From 48c463680b51fa767b4cd7bd62865f192d0354ac Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 6 Feb 2021 18:30:32 +0100 Subject: Reintroduce interface to saemix Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed. --- .travis.yml | 2 -- 1 file changed, 2 deletions(-) (limited to '.travis.yml') diff --git a/.travis.yml b/.travis.yml index 282f1302..6c03b451 100644 --- a/.travis.yml +++ b/.travis.yml @@ -11,8 +11,6 @@ addons: cache: packages repos: CRAN: https://cloud.r-project.org -r_github_packages: - - saemixdevelopment/saemixextension@master script: - R CMD build . - R CMD check --no-tests mkin_*.tar.gz -- cgit v1.2.1 From c6eb6b2bb598002523c3d34d71b0e4a99671ccd6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 9 Jun 2021 16:53:31 +0200 Subject: Rudimentary support for setting up nlmixr models - All degradation models are specified as ODE models. This appears to be fast enough - Error models are being translated to nlmixr as close to the mkin error model as possible. When using the 'saem' backend, it appears not to be possible to use the same error model for more than one observed variable - No support yet for models with parallel formation of metabolites, where the ilr transformation is used in mkin per default - There is a bug in nlmixr which appears to be triggered if the data are not balanced, see nlmixrdevelopment/nlmixr#530 - There is a print and a plot method, the summary method is not finished --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) (limited to '.travis.yml') diff --git a/.travis.yml b/.travis.yml index 6c03b451..60e37230 100644 --- a/.travis.yml +++ b/.travis.yml @@ -11,6 +11,8 @@ addons: cache: packages repos: CRAN: https://cloud.r-project.org +r_github_packages: + - jranke/saemixextension@warp_combined script: - R CMD build . - R CMD check --no-tests mkin_*.tar.gz -- cgit v1.2.1 From 1848f6a9c6f763b6ad32df8c5b58e27b30880ea4 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 11 Jun 2021 12:04:19 +0200 Subject: Add system requirements for symengine on Travis nlmixr depends on symengine --- .travis.yml | 1 + 1 file changed, 1 insertion(+) (limited to '.travis.yml') diff --git a/.travis.yml b/.travis.yml index 60e37230..1e2fe241 100644 --- a/.travis.yml +++ b/.travis.yml @@ -8,6 +8,7 @@ addons: packages: - gcc - libgit2-dev + - libmpfr-dev cache: packages repos: CRAN: https://cloud.r-project.org -- cgit v1.2.1 From 2c0721983e8d0b090141882c49780fe50d8fdcde Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 11 Jun 2021 13:46:23 +0200 Subject: Attempt to satisfy nlme version requirement on travis --- .travis.yml | 1 + 1 file changed, 1 insertion(+) (limited to '.travis.yml') diff --git a/.travis.yml b/.travis.yml index 1e2fe241..bc39faf9 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,6 +12,7 @@ addons: cache: packages repos: CRAN: https://cloud.r-project.org +r_packages: nlme r_github_packages: - jranke/saemixextension@warp_combined script: -- cgit v1.2.1 From 1aeb2c5e3dc4782f0cc7279bf16b9ba06a08f328 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 11 Jun 2021 14:03:43 +0200 Subject: Add packages necessary for shell commands on travis --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.travis.yml') diff --git a/.travis.yml b/.travis.yml index bc39faf9..8f4e1566 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,7 +12,7 @@ addons: cache: packages repos: CRAN: https://cloud.r-project.org -r_packages: nlme +r_packages: nlme devtools codecov r_github_packages: - jranke/saemixextension@warp_combined script: -- cgit v1.2.1 From 6f78e98e81cbdda9a3caf90641a66df52afb37ac Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 11 Jun 2021 14:36:30 +0200 Subject: Fix travis syntax --- .travis.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to '.travis.yml') diff --git a/.travis.yml b/.travis.yml index 8f4e1566..906010f4 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,7 +12,10 @@ addons: cache: packages repos: CRAN: https://cloud.r-project.org -r_packages: nlme devtools codecov +r_packages: + - nlme + - devtools + - codecov r_github_packages: - jranke/saemixextension@warp_combined script: -- cgit v1.2.1 From 8bf6bd4289f1a0618376406a6a44dd99aedc692f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 11 Jun 2021 14:54:46 +0200 Subject: Fix package name for travis config... --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.travis.yml') diff --git a/.travis.yml b/.travis.yml index 906010f4..0ae488cb 100644 --- a/.travis.yml +++ b/.travis.yml @@ -15,7 +15,7 @@ repos: r_packages: - nlme - devtools - - codecov + - covr r_github_packages: - jranke/saemixextension@warp_combined script: -- cgit v1.2.1 From fbef7bb4585b1fe1f4dc883aa8c017de3d6d8c23 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Sep 2021 09:01:35 +0200 Subject: Try to make remotes on travis work again This tries to unset the environment variable GITHUB_PAT which seems to get in the way for installing using remotes::install_github on travis. --- .travis.yml | 1 + 1 file changed, 1 insertion(+) (limited to '.travis.yml') diff --git a/.travis.yml b/.travis.yml index 09e361c4..cbc491a9 100644 --- a/.travis.yml +++ b/.travis.yml @@ -16,6 +16,7 @@ r_packages: - devtools - covr - vdiffr +env: GITHUB_PAT= r_github_packages: - jranke/saemixextension@warp_combined script: -- cgit v1.2.1 From 450f3fe33af3c0cc9838f54ca090603727d0f783 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Sep 2021 09:31:00 +0200 Subject: Try to diagnose the problem with remotes --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) (limited to '.travis.yml') diff --git a/.travis.yml b/.travis.yml index cbc491a9..91cf3d9b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -16,10 +16,12 @@ r_packages: - devtools - covr - vdiffr +before_script: echo $GITHUB_PAT env: GITHUB_PAT= r_github_packages: - jranke/saemixextension@warp_combined script: + - echo $GITHUB_PAT - R CMD build . - R CMD check --no-tests mkin_*.tar.gz - Rscript -e 'devtools::test()' -- cgit v1.2.1 From e0ca5972b4a300b93a9fe6b44345eeb19d574149 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Sep 2021 09:56:35 +0200 Subject: Remove GITHUB_PAT from .travis.yml I found that I can create a PAT with no extra privileges, thanks to https://itsalocke.com/blog/using-travis-make-sure-you-use-a-github-pat/ so I will add this to my travis account. --- .travis.yml | 3 --- 1 file changed, 3 deletions(-) (limited to '.travis.yml') diff --git a/.travis.yml b/.travis.yml index 91cf3d9b..09e361c4 100644 --- a/.travis.yml +++ b/.travis.yml @@ -16,12 +16,9 @@ r_packages: - devtools - covr - vdiffr -before_script: echo $GITHUB_PAT -env: GITHUB_PAT= r_github_packages: - jranke/saemixextension@warp_combined script: - - echo $GITHUB_PAT - R CMD build . - R CMD check --no-tests mkin_*.tar.gz - Rscript -e 'devtools::test()' -- cgit v1.2.1 From e83e7c7c0aec23132a1a15c54cb8a8e0fe104ceb Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 17 Nov 2021 11:13:33 +0100 Subject: Use the official master branch of saemix As my changes were merged meanwhile --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.travis.yml') diff --git a/.travis.yml b/.travis.yml index 09e361c4..84c6d7c5 100644 --- a/.travis.yml +++ b/.travis.yml @@ -17,7 +17,7 @@ r_packages: - covr - vdiffr r_github_packages: - - jranke/saemixextension@warp_combined + - saemixdevelopment/saemixextension script: - R CMD build . - R CMD check --no-tests mkin_*.tar.gz -- cgit v1.2.1