(venv) HMDC-beamish:ec2 pdurbin$ ./ec2-create-instance.sh using default repo: https://github.com/IQSS/dataverse.git using default branch develop using ami-0408f4c4a072e3fb9 using t3a.large using dataverse-sg security group using key_name: key-pdurbin-F85C423E Your newly created private key file is "/Users/pdurbin/key-pdurbin-F85C423E.pem". Keep it secret. Keep it safe. Creating EC2 instance Instance ID: i-018e4537494a706b1 When you are done, please terminate your instance with: aws ec2 terminate-instances --instance-ids i-018e4537494a706b1 giving instance 90 seconds to wake up... End creating EC2 instance New instance created with ID "i-018e4537494a706b1". To ssh into it: ssh -i /Users/pdurbin/key-pdurbin-F85C423E.pem rocky@ec2-18-233-166-106.compute-1.amazonaws.com Please wait at least 15 minutes while the branch "develop" from https://github.com/IQSS/dataverse.git is being deployed. Warning: Permanently added 'ec2-18-233-166-106.compute-1.amazonaws.com' (ED25519) to the list of known hosts. Activate the web console with: systemctl enable --now cockpit.socket Importing GPG key 0x6D745A60: Userid : "Release Engineering " Fingerprint: 7051 C470 A929 F454 CEBE 37B7 15AF 5DAC 6D74 5A60 From : /etc/pki/rpm-gpg/RPM-GPG-KEY-rockyofficial Installed: epel-release-8-18.el8.noarch Importing GPG key 0x2F86D6A1: Userid : "Fedora EPEL (8) " Fingerprint: 94E2 79EB 8D8F 25B2 1810 ADF1 21EA 45AB 2F86 D6A1 From : /etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-8 Installed: ansible-8.3.0-1.el8.noarch ansible-core-2.15.3-1.el8.x86_64 emacs-filesystem-1:26.1-11.el8.noarch git-2.39.3-1.el8_8.x86_64 git-core-2.39.3-1.el8_8.x86_64 git-core-doc-2.39.3-1.el8_8.noarch mpdecimal-2.5.1-3.el8.x86_64 perl-Carp-1.42-396.el8.noarch perl-Data-Dumper-2.167-399.el8.x86_64 perl-Digest-1.17-395.el8.noarch perl-Digest-MD5-2.55-396.el8.x86_64 perl-Encode-4:2.97-3.el8.x86_64 perl-Errno-1.28-422.el8.x86_64 perl-Error-1:0.17025-2.el8.noarch perl-Exporter-5.72-396.el8.noarch perl-File-Path-2.15-2.el8.noarch perl-File-Temp-0.230.600-1.el8.noarch perl-Getopt-Long-1:2.50-4.el8.noarch perl-Git-2.39.3-1.el8_8.noarch perl-HTTP-Tiny-0.074-2.el8_9.1.noarch perl-IO-1.38-422.el8.x86_64 perl-IO-Socket-IP-0.39-5.el8.noarch perl-IO-Socket-SSL-2.066-4.module+el8.9.0+1517+e71a7a62.noarch perl-MIME-Base64-3.15-396.el8.x86_64 perl-Mozilla-CA-20160104-7.module+el8.9.0+1521+0101edce.noarch perl-Net-SSLeay-1.88-2.module+el8.9.0+1517+e71a7a62.x86_64 perl-PathTools-3.74-1.el8.x86_64 perl-Pod-Escapes-1:1.07-395.el8.noarch perl-Pod-Perldoc-3.28-396.el8.noarch perl-Pod-Simple-1:3.35-395.el8.noarch perl-Pod-Usage-4:1.69-395.el8.noarch perl-Scalar-List-Utils-3:1.49-2.el8.x86_64 perl-Socket-4:2.027-3.el8.x86_64 perl-Storable-1:3.11-3.el8.x86_64 perl-Term-ANSIColor-4.06-396.el8.noarch perl-Term-Cap-1.17-395.el8.noarch perl-TermReadKey-2.37-7.el8.x86_64 perl-Text-ParseWords-3.30-395.el8.noarch perl-Text-Tabs+Wrap-2013.0523-395.el8.noarch perl-Time-Local-1:1.280-1.el8.noarch perl-URI-1.73-3.el8.noarch perl-Unicode-Normalize-1.25-396.el8.x86_64 perl-constant-1.33-396.el8.noarch perl-interpreter-4:5.26.3-422.el8.x86_64 perl-libnet-3.11-3.el8.noarch perl-libs-4:5.26.3-422.el8.x86_64 perl-macros-4:5.26.3-422.el8.x86_64 perl-parent-1:0.237-1.el8.noarch perl-podlators-4.11-1.el8.noarch perl-threads-1:2.21-2.el8.x86_64 perl-threads-shared-1.58-2.el8.x86_64 python3-jmespath-0.9.0-11.el8.noarch python3.11-3.11.5-1.el8_9.x86_64 python3.11-cffi-1.15.1-1.el8.x86_64 python3.11-cryptography-37.0.2-5.el8.x86_64 python3.11-libs-3.11.5-1.el8_9.x86_64 python3.11-pip-wheel-22.3.1-4.el8_9.1.noarch python3.11-ply-3.11-1.el8.noarch python3.11-pycparser-2.20-1.el8.noarch python3.11-pyyaml-6.0-1.el8.x86_64 python3.11-setuptools-wheel-65.5.1-2.el8.noarch sshpass-1.09-4.el8.x86_64 Cloning into 'dataverse'... [WARNING]: Found variable using reserved name: any_errors_fatal PLAY [Install Dataverse] ******************************************************* TASK [Gathering Facts] ********************************************************* ok: [localhost] TASK [dataverse : begin dataverse ansible role] ******************************** ok: [localhost] => { "msg": "##### BEGIN ANSIBLE ROLE #####" } TASK [dataverse : RHEL8 and RockyLinux don't play nice with postgresql9.6] ***** skipping: [localhost] TASK [dataverse : RHEL9 and RockyLinux likely require PG13] ******************** skipping: [localhost] TASK [dataverse : Shibboleth requires AJP] ************************************* skipping: [localhost] TASK [dataverse : squawk] ****************************************************** skipping: [localhost] TASK [dataverse : bail] ******************************************************** skipping: [localhost] TASK [dataverse : install prerequisite packages] ******************************* ok: [localhost] => { "msg": "##### INSTALL PREREQUISITE PACKAGES #####" } TASK [dataverse : yum clean all] *********************************************** changed: [localhost] TASK [dataverse : let's use the closest mirror] ******************************** skipping: [localhost] TASK [dataverse : let's use the fastest mirror] ******************************** changed: [localhost] TASK [dataverse : makecache on RedHat] ***************************************** skipping: [localhost] TASK [dataverse : makecache] *************************************************** skipping: [localhost] TASK [dataverse : ensure EPEL repository for RedHat/Rocky] ********************* changed: [localhost] TASK [dataverse : install some necessary packages] ***************************** changed: [localhost] TASK [dataverse : RHEL/Rocky 8.6-packaged Ansible wants Python-3.8] ************ changed: [localhost] TASK [dataverse : RHEL/Rocky 9 provides Python-3.9] **************************** skipping: [localhost] TASK [dataverse : install java-nnn-openjdk and other packages for RedHat/Rocky] *** changed: [localhost] TASK [dataverse : install java-nnn-openjdk and other packages for Debian/Ubuntu.] *** skipping: [localhost] TASK [dataverse : install GraphicsMagic on RHEL/Rocky for thumbnail generation] *** skipping: [localhost] TASK [dataverse : install GraphicsMagic on Debian/Ubuntu for thumbnail generation] *** skipping: [localhost] TASK [dataverse : install curl on Debian/Ubuntu] ******************************* skipping: [localhost] TASK [dataverse : ensure payara service group exists] ************************** changed: [localhost] TASK [dataverse : ensure payara service account exists] ************************ changed: [localhost] TASK [dataverse : create dataverse misc files directory for language and handle and other similar auxilliary files] *** changed: [localhost] TASK [dataverse : construct payara_dir] **************************************** ok: [localhost] TASK [dataverse : construct dataverse_raw_repo (githubusercontent) URL] ******** ok: [localhost] TASK [dataverse : install script(s) necessary for various ansible subtasks] **** changed: [localhost] => (item=asadmin-create-or-replace-option.sh) changed: [localhost] => (item=asadmin-create-or-replace-password-alias.sh) TASK [dataverse : install rserve] ********************************************** ok: [localhost] => { "msg": "##### BEGIN RSERVE INSTALLATION #####" } TASK [dataverse : ensure EPEL is installed] ************************************ ok: [localhost] TASK [dataverse : RHEL8/9 need codeready-builder] ****************************** skipping: [localhost] TASK [dataverse : Rocky 8 needs powertools] ************************************ changed: [localhost] TASK [dataverse : Rocky 9 calls it crb] **************************************** skipping: [localhost] TASK [dataverse : install base packages] *************************************** changed: [localhost] TASK [dataverse : install base packages on Debian/Ubuntu] ********************** skipping: [localhost] TASK [dataverse : detect number of system cores] ******************************* ok: [localhost] TASK [dataverse : ensure .R exists] ******************************************** changed: [localhost] TASK [dataverse : set in .R/Makevars] ****************************************** changed: [localhost] TASK [dataverse : detect installed R modules] ********************************** ok: [localhost] => (item=R2HTML) ok: [localhost] => (item=rjson) ok: [localhost] => (item=DescTools) ok: [localhost] => (item=Rserve) ok: [localhost] => (item=haven) TASK [dataverse : process module detection output] ***************************** ok: [localhost] TASK [dataverse : debug] ******************************************************* ok: [localhost] => { "msg": "The following modules are not installed -- ['R2HTML', 'rjson', 'DescTools', 'Rserve', 'haven']" } TASK [dataverse : install R modules] ******************************************* changed: [localhost] => (item=R2HTML) changed: [localhost] => (item=rjson) failed: [localhost] (item=DescTools) => {"ansible_loop_var": "item", "changed": true, "cmd": ["/usr/bin/Rscript", "--slave", "--no-save", "--no-restore-history", "-e", "install.packages('DescTools', repos=c('https://cloud.r-project.org/'), Ncpus='2', quiet=TRUE); if(!library('DescTools', character.only=TRUE, logical.return=TRUE)){quit(status=1, save='no')};"], "delta": "0:04:32.445029", "end": "2024-05-28 18:16:09.118458", "item": "DescTools", "msg": "non-zero return code", "rc": 1, "start": "2024-05-28 18:11:36.673429", "stderr": "also installing the dependencies ‘glue’, ‘utf8’, ‘sys’, ‘proxy’, ‘rematch’, ‘fansi’, ‘lifecycle’, ‘magrittr’, ‘pillar’, ‘pkgconfig’, ‘rlang’, ‘vctrs’, ‘crayon’, ‘hms’, ‘prettyunits’, ‘askpass’, ‘rootSolve’, ‘e1071’, ‘lmom’, ‘cellranger’, ‘tibble’, ‘cpp11’, ‘progress’, ‘curl’, ‘jsonlite’, ‘mime’, ‘openssl’, ‘R6’, ‘mvtnorm’, ‘expm’, ‘Rcpp’, ‘rstudioapi’, ‘Exact’, ‘gld’, ‘data.table’, ‘readxl’, ‘httr’, ‘withr’, ‘cli’\n\nUpdating HTML index of packages in '.Library'\nMaking 'packages.html' ... done\nWarning message:\nIn install.packages(\"DescTools\", repos = c(\"https://cloud.r-project.org/\"), :\n installation of package ‘DescTools’ failed\nWarning message:\nIn library(\"DescTools\", character.only = TRUE, logical.return = TRUE) :\n there is no package called ‘DescTools’", "stderr_lines": ["also installing the dependencies ‘glue’, ‘utf8’, ‘sys’, ‘proxy’, ‘rematch’, ‘fansi’, ‘lifecycle’, ‘magrittr’, ‘pillar’, ‘pkgconfig’, ‘rlang’, ‘vctrs’, ‘crayon’, ‘hms’, ‘prettyunits’, ‘askpass’, ‘rootSolve’, ‘e1071’, ‘lmom’, ‘cellranger’, ‘tibble’, ‘cpp11’, ‘progress’, ‘curl’, ‘jsonlite’, ‘mime’, ‘openssl’, ‘R6’, ‘mvtnorm’, ‘expm’, ‘Rcpp’, ‘rstudioapi’, ‘Exact’, ‘gld’, ‘data.table’, ‘readxl’, ‘httr’, ‘withr’, ‘cli’", "", "Updating HTML index of packages in '.Library'", "Making 'packages.html' ... done", "Warning message:", "In install.packages(\"DescTools\", repos = c(\"https://cloud.r-project.org/\"), :", " installation of package ‘DescTools’ failed", "Warning message:", "In library(\"DescTools\", character.only = TRUE, logical.return = TRUE) :", " there is no package called ‘DescTools’"], "stdout": "* installing *source* package ‘DescTools’ ...\n** package ‘DescTools’ successfully unpacked and MD5 sums checked\n** using staged installation\n** libs\nusing C compiler: ‘gcc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20)’\nusing Fortran compiler: ‘GNU Fortran (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20)’\nusing C++ compiler: ‘g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20)’\nusing C++17\nmake[1]: Entering directory '/tmp/RtmpPsC4Q9/R.INSTALLc52833932926/DescTools/src'\ngcc -I\"/usr/include/R\" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c ADinf.c -o ADinf.o\ngcc -I\"/usr/include/R\" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c AnDarl.c -o AnDarl.o\ng++ -std=gnu++17 -I\"/usr/include/R\" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o\ng++ -std=gnu++17 -I\"/usr/include/R\" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c aux_fct.cpp -o aux_fct.o\naux_fct.cpp: In function ‘Rcpp::List n_pow_sum(Rcpp::NumericVector)’:\naux_fct.cpp:205:23: error: ‘reduce’ is not a member of ‘std’\n double mean = std::reduce(x.begin(), x.end(), 0.0, std::plus()) / x.size();\n ^~~~~~\naux_fct.cpp:205:23: note: suggested alternative: ‘replace’\n double mean = std::reduce(x.begin(), x.end(), 0.0, std::plus()) / x.size();\n ^~~~~~\n replace\nmake[1]: *** [/usr/lib64/R/etc/Makeconf:204: aux_fct.o] Error 1\nmake[1]: *** Waiting for unfinished jobs....\nmake[1]: Leaving directory '/tmp/RtmpPsC4Q9/R.INSTALLc52833932926/DescTools/src'\nERROR: compilation failed for package ‘DescTools’\n* removing ‘/usr/lib64/R/library/DescTools’", "stdout_lines": ["* installing *source* package ‘DescTools’ ...", "** package ‘DescTools’ successfully unpacked and MD5 sums checked", "** using staged installation", "** libs", "using C compiler: ‘gcc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20)’", "using Fortran compiler: ‘GNU Fortran (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20)’", "using C++ compiler: ‘g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20)’", "using C++17", "make[1]: Entering directory '/tmp/RtmpPsC4Q9/R.INSTALLc52833932926/DescTools/src'", "gcc -I\"/usr/include/R\" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c ADinf.c -o ADinf.o", "gcc -I\"/usr/include/R\" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c AnDarl.c -o AnDarl.o", "g++ -std=gnu++17 -I\"/usr/include/R\" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o", "g++ -std=gnu++17 -I\"/usr/include/R\" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c aux_fct.cpp -o aux_fct.o", "aux_fct.cpp: In function ‘Rcpp::List n_pow_sum(Rcpp::NumericVector)’:", "aux_fct.cpp:205:23: error: ‘reduce’ is not a member of ‘std’", " double mean = std::reduce(x.begin(), x.end(), 0.0, std::plus()) / x.size();", " ^~~~~~", "aux_fct.cpp:205:23: note: suggested alternative: ‘replace’", " double mean = std::reduce(x.begin(), x.end(), 0.0, std::plus()) / x.size();", " ^~~~~~", " replace", "make[1]: *** [/usr/lib64/R/etc/Makeconf:204: aux_fct.o] Error 1", "make[1]: *** Waiting for unfinished jobs....", "make[1]: Leaving directory '/tmp/RtmpPsC4Q9/R.INSTALLc52833932926/DescTools/src'", "ERROR: compilation failed for package ‘DescTools’", "* removing ‘/usr/lib64/R/library/DescTools’"]} changed: [localhost] => (item=Rserve) changed: [localhost] => (item=haven) NO MORE HOSTS LEFT ************************************************************* PLAY RECAP ********************************************************************* localhost : ok=25 changed=14 unreachable=0 failed=1 skipped=15 rescued=0 ignored=0 (venv) HMDC-beamish:ec2 pdurbin$