Dear Paul and the coot community I am trying to compile coot-1 on Ubuntu 20.04 using Coot 1 (GTK-+-3-based) From Scratch script build-it-3-3 This started by creating auto-build directory and downloading several dependencies and then It stopped with this error --see below
"PATH is now: /home/rajiv/autobuild/Linux-rajiv-vm-pre-release-gtk3/bin:/home/rajiv/.local/UCSF-Chimera64-2022-07-01/bin:/home/rajiv/anaconda3/bin:/home/rajiv/anaconda3/condabin:/home/rajiv/pymol-open-source-build/bin:/usr/local/phenix-1.19.2-4158/build/bin:/home/rajiv/ccpEM/ccpem-20210902/bin:/home/rajiv/ccp4/ccp4-7.1/etc:/home/rajiv/ccp4/ccp4-7.1/bin:/home/rajiv/.aspera/connect/bin:/home/rajiv/.local/bin:/home/rajiv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc AUTOBUILD_BUILD is /home/rajiv/autobuild/building AUTOBUILD_SOURCES is /home/rajiv/autobuild/building/sources INFO:: redirecting std output to /home/rajiv/public_html/build-logs/Linux-rajiv-vm/build.log awk: not an option: --version ls: cannot access '/home/rajiv/autobuild/Linux-rajiv-vm-gtk3/include/ltdl.h': No such file or directory build-it-3-3: line 2090: /home/rajiv/autobuild/Linux-rajiv-vm-gtk3/bin/gsl-config: No such file or directory URL transformed to HTTPS due to an HSTS policy --2022-07-07 05:25:47-- https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/libccp4-6.5.1.tar.gz Resolving www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)... 131.111.85.100 Connecting to www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)|131.111.85.100|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 947521 (925K) [application/x-gzip] Saving to: ‘/home/rajiv/autobuild/building/sources/libccp4-6.5.1.tar.gz’ libccp4-6.5.1.tar.gz 100%[===============================================================================================================>] 925.31K 217KB/s in 4.3s 2022-07-07 05:25:53 (217 KB/s) - ‘/home/rajiv/autobuild/building/sources/libccp4-6.5.1.tar.gz’ saved [947521/947521] URL transformed to HTTPS due to an HSTS policy --2022-07-07 05:26:01-- https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/mmdb2-2.0.22.tar.gz Resolving www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)... 131.111.85.100 Connecting to www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)|131.111.85.100|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 737837 (721K) [application/x-gzip] Saving to: ‘/home/rajiv/autobuild/building/sources/mmdb2-2.0.22.tar.gz’ mmdb2-2.0.22.tar.gz 100%[===============================================================================================================>] 720.54K 168KB/s in 4.3s 2022-07-07 05:26:06 (168 KB/s) - ‘/home/rajiv/autobuild/building/sources/mmdb2-2.0.22.tar.gz’ saved [737837/737837] URL transformed to HTTPS due to an HSTS policy --2022-07-07 05:26:24-- https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/ssm-1.4.tar.gz Resolving www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)... 131.111.85.100 Connecting to www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)|131.111.85.100|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 426685 (417K) [application/x-gzip] Saving to: ‘/home/rajiv/autobuild/building/sources/ssm-1.4.tar.gz’ ssm-1.4.tar.gz 100%[===============================================================================================================>] 416.68K 133KB/s in 3.1s 2022-07-07 05:26:29 (133 KB/s) - ‘/home/rajiv/autobuild/building/sources/ssm-1.4.tar.gz’ saved [426685/426685] URL transformed to HTTPS due to an HSTS policy --2022-07-07 05:26:37-- https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/fftw-2.1.5.tar.gz Resolving www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)... 131.111.85.100 Connecting to www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)|131.111.85.100|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1256888 (1.2M) [application/x-gzip] Saving to: ‘/home/rajiv/autobuild/building/sources/fftw-2.1.5.tar.gz’ fftw-2.1.5.tar.gz 100%[===============================================================================================================>] 1.20M 226KB/s in 5.7s 2022-07-07 05:26:44 (217 KB/s) - ‘/home/rajiv/autobuild/building/sources/fftw-2.1.5.tar.gz’ saved [1256888/1256888] URL transformed to HTTPS due to an HSTS policy --2022-07-07 05:27:19-- https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/clipper-2.1.20180802.tar.gz Resolving www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)... 131.111.85.100 Connecting to www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)|131.111.85.100|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 4238748 (4.0M) [application/x-gzip] Saving to: ‘/home/rajiv/autobuild/building/sources/clipper-2.1.20180802.tar.gz’ clipper-2.1.20180802.tar.gz 100%[===============================================================================================================>] 4.04M 311KB/s in 15s 2022-07-07 05:27:35 (277 KB/s) - ‘/home/rajiv/autobuild/building/sources/clipper-2.1.20180802.tar.gz’ saved [4238748/4238748] URL transformed to HTTPS due to an HSTS policy --2022-07-07 05:27:35-- https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/clipper-configure-2.patch Resolving www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)... 131.111.85.100 Connecting to www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)|131.111.85.100|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 5888 (5.8K) Saving to: ‘/home/rajiv/autobuild/building/sources/clipper-configure-2.patch’ clipper-configure-2.patch 100%[===============================================================================================================>] 5.75K --.-KB/s in 0s 2022-07-07 05:27:36 (130 MB/s) - ‘/home/rajiv/autobuild/building/sources/clipper-configure-2.patch’ saved [5888/5888] --2022-07-07 05:30:54-- ftp://ftp.gnu.org/gnu/readline/readline-6.3.tar.gz => ‘/home/rajiv/autobuild/building/sources/.listing’ Resolving ftp.gnu.org (ftp.gnu.org)... 209.51.188.20, 2001:470:142:3::b Connecting to ftp.gnu.org (ftp.gnu.org)|209.51.188.20|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /gnu/readline ... done. ==> PASV ... done. ==> LIST ... done. .listing [ <=> ] 6.27K --.-KB/s in 0.001s 2022-07-07 05:30:57 (8.43 MB/s) - ‘/home/rajiv/autobuild/building/sources/.listing’ saved [6424] Removed ‘/home/rajiv/autobuild/building/sources/.listing’. --2022-07-07 05:30:57-- ftp://ftp.gnu.org/gnu/readline/readline-6.3.tar.gz => ‘/home/rajiv/autobuild/building/sources/readline-6.3.tar.gz’ ==> CWD not required. ==> PASV ... done. ==> RETR readline-6.3.tar.gz ... done. Length: 2468560 (2.4M) readline-6.3.tar.gz 100%[===============================================================================================================>] 2.35M 1.31MB/s in 1.8s 2022-07-07 05:31:00 (1.31 MB/s) - ‘/home/rajiv/autobuild/building/sources/readline-6.3.tar.gz’ saved [2468560] URL transformed to HTTPS due to an HSTS policy --2022-07-07 05:31:00-- https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/readline-5.1.patch Resolving www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)... 131.111.85.100 Connecting to www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)|131.111.85.100|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1665 (1.6K) [application/x-troff-man] Saving to: ‘/home/rajiv/autobuild/building/sources/readline-5.1.patch’ readline-5.1.patch 100%[===============================================================================================================>] 1.63K --.-KB/s in 0s 2022-07-07 05:31:01 (178 MB/s) - ‘/home/rajiv/autobuild/building/sources/readline-5.1.patch’ saved [1665/1665] URL transformed to HTTPS due to an HSTS policy --2022-07-07 05:31:31-- https://www.python.org/ftp/python/3.9.12/Python-3.9.12.tgz Resolving www.python.org (www.python.org)... 146.75.112.223, 2a04:4e42:1a::223 Connecting to www.python.org (www.python.org)|146.75.112.223|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 26338472 (25M) [application/octet-stream] Saving to: ‘/home/rajiv/autobuild/building/sources/Python-3.9.12.tgz’ Python-3.9.12.tgz 100%[===============================================================================================================>] 25.12M 9.72MB/s in 2.6s 2022-07-07 05:31:34 (9.72 MB/s) - ‘/home/rajiv/autobuild/building/sources/Python-3.9.12.tgz’ saved [26338472/26338472] --2022-07-07 05:38:20-- http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2 Resolving www.mirrorservice.org (www.mirrorservice.org)... 212.219.56.184, 2001:630:341:12::184 Connecting to www.mirrorservice.org (www.mirrorservice.org)|212.219.56.184|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 2386766 (2.3M) [application/x-bzip2] Saving to: ‘/home/rajiv/autobuild/building/sources/gmp-6.1.2.tar.bz2’ gmp-6.1.2.tar.bz2 100%[===============================================================================================================>] 2.28M 1.16MB/s in 2.0s 2022-07-07 05:38:23 (1.16 MB/s) - ‘/home/rajiv/autobuild/building/sources/gmp-6.1.2.tar.bz2’ saved [2386766/2386766] --2022-07-07 05:39:31-- http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/libtool/libtool-2.4.6.tar.gz Resolving www.mirrorservice.org (www.mirrorservice.org)... 212.219.56.184, 2001:630:341:12::184 Connecting to www.mirrorservice.org (www.mirrorservice.org)|212.219.56.184|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 1806697 (1.7M) [application/x-gzip] Saving to: ‘/home/rajiv/autobuild/building/sources/libtool-2.4.6.tar.gz’ libtool-2.4.6.tar.gz 100%[===============================================================================================================>] 1.72M 880KB/s in 2.0s 2022-07-07 05:39:34 (880 KB/s) - ‘/home/rajiv/autobuild/building/sources/libtool-2.4.6.tar.gz’ saved [1806697/1806697] --2022-07-07 05:41:13-- http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/gsl/gsl-1.16.tar.gz Resolving www.mirrorservice.org (www.mirrorservice.org)... 212.219.56.184, 2001:630:341:12::184 Connecting to www.mirrorservice.org (www.mirrorservice.org)|212.219.56.184|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 3534080 (3.4M) [application/x-gzip] Saving to: ‘/home/rajiv/autobuild/building/sources/gsl-1.16.tar.gz’ gsl-1.16.tar.gz 100%[===============================================================================================================>] 3.37M 1.06MB/s in 3.2s 2022-07-07 05:41:17 (1.06 MB/s) - ‘/home/rajiv/autobuild/building/sources/gsl-1.16.tar.gz’ saved [3534080/3534080] --2022-07-07 05:43:26-- https://boostorg.jfrog.io/artifactory/main/release/1.74.0/source/boost_1_74_0.tar.gz Resolving boostorg.jfrog.io (boostorg.jfrog.io)... 54.148.95.135, 52.39.121.184, 54.186.188.26, ... Connecting to boostorg.jfrog.io (boostorg.jfrog.io)|54.148.95.135|:443... connected. HTTP request sent, awaiting response... 302 Location: https://jfrog-prod-usw2-shared-oregon-main.s3.amazonaws.com/aol-boostorg/filestore/10/107cebeec706988639cf2932fc0ce43200de4c0a?X-Artifactory-repositoryKey=main&X-Artifactory-projectKey=default&x-jf-traceId=47fd0eb9ae8c3cf5&response-content-disposition=attachment%3Bfilename%3D%22boost_1_74_0.tar.gz%22&response-content-type=application%2Fx-gzip&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20220706T204327Z&X-Amz-SignedHeaders=host&X-Amz-Expires=60&X-Amz-Credential=AKIASG3IHPL63WBBRCUD%2F20220706%2Fus-west-2%2Fs3%2Faws4_request&X-Amz-Signature=5b31b1aabed47a5520c15b4b4c89ce918fb4a510b3b5a5ce709e0c2ef24b3160 [following] --2022-07-07 05:43:27-- https://jfrog-prod-usw2-shared-oregon-main.s3.amazonaws.com/aol-boostorg/filestore/10/107cebeec706988639cf2932fc0ce43200de4c0a?X-Artifactory-repositoryKey=main&X-Artifactory-projectKey=default&x-jf-traceId=47fd0eb9ae8c3cf5&response-content-disposition=attachment%3Bfilename%3D%22boost_1_74_0.tar.gz%22&response-content-type=application%2Fx-gzip&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20220706T204327Z&X-Amz-SignedHeaders=host&X-Amz-Expires=60&X-Amz-Credential=AKIASG3IHPL63WBBRCUD%2F20220706%2Fus-west-2%2Fs3%2Faws4_request&X-Amz-Signature=5b31b1aabed47a5520c15b4b4c89ce918fb4a510b3b5a5ce709e0c2ef24b3160 Resolving jfrog-prod-usw2-shared-oregon-main.s3.amazonaws.com (jfrog-prod-usw2-shared-oregon-main.s3.amazonaws.com)... 52.92.179.41 Connecting to jfrog-prod-usw2-shared-oregon-main.s3.amazonaws.com (jfrog-prod-usw2-shared-oregon-main.s3.amazonaws.com)|52.92.179.41|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 129348951 (123M) [application/x-gzip] Saving to: ‘/home/rajiv/autobuild/building/sources/boost_1_74_0.tar.gz’ boost_1_74_0.tar.gz 100%[===============================================================================================================>] 123.36M 3.40MB/s in 55s 2022-07-07 05:44:23 (2.26 MB/s) - ‘/home/rajiv/autobuild/building/sources/boost_1_74_0.tar.gz’ saved [129348951/129348951] --2022-07-07 05:48:02-- https://download-fallback.gnome.org/sources/goocanvas/2.0/goocanvas-2.0.4.tar.xz Resolving download-fallback.gnome.org (download-fallback.gnome.org)... 89.187.162.133, 89.187.162.137, 89.187.162.142, ... Connecting to download-fallback.gnome.org (download-fallback.gnome.org)|89.187.162.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 584272 (571K) [application/octet-stream] Saving to: ‘/home/rajiv/autobuild/building/sources/goocanvas-2.0.4.tar.xz’ goocanvas-2.0.4.tar.xz 100%[===============================================================================================================>] 570.58K 688KB/s in 0.8s 2022-07-07 05:48:04 (688 KB/s) - ‘/home/rajiv/autobuild/building/sources/goocanvas-2.0.4.tar.xz’ saved [584272/584272] --2022-07-07 05:48:49-- http://skuld.bmsc.washington.edu/raster3d/Raster3D_3.0-7.tar.gz Resolving skuld.bmsc.washington.edu (skuld.bmsc.washington.edu)... 128.95.235.53 Connecting to skuld.bmsc.washington.edu (skuld.bmsc.washington.edu)|128.95.235.53|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 1729798 (1.6M) [application/x-gzip] Saving to: ‘/home/rajiv/autobuild/building/sources/Raster3D_3.0-7.tar.gz’ Raster3D_3.0-7.tar.gz 100%[===============================================================================================================>] 1.65M 475KB/s in 3.6s 2022-07-07 05:48:53 (475 KB/s) - ‘/home/rajiv/autobuild/building/sources/Raster3D_3.0-7.tar.gz’ saved [1729798/1729798] URL transformed to HTTPS due to an HSTS policy --2022-07-07 05:49:11-- https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/glm-0.9.9.2.tar.gz Resolving www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)... 131.111.85.100 Connecting to www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)|131.111.85.100|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 4572279 (4.4M) [application/x-gzip] Saving to: ‘/home/rajiv/autobuild/building/sources/glm-0.9.9.2.tar.gz’ glm-0.9.9.2.tar.gz 100%[===============================================================================================================>] 4.36M 292KB/s in 17s 2022-07-07 05:49:29 (259 KB/s) - ‘/home/rajiv/autobuild/building/sources/glm-0.9.9.2.tar.gz’ saved [4572279/4572279] ls: cannot access '/home/rajiv/autobuild/Linux-rajiv-vm-gtk3/lib/python3.9/site-packages/numpy-*/numpy/lib/_version.py': No such file or directory guile-config - Guile version 2.2.7" I wonder how to proceed past this. Appreciate your support. Best, Rajiv ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
