pkg-config search path. Perhaps you should add the directory containing `libxml-2.0.pc' to the PKG_CONFIG_PATH environment variable No package 'libxml-2.0' found Using PKG_CFLAGS= Using PKG_LIBS=-lxml2 ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libxml-2.0 was not found. Try installing: * deb: libxml2-dev (Debian, Ubuntu, etc) * rpm: libxml2-devel (Fedora, CentOS, RHEL) * csw: libxml2_dev (Solaris) If libxml-2.0 is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------------------------------------------------- ERROR: configuration failed for package ‘xml2’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/xml2’ Warning in install.packages : installation of package ‘xml2’ had non-zero exit status ERROR: dependency ‘nloptr’ is not available for package ‘lme4’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/lme4’ Warning in install.packages : installation of package ‘lme4’ had non-zero exit status ERROR: dependency ‘curl’ is not available for package ‘httr’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/httr’ Warning in install.packages : installation of package ‘httr’ had non-zero exit status ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/pbkrtest’ Warning in install.packages : installation of package ‘pbkrtest’ had non-zero exit status ERROR: dependency ‘httr’ is not available for package ‘gargle’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/gargle’ Warning in install.packages : installation of package ‘gargle’ had non-zero exit status ERROR: dependencies ‘httr’, ‘xml2’ are not available for package ‘rvest’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/rvest’ Warning in install.packages : installation of package ‘rvest’ had non-zero exit status ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/car’ Warning in install.packages : installation of package ‘car’ had non-zero exit status ERROR: dependencies ‘gargle’, ‘httr’ are not available for package ‘googledrive’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/googledrive’ Warning in install.packages : installation of package ‘googledrive’ had non-zero exit status ERROR: dependency ‘car’ is not available for package ‘rstatix’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/rstatix’ Warning in install.packages : installation of package ‘rstatix’ had non-zero exit status ERROR: dependency ‘car’ is not available for package ‘FactoMineR’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/FactoMineR’ Warning in install.packages : installation of package ‘FactoMineR’ had non-zero exit status ERROR: dependencies ‘curl’, ‘gargle’, ‘googledrive’, ‘httr’ are not available for package ‘googlesheets4’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/googlesheets4’ Warning in install.packages : installation of package ‘googlesheets4’ had non-zero exit status ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/ggpubr’ Warning in install.packages : installation of package ‘ggpubr’ had non-zero exit status ERROR: dependencies ‘googledrive’, ‘googlesheets4’, ‘httr’, ‘rvest’, ‘xml2’ are not available for package ‘tidyverse’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/tidyverse’ Warning in install.packages : installation of package ‘tidyverse’ had non-zero exit status ERROR: dependencies ‘FactoMineR’, ‘ggpubr’ are not available for package ‘factoextra’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/factoextra’ Warning in install.packages : installation of package ‘factoextra’ had non-zero exit status The downloaded source packages are in ‘/tmp/RtmpSFb6Sy/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01) Installing package(s) 'DESeq2' also installing the dependencies ‘Biostrings’, ‘curl’, ‘RCurl’, ‘KEGGREST’, ‘XML’, ‘httr’, ‘GenomeInfoDb’, ‘AnnotationDbi’, ‘annotate’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Biostrings_2.62.0.tar.gz' Content type 'application/octet-stream' length 12645827 bytes (12.1 MB) ================================================== downloaded 12.1 MB trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz' Content type 'application/x-gzip' length 670416 bytes (654 KB) ================================================== downloaded 654 KB trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.9.tar.gz' Content type 'application/x-gzip' length 731611 bytes (714 KB) ================================================== downloaded 714 KB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/KEGGREST_1.34.0.tar.gz' Content type 'application/octet-stream' length 25778 bytes (25 KB) ================================================== downloaded 25 KB trying URL 'https://cloud.r-project.org/src/contrib/XML_3.99-0.11.tar.gz' Content type 'application/x-gzip' length 970681 bytes (947 KB) ================================================== downloaded 947 KB trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.4.tar.gz' Content type 'application/x-gzip' length 161140 bytes (157 KB) ================================================== downloaded 157 KB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomeInfoDb_1.30.1.tar.gz' Content type 'application/octet-stream' length 3457147 bytes (3.3 MB) ================================================== downloaded 3.3 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/AnnotationDbi_1.56.2.tar.gz' Content type 'application/octet-stream' length 4330396 bytes (4.1 MB) ================================================== downloaded 4.1 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/annotate_1.72.0.tar.gz' Content type 'application/octet-stream' length 1723060 bytes (1.6 MB) ================================================== downloaded 1.6 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomicRanges_1.46.1.tar.gz' Content type 'application/octet-stream' length 1171939 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/SummarizedExperiment_1.24.0.tar.gz' Content type 'application/octet-stream' length 1524667 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/genefilter_1.76.0.tar.gz' Content type 'application/octet-stream' length 807639 bytes (788 KB) ================================================== downloaded 788 KB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/geneplotter_1.72.0.tar.gz' Content type 'application/octet-stream' length 1437803 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DESeq2_1.34.0.tar.gz' Content type 'application/octet-stream' length 2088431 bytes (2.0 MB) ================================================== downloaded 2.0 MB * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Using PKG_CFLAGS= Using PKG_LIBS=-lcurl ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libcurl was not found. Try installing: * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc) * rpm: libcurl-devel (Fedora, CentOS, RHEL) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------------------------------------------------- ERROR: configuration failed for package ‘curl’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/curl’ * installing *source* package ‘RCurl’ ... ** package ‘RCurl’ successfully unpacked and MD5 sums checked ** using staged installation checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ‘RCurl’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/RCurl’ * installing *source* package ‘XML’ ... ** package ‘XML’ successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package ‘XML’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/XML’ ERROR: dependency ‘curl’ is not available for package ‘httr’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/httr’ ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/GenomeInfoDb’ ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘Biostrings’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/Biostrings’ ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/GenomicRanges’ ERROR: dependencies ‘httr’, ‘Biostrings’ are not available for package ‘KEGGREST’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/KEGGREST’ ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/SummarizedExperiment’ ERROR: dependency ‘KEGGREST’ is not available for package ‘AnnotationDbi’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/AnnotationDbi’ ERROR: dependencies ‘AnnotationDbi’, ‘XML’, ‘httr’ are not available for package ‘annotate’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/annotate’ ERROR: dependencies ‘AnnotationDbi’, ‘annotate’ are not available for package ‘genefilter’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/genefilter’ ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘geneplotter’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/geneplotter’ ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/DESeq2’ The downloaded source packages are in ‘/tmp/RtmpSFb6Sy/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: cluster, foreign, MASS, Matrix, mgcv, nlme, nnet, survival 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01) Installing package(s) 'DEGreport' Warning: dependency ‘lasso2’ is not available also installing the dependencies ‘Biostrings’, ‘curl’, ‘KEGGREST’, ‘XML’, ‘httr’, ‘AnnotationDbi’, ‘annotate’, ‘RCurl’, ‘GenomicRanges’, ‘genefilter’, ‘geneplotter’, ‘GenomeInfoDb’, ‘DESeq2’, ‘SummarizedExperiment’ trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Biostrings_2.62.0.tar.gz' Content type 'application/octet-stream' length 12645827 bytes (12.1 MB) ================================================== downloaded 12.1 MB trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz' Content type 'application/x-gzip' length 670416 bytes (654 KB) ================================================== downloaded 654 KB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/KEGGREST_1.34.0.tar.gz' Content type 'application/octet-stream' length 25778 bytes (25 KB) ================================================== downloaded 25 KB trying URL 'https://cloud.r-project.org/src/contrib/XML_3.99-0.11.tar.gz' Content type 'application/x-gzip' length 970681 bytes (947 KB) ================================================== downloaded 947 KB trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.4.tar.gz' Content type 'application/x-gzip' length 161140 bytes (157 KB) ================================================== downloaded 157 KB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/AnnotationDbi_1.56.2.tar.gz' Content type 'application/octet-stream' length 4330396 bytes (4.1 MB) ================================================== downloaded 4.1 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/annotate_1.72.0.tar.gz' Content type 'application/octet-stream' length 1723060 bytes (1.6 MB) ================================================== downloaded 1.6 MB trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.9.tar.gz' Content type 'application/x-gzip' length 731611 bytes (714 KB) ================================================== downloaded 714 KB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomicRanges_1.46.1.tar.gz' Content type 'application/octet-stream' length 1171939 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/genefilter_1.76.0.tar.gz' Content type 'application/octet-stream' length 807639 bytes (788 KB) ================================================== downloaded 788 KB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/geneplotter_1.72.0.tar.gz' Content type 'application/octet-stream' length 1437803 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomeInfoDb_1.30.1.tar.gz' Content type 'application/octet-stream' length 3457147 bytes (3.3 MB) ================================================== downloaded 3.3 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DESeq2_1.34.0.tar.gz' Content type 'application/octet-stream' length 2088431 bytes (2.0 MB) ================================================== downloaded 2.0 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/SummarizedExperiment_1.24.0.tar.gz' Content type 'application/octet-stream' length 1524667 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DEGreport_1.30.3.tar.gz' Content type 'application/octet-stream' length 20097260 bytes (19.2 MB) ================================================== downloaded 19.2 MB * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Using PKG_CFLAGS= Using PKG_LIBS=-lcurl ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libcurl was not found. Try installing: * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc) * rpm: libcurl-devel (Fedora, CentOS, RHEL) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------------------------------------------------- ERROR: configuration failed for package ‘curl’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/curl’ * installing *source* package ‘XML’ ... ** package ‘XML’ successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package ‘XML’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/XML’ * installing *source* package ‘RCurl’ ... ** package ‘RCurl’ successfully unpacked and MD5 sums checked ** using staged installation checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ‘RCurl’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/RCurl’ ERROR: dependency ‘curl’ is not available for package ‘httr’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/httr’ ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/GenomeInfoDb’ ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘Biostrings’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/Biostrings’ ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/GenomicRanges’ ERROR: dependencies ‘httr’, ‘Biostrings’ are not available for package ‘KEGGREST’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/KEGGREST’ ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/SummarizedExperiment’ ERROR: dependency ‘KEGGREST’ is not available for package ‘AnnotationDbi’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/AnnotationDbi’ ERROR: dependencies ‘AnnotationDbi’, ‘XML’, ‘httr’ are not available for package ‘annotate’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/annotate’ ERROR: dependencies ‘AnnotationDbi’, ‘annotate’ are not available for package ‘genefilter’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/genefilter’ ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘geneplotter’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/geneplotter’ ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/DESeq2’ ERROR: dependencies ‘DESeq2’, ‘lasso2’, ‘SummarizedExperiment’ are not available for package ‘DEGreport’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/DEGreport’ The downloaded source packages are in ‘/tmp/RtmpSFb6Sy/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: cluster, foreign, MASS, Matrix, mgcv, nlme, nnet, survival 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01) Installing package(s) 'pathview' also installing the dependencies ‘curl’, ‘GenomeInfoDb’, ‘RCurl’, ‘httr’, ‘Biostrings’, ‘KEGGgraph’, ‘XML’, ‘AnnotationDbi’, ‘org.Hs.eg.db’, ‘KEGGREST’ trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz' Content type 'application/x-gzip' length 670416 bytes (654 KB) ================================================== downloaded 654 KB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomeInfoDb_1.30.1.tar.gz' Content type 'application/octet-stream' length 3457147 bytes (3.3 MB) ================================================== downloaded 3.3 MB trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.9.tar.gz' Content type 'application/x-gzip' length 731611 bytes (714 KB) ================================================== downloaded 714 KB trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.4.tar.gz' Content type 'application/x-gzip' length 161140 bytes (157 KB) ================================================== downloaded 157 KB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Biostrings_2.62.0.tar.gz' Content type 'application/octet-stream' length 12645827 bytes (12.1 MB) ================================================== downloaded 12.1 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/KEGGgraph_1.54.0.tar.gz' Content type 'application/octet-stream' length 1462164 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://cloud.r-project.org/src/contrib/XML_3.99-0.11.tar.gz' Content type 'application/x-gzip' length 970681 bytes (947 KB) ================================================== downloaded 947 KB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/AnnotationDbi_1.56.2.tar.gz' Content type 'application/octet-stream' length 4330396 bytes (4.1 MB) ================================================== downloaded 4.1 MB trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/org.Hs.eg.db_3.14.0.tar.gz' Content type 'application/octet-stream' length 82195112 bytes (78.4 MB) ================================================== downloaded 78.4 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/KEGGREST_1.34.0.tar.gz' Content type 'application/octet-stream' length 25778 bytes (25 KB) ================================================== downloaded 25 KB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/pathview_1.34.0.tar.gz' Content type 'application/octet-stream' length 2254509 bytes (2.2 MB) ================================================== downloaded 2.2 MB * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Using PKG_CFLAGS= Using PKG_LIBS=-lcurl ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libcurl was not found. Try installing: * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc) * rpm: libcurl-devel (Fedora, CentOS, RHEL) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------------------------------------------------- ERROR: configuration failed for package ‘curl’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/curl’ * installing *source* package ‘RCurl’ ... ** package ‘RCurl’ successfully unpacked and MD5 sums checked ** using staged installation checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ‘RCurl’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/RCurl’ * installing *source* package ‘XML’ ... ** package ‘XML’ successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package ‘XML’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/XML’ ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/GenomeInfoDb’ ERROR: dependency ‘curl’ is not available for package ‘httr’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/httr’ ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘KEGGgraph’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/KEGGgraph’ ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘Biostrings’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/Biostrings’ ERROR: dependencies ‘httr’, ‘Biostrings’ are not available for package ‘KEGGREST’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/KEGGREST’ ERROR: dependency ‘KEGGREST’ is not available for package ‘AnnotationDbi’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/AnnotationDbi’ ERROR: dependency ‘AnnotationDbi’ is not available for package ‘org.Hs.eg.db’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/org.Hs.eg.db’ ERROR: dependencies ‘KEGGgraph’, ‘XML’, ‘AnnotationDbi’, ‘org.Hs.eg.db’, ‘KEGGREST’ are not available for package ‘pathview’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/pathview’ The downloaded source packages are in ‘/tmp/RtmpSFb6Sy/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: cluster, foreign, MASS, Matrix, mgcv, nlme, nnet, survival Error in library(package, character.only = TRUE) : there is no package called ‘factoextra’ In addition: There were 40 warnings (use warnings() to see them)

Okay, fresh Linux install. Version of R is 4.1.2. Here is the stdout of running source(DifferentialExpressionFunctions.R).

> source("DifferentialExpressionFunctions.R")
Installing packages into ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
also installing the dependencies ‘nloptr’, ‘pbkrtest’, ‘lme4’, ‘car’, ‘rstatix’, ‘gargle’, ‘curl’, ‘FactoMineR’, ‘ggpubr’, ‘googledrive’, ‘googlesheets4’, ‘httr’, ‘rvest’, ‘xml2’

trying URL 'https://cloud.r-project.org/src/contrib/nloptr_2.0.3.tar.gz'
Content type 'application/x-gzip' length 2219877 bytes (2.1 MB)
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downloaded 2.1 MB

trying URL 'https://cloud.r-project.org/src/contrib/pbkrtest_0.5.1.tar.gz'
Content type 'application/x-gzip' length 246327 bytes (240 KB)
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downloaded 240 KB

trying URL 'https://cloud.r-project.org/src/contrib/lme4_1.1-30.tar.gz'
Content type 'application/x-gzip' length 3307884 bytes (3.2 MB)
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downloaded 3.2 MB

trying URL 'https://cloud.r-project.org/src/contrib/car_3.1-0.tar.gz'
Content type 'application/x-gzip' length 569914 bytes (556 KB)
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downloaded 556 KB

trying URL 'https://cloud.r-project.org/src/contrib/rstatix_0.7.0.tar.gz'
Content type 'application/x-gzip' length 402481 bytes (393 KB)
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downloaded 393 KB

trying URL 'https://cloud.r-project.org/src/contrib/gargle_1.2.1.tar.gz'
Content type 'application/x-gzip' length 312943 bytes (305 KB)
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downloaded 305 KB

trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz'
Content type 'application/x-gzip' length 670416 bytes (654 KB)
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downloaded 654 KB

trying URL 'https://cloud.r-project.org/src/contrib/FactoMineR_2.6.tar.gz'
Content type 'application/x-gzip' length 2831505 bytes (2.7 MB)
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downloaded 2.7 MB

trying URL 'https://cloud.r-project.org/src/contrib/ggpubr_0.4.0.tar.gz'
Content type 'application/x-gzip' length 2689307 bytes (2.6 MB)
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downloaded 2.6 MB

trying URL 'https://cloud.r-project.org/src/contrib/googledrive_2.0.0.tar.gz'
Content type 'application/x-gzip' length 1593656 bytes (1.5 MB)
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downloaded 1.5 MB

trying URL 'https://cloud.r-project.org/src/contrib/googlesheets4_1.0.1.tar.gz'
Content type 'application/x-gzip' length 223314 bytes (218 KB)
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downloaded 218 KB

trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.4.tar.gz'
Content type 'application/x-gzip' length 161140 bytes (157 KB)
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downloaded 157 KB

trying URL 'https://cloud.r-project.org/src/contrib/rvest_1.0.3.tar.gz'
Content type 'application/x-gzip' length 94659 bytes (92 KB)
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downloaded 92 KB

trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.3.3.tar.gz'
Content type 'application/x-gzip' length 283965 bytes (277 KB)
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downloaded 277 KB

trying URL 'https://cloud.r-project.org/src/contrib/factoextra_1.0.7.tar.gz'
Content type 'application/x-gzip' length 1386480 bytes (1.3 MB)
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downloaded 1.3 MB

trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.3.2.tar.gz'
Content type 'application/x-gzip' length 702514 bytes (686 KB)
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downloaded 686 KB

* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
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 the compiler supports GNU C++... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking for g++ -std=gnu++14 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++14 accepts -g... (cached) yes
checking for g++ -std=gnu++14 option to enable C++11 features... (cached) none needed
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows NLopt... no
checking for cmake... no

------------------ CMAKE NOT FOUND --------------------

CMake was not found on the PATH. Please install CMake:

 - sudo yum install cmake          (Fedora/CentOS; inside a terminal)
 - sudo apt install cmake          (Debian/Ubuntu; inside a terminal).
 - sudo pacman -S cmake            (Arch Linux; inside a terminal).
 - sudo brew install cmake         (MacOS; inside a terminal with Homebrew)
 - sudo port install cmake         (MacOS; inside a terminal with MacPorts)

Alternatively install CMake from: <https://cmake.org/>

-------------------------------------------------------

ERROR: configuration failed for package ‘nloptr’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/nloptr’
Warning in install.packages :
  installation of package ‘nloptr’ had non-zero exit status
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/curl’
Warning in install.packages :
  installation of package ‘curl’ had non-zero exit status
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
** using staged installation
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lxml2
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
 * deb: libxml2-dev (Debian, Ubuntu, etc)
 * rpm: libxml2-devel (Fedora, CentOS, RHEL)
 * csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘xml2’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/xml2’
Warning in install.packages :
  installation of package ‘xml2’ had non-zero exit status
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/lme4’
Warning in install.packages :
  installation of package ‘lme4’ had non-zero exit status
ERROR: dependency ‘curl’ is not available for package ‘httr’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/httr’
Warning in install.packages :
  installation of package ‘httr’ had non-zero exit status
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/pbkrtest’
Warning in install.packages :
  installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependency ‘httr’ is not available for package ‘gargle’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/gargle’
Warning in install.packages :
  installation of package ‘gargle’ had non-zero exit status
ERROR: dependencies ‘httr’, ‘xml2’ are not available for package ‘rvest’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/rvest’
Warning in install.packages :
  installation of package ‘rvest’ had non-zero exit status
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/car’
Warning in install.packages :
  installation of package ‘car’ had non-zero exit status
ERROR: dependencies ‘gargle’, ‘httr’ are not available for package ‘googledrive’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/googledrive’
Warning in install.packages :
  installation of package ‘googledrive’ had non-zero exit status
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/rstatix’
Warning in install.packages :
  installation of package ‘rstatix’ had non-zero exit status
ERROR: dependency ‘car’ is not available for package ‘FactoMineR’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/FactoMineR’
Warning in install.packages :
  installation of package ‘FactoMineR’ had non-zero exit status
ERROR: dependencies ‘curl’, ‘gargle’, ‘googledrive’, ‘httr’ are not available for package ‘googlesheets4’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/googlesheets4’
Warning in install.packages :
  installation of package ‘googlesheets4’ had non-zero exit status
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/ggpubr’
Warning in install.packages :
  installation of package ‘ggpubr’ had non-zero exit status
ERROR: dependencies ‘googledrive’, ‘googlesheets4’, ‘httr’, ‘rvest’, ‘xml2’ are not available for package ‘tidyverse’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/tidyverse’
Warning in install.packages :
  installation of package ‘tidyverse’ had non-zero exit status
ERROR: dependencies ‘FactoMineR’, ‘ggpubr’ are not available for package ‘factoextra’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/factoextra’
Warning in install.packages :
  installation of package ‘factoextra’ had non-zero exit status

The downloaded source packages are in
  ‘/tmp/RtmpSFb6Sy/downloaded_packages’
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
Installing package(s) 'DESeq2'
also installing the dependencies ‘Biostrings’, ‘curl’, ‘RCurl’, ‘KEGGREST’, ‘XML’, ‘httr’, ‘GenomeInfoDb’, ‘AnnotationDbi’, ‘annotate’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Biostrings_2.62.0.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.9.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/KEGGREST_1.34.0.tar.gz'
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Content type 'application/x-gzip' length 970681 bytes (947 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.4.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomeInfoDb_1.30.1.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/AnnotationDbi_1.56.2.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/annotate_1.72.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomicRanges_1.46.1.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/SummarizedExperiment_1.24.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/genefilter_1.76.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/geneplotter_1.72.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DESeq2_1.34.0.tar.gz'
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* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/curl’
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/RCurl’
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/XML’
ERROR: dependency ‘curl’ is not available for package ‘httr’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/httr’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/GenomeInfoDb’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘Biostrings’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/Biostrings’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/GenomicRanges’
ERROR: dependencies ‘httr’, ‘Biostrings’ are not available for package ‘KEGGREST’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/KEGGREST’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/SummarizedExperiment’
ERROR: dependency ‘KEGGREST’ is not available for package ‘AnnotationDbi’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/AnnotationDbi’
ERROR: dependencies ‘AnnotationDbi’, ‘XML’, ‘httr’ are not available for package ‘annotate’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/annotate’
ERROR: dependencies ‘AnnotationDbi’, ‘annotate’ are not available for package ‘genefilter’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/genefilter’
ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘geneplotter’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/geneplotter’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/DESeq2’

The downloaded source packages are in
  ‘/tmp/RtmpSFb6Sy/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    cluster, foreign, MASS, Matrix, mgcv, nlme, nnet, survival
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
Installing package(s) 'DEGreport'
Warning: dependency ‘lasso2’ is not available
also installing the dependencies ‘Biostrings’, ‘curl’, ‘KEGGREST’, ‘XML’, ‘httr’, ‘AnnotationDbi’, ‘annotate’, ‘RCurl’, ‘GenomicRanges’, ‘genefilter’, ‘geneplotter’, ‘GenomeInfoDb’, ‘DESeq2’, ‘SummarizedExperiment’

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Biostrings_2.62.0.tar.gz'
Content type 'application/octet-stream' length 12645827 bytes (12.1 MB)
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downloaded 12.1 MB

trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz'
Content type 'application/x-gzip' length 670416 bytes (654 KB)
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/KEGGREST_1.34.0.tar.gz'
Content type 'application/octet-stream' length 25778 bytes (25 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/XML_3.99-0.11.tar.gz'
Content type 'application/x-gzip' length 970681 bytes (947 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.4.tar.gz'
Content type 'application/x-gzip' length 161140 bytes (157 KB)
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/AnnotationDbi_1.56.2.tar.gz'
Content type 'application/octet-stream' length 4330396 bytes (4.1 MB)
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/annotate_1.72.0.tar.gz'
Content type 'application/octet-stream' length 1723060 bytes (1.6 MB)
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trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.9.tar.gz'
Content type 'application/x-gzip' length 731611 bytes (714 KB)
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomicRanges_1.46.1.tar.gz'
Content type 'application/octet-stream' length 1171939 bytes (1.1 MB)
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downloaded 1.1 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/genefilter_1.76.0.tar.gz'
Content type 'application/octet-stream' length 807639 bytes (788 KB)
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/geneplotter_1.72.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomeInfoDb_1.30.1.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DESeq2_1.34.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/SummarizedExperiment_1.24.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DEGreport_1.30.3.tar.gz'
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* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/curl’
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/XML’
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/RCurl’
ERROR: dependency ‘curl’ is not available for package ‘httr’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/httr’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/GenomeInfoDb’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘Biostrings’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/Biostrings’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/GenomicRanges’
ERROR: dependencies ‘httr’, ‘Biostrings’ are not available for package ‘KEGGREST’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/KEGGREST’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/SummarizedExperiment’
ERROR: dependency ‘KEGGREST’ is not available for package ‘AnnotationDbi’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/AnnotationDbi’
ERROR: dependencies ‘AnnotationDbi’, ‘XML’, ‘httr’ are not available for package ‘annotate’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/annotate’
ERROR: dependencies ‘AnnotationDbi’, ‘annotate’ are not available for package ‘genefilter’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/genefilter’
ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘geneplotter’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/geneplotter’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/DESeq2’
ERROR: dependencies ‘DESeq2’, ‘lasso2’, ‘SummarizedExperiment’ are not available for package ‘DEGreport’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/DEGreport’

The downloaded source packages are in
  ‘/tmp/RtmpSFb6Sy/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    cluster, foreign, MASS, Matrix, mgcv, nlme, nnet, survival
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
Installing package(s) 'pathview'
also installing the dependencies ‘curl’, ‘GenomeInfoDb’, ‘RCurl’, ‘httr’, ‘Biostrings’, ‘KEGGgraph’, ‘XML’, ‘AnnotationDbi’, ‘org.Hs.eg.db’, ‘KEGGREST’

trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz'
Content type 'application/x-gzip' length 670416 bytes (654 KB)
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomeInfoDb_1.30.1.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.9.tar.gz'
Content type 'application/x-gzip' length 731611 bytes (714 KB)
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downloaded 714 KB

trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.4.tar.gz'
Content type 'application/x-gzip' length 161140 bytes (157 KB)
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trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Biostrings_2.62.0.tar.gz'
Content type 'application/octet-stream' length 12645827 bytes (12.1 MB)
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downloaded 12.1 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/KEGGgraph_1.54.0.tar.gz'
Content type 'application/octet-stream' length 1462164 bytes (1.4 MB)
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downloaded 1.4 MB

trying URL 'https://cloud.r-project.org/src/contrib/XML_3.99-0.11.tar.gz'
Content type 'application/x-gzip' length 970681 bytes (947 KB)
==================================================
downloaded 947 KB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/AnnotationDbi_1.56.2.tar.gz'
Content type 'application/octet-stream' length 4330396 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/org.Hs.eg.db_3.14.0.tar.gz'
Content type 'application/octet-stream' length 82195112 bytes (78.4 MB)
==================================================
downloaded 78.4 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/KEGGREST_1.34.0.tar.gz'
Content type 'application/octet-stream' length 25778 bytes (25 KB)
==================================================
downloaded 25 KB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/pathview_1.34.0.tar.gz'
Content type 'application/octet-stream' length 2254509 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/curl’
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/RCurl’
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/XML’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/GenomeInfoDb’
ERROR: dependency ‘curl’ is not available for package ‘httr’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/httr’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘KEGGgraph’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/KEGGgraph’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘Biostrings’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/Biostrings’
ERROR: dependencies ‘httr’, ‘Biostrings’ are not available for package ‘KEGGREST’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/KEGGREST’
ERROR: dependency ‘KEGGREST’ is not available for package ‘AnnotationDbi’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/AnnotationDbi’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘org.Hs.eg.db’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/org.Hs.eg.db’
ERROR: dependencies ‘KEGGgraph’, ‘XML’, ‘AnnotationDbi’, ‘org.Hs.eg.db’, ‘KEGGREST’ are not available for package ‘pathview’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/pathview’

The downloaded source packages are in
  ‘/tmp/RtmpSFb6Sy/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    cluster, foreign, MASS, Matrix, mgcv, nlme, nnet, survival
Error in library(package, character.only = TRUE) : 
  there is no package called ‘factoextra’
In addition: There were 40 warnings (use warnings() to see them)

There are errors, some of them we have seen before.

Many of the same errors occurred as we have seen previously in this thread, and were similarly solved. I won't repeat those solutions.

> source("DifferentialExpressionFunctions.R") Installing package into ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1’ (as ‘lib’ is unspecified) also installing the dependencies ‘gargle’, ‘googledrive’, ‘googlesheets4’, ‘rvest’ trying URL 'https://cloud.r-project.org/src/contrib/gargle_1.2.1.tar.gz' Content type 'application/x-gzip' length 312943 bytes (305 KB) ================================================== downloaded 305 KB trying URL 'https://cloud.r-project.org/src/contrib/googledrive_2.0.0.tar.gz' Content type 'application/x-gzip' length 1593656 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://cloud.r-project.org/src/contrib/googlesheets4_1.0.1.tar.gz' Content type 'application/x-gzip' length 223314 bytes (218 KB) ================================================== downloaded 218 KB trying URL 'https://cloud.r-project.org/src/contrib/rvest_1.0.3.tar.gz' Content type 'application/x-gzip' length 94659 bytes (92 KB) ================================================== downloaded 92 KB trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.3.2.tar.gz' Content type 'application/x-gzip' length 702514 bytes (686 KB) ================================================== downloaded 686 KB * installing *source* package ‘gargle’ ... ** package ‘gargle’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gargle) * installing *source* package ‘rvest’ ... ** package ‘rvest’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rvest) * installing *source* package ‘googledrive’ ... ** package ‘googledrive’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (googledrive) * installing *source* package ‘googlesheets4’ ... ** package ‘googlesheets4’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (googlesheets4) * installing *source* package ‘tidyverse’ ... ** package ‘tidyverse’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tidyverse) The downloaded source packages are in ‘/tmp/RtmpSFb6Sy/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01) Installing package(s) 'DEGreport' Warning: dependency ‘lasso2’ is not available trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DEGreport_1.30.3.tar.gz' Content type 'application/octet-stream' length 20097260 bytes (19.2 MB) ================================================== downloaded 19.2 MB ERROR: dependency ‘lasso2’ is not available for package ‘DEGreport’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/DEGreport’ The downloaded source packages are in ‘/tmp/RtmpSFb6Sy/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: cluster, foreign, MASS, Matrix, mgcv, nlme, nnet, survival path: /usr/lib/R/site-library packages: BH, blob, broom, callr, car, caret, checkmate, chron, classInt, cli, colorspace, commonmark, conquer, covr, crayon, curl, CVST, DBI, dbplyr, ddalpha, dendextend, DEoptimR, desc, dimRed, dplyr, DT, e1071, ellipse, evaluate, FactoMineR, fansi, farver, filehash, FNN, forcats, furrr, future, future.apply, gdata, generics, geometry, ggplot2, gh, gitcreds, globals, glue, gplots, gtable, gtools, haven, Hmisc, hms, htmlTable, htmltools, httpuv, httr, igraph, interp, ipred, isoband, jsonlite, kernlab, knitr, ks, latticeExtra, lifecycle, linprog, littler, lme4, lobstr, lpSolve, lwgeom, magrittr, maptools, MatrixModels, matrixStats, mclust, mda, mets, mockr, modeldata, multcomp, nloptr, openssl, palmerpenguins, parallelly, pillar, pkgload, plotmo, pls, plyr, polynom, pracma, processx, progressr, proxy, ps, purrr, quantmod, quantreg, ragg, raster, RColorBrewer, Rcpp, RcppArmadillo, RcppEigen, readr, readxl, recipes, rgdal, rgl, rlang, rmarkdown, robustbase, RPostgreSQL, rprojroot, rsample, RSpectra, RSQLite, rstudioapi, s2, sandwich, sass, scales, scatterplot3d, setRNG, sf, sfsmisc, shiny, sodium, sp, spatstat, spatstat.core, spatstat.data, spatstat.geom, spatstat.linnet, spatstat.sparse, spatstat.utils, statmod, stringi, stringr, terra, testthat, TH.data, tibble, tidyr, tidyselect, timeDate, timereg, timeSeries, tinytex, tseries, tzdb, vctrs, vdiffr, viridisLite, vroom, waldo, withr, wkutils, xfun, XML, zip, zoo 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01) Installing package(s) 'pathview' also installing the dependencies ‘KEGGgraph’, ‘org.Hs.eg.db’ trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/KEGGgraph_1.54.0.tar.gz' Content type 'application/octet-stream' length 1462164 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/org.Hs.eg.db_3.14.0.tar.gz' Content type 'application/octet-stream' length 82195112 bytes (78.4 MB) ================================================== downloaded 78.4 MB trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/pathview_1.34.0.tar.gz' Content type 'application/octet-stream' length 2254509 bytes (2.2 MB) ================================================== downloaded 2.2 MB * installing *source* package ‘KEGGgraph’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (KEGGgraph) * installing *source* package ‘org.Hs.eg.db’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (org.Hs.eg.db) * installing *source* package ‘pathview’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (pathview) The downloaded source packages are in ‘/tmp/RtmpSFb6Sy/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: cluster, foreign, MASS, Matrix, mgcv, nlme, nnet, survival path: /usr/lib/R/site-library packages: BH, blob, broom, callr, car, caret, checkmate, chron, classInt, cli, colorspace, commonmark, conquer, covr, crayon, curl, CVST, DBI, dbplyr, ddalpha, dendextend, DEoptimR, desc, dimRed, dplyr, DT, e1071, ellipse, evaluate, FactoMineR, fansi, farver, filehash, FNN, forcats, furrr, future, future.apply, gdata, generics, geometry, ggplot2, gh, gitcreds, globals, glue, gplots, gtable, gtools, haven, Hmisc, hms, htmlTable, htmltools, httpuv, httr, igraph, interp, ipred, isoband, jsonlite, kernlab, knitr, ks, latticeExtra, lifecycle, linprog, littler, lme4, lobstr, lpSolve, lwgeom, magrittr, maptools, MatrixModels, matrixStats, mclust, mda, mets, mockr, modeldata, multcomp, nloptr, openssl, palmerpenguins, parallelly, pillar, pkgload, plotmo, pls, plyr, polynom, pracma, processx, progressr, proxy, ps, purrr, quantmod, quantreg, ragg, raster, RColorBrewer, Rcpp, RcppArmadillo, RcppEigen, readr, readxl, recipes, rgdal, rgl, rlang, rmarkdown, robustbase, RPostgreSQL, rprojroot, rsample, RSpectra, RSQLite, rstudioapi, s2, sandwich, sass, scales, scatterplot3d, setRNG, sf, sfsmisc, shiny, sodium, sp, spatstat, spatstat.core, spatstat.data, spatstat.geom, spatstat.linnet, spatstat.sparse, spatstat.utils, statmod, stringi, stringr, terra, testthat, TH.data, tibble, tidyr, tidyselect, timeDate, timereg, timeSeries, tinytex, tseries, tzdb, vctrs, vdiffr, viridisLite, vroom, waldo, withr, wkutils, xfun, XML, zip, zoo Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa ── Attaching packages ───────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.2 ── ✔ tibble 3.1.8 ✔ dplyr 1.0.10 ✔ tidyr 1.2.1 ✔ stringr 1.4.1 ✔ readr 2.1.3 ✔ forcats 0.5.2 ✔ purrr 0.3.5 ── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::collapse() masks IRanges::collapse() ✖ dplyr::combine() masks Biobase::combine(), BiocGenerics::combine() ✖ dplyr::count() masks matrixStats::count() ✖ dplyr::desc() masks IRanges::desc() ✖ tidyr::expand() masks S4Vectors::expand(), Matrix::expand() ✖ dplyr::filter() masks stats::filter() ✖ dplyr::first() masks S4Vectors::first() ✖ dplyr::lag() masks stats::lag() ✖ tidyr::pack() masks Matrix::pack() ✖ readr::parse_date() masks curl::parse_date() ✖ BiocGenerics::Position() masks ggplot2::Position(), base::Position() ✖ purrr::reduce() masks GenomicRanges::reduce(), IRanges::reduce() ✖ dplyr::rename() masks S4Vectors::rename() ✖ dplyr::slice() masks IRanges::slice() ✖ tidyr::unpack() masks Matrix::unpack() Error in library(package, character.only = TRUE) : there is no package called ‘DEGreport’ In addition: Warning message: In install.packages(...) : installation of package ‘DEGreport’ had non-zero exit status

> BiocManager::install("DEGreport", force=TRUE) 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01) Installing package(s) 'DEGreport' Warning: dependency ‘lasso2’ is not available trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DEGreport_1.30.3.tar.gz' Content type 'application/octet-stream' length 20097260 bytes (19.2 MB) ================================================== downloaded 19.2 MB ERROR: dependency ‘lasso2’ is not available for package ‘DEGreport’ * removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/4.1/DEGreport’ The downloaded source packages are in ‘/tmp/RtmpSFb6Sy/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: cluster, foreign, MASS, Matrix, mgcv, nlme, nnet, survival path: /usr/lib/R/site-library packages: BH, blob, broom, callr, car, caret, checkmate, chron, classInt, cli, colorspace, commonmark, conquer, covr, crayon, curl, CVST, DBI, dbplyr, ddalpha, dendextend, DEoptimR, desc, dimRed, dplyr, DT, e1071, ellipse, evaluate, FactoMineR, fansi, farver, filehash, FNN, forcats, furrr, future, future.apply, gdata, generics, geometry, ggplot2, gh, gitcreds, globals, glue, gplots, gtable, gtools, haven, Hmisc, hms, htmlTable, htmltools, httpuv, httr, igraph, interp, ipred, isoband, jsonlite, kernlab, knitr, ks, latticeExtra, lifecycle, linprog, littler, lme4, lobstr, lpSolve, lwgeom, magrittr, maptools, MatrixModels, matrixStats, mclust, mda, mets, mockr, modeldata, multcomp, nloptr, openssl, palmerpenguins, parallelly, pillar, pkgload, plotmo, pls, plyr, polynom, pracma, processx, progressr, proxy, ps, purrr, quantmod, quantreg, ragg, raster, RColorBrewer, Rcpp, RcppArmadillo, RcppEigen, readr, readxl, recipes, rgdal, rgl, rlang, rmarkdown, robustbase, RPostgreSQL, rprojroot, rsample, RSpectra, RSQLite, rstudioapi, s2, sandwich, sass, scales, scatterplot3d, setRNG, sf, sfsmisc, shiny, sodium, sp, spatstat, spatstat.core, spatstat.data, spatstat.geom, spatstat.linnet, spatstat.sparse, spatstat.utils, statmod, stringi, stringr, terra, testthat, TH.data, tibble, tidyr, tidyselect, timeDate, timereg, timeSeries, tinytex, tseries, tzdb, vctrs, vdiffr, viridisLite, vroom, waldo, withr, wkutils, xfun, XML, zip, zoo Warning message: In install.packages(...) : installation of package ‘DEGreport’ had non-zero exit status

dfossl / RaderLabCode

Initialization script fails #1