Closed gallardoalba closed 1 year ago
HajkD
commented
1 year ago Hi @gallardoalba
Thank you very much for reaching out!
@LotharukpongJS Would it be possible to help here?
If it is more tricky to solve, I will be back to office on 3rd July and will look into this.
With many thanks and very best wishes, Hajk
gallardoalba
commented
1 year ago Hi @gallardoalba
Thank you very much for reaching out!
@LotharukpongJS Would it be possible to help here?
If it is more tricky to solve, I will be back to office on 3rd July and will look into this.
With many thanks and very best wishes, Hajk
Thanks a lot! I'm planing to create a Galaxy training for the tool, so probably will stay in touch.
Regards
LotharukpongJS
commented
1 year ago Hi @gallardoalba ,
I had a look at your recipe file and building it was fine until there was an RcppArmadillo dependency error. I am not sure if this is due to the R version I am using. Is this an error you have noticed?
I will update my R and check again tomorrow. Conda-build takes a very long time so I sadly couldn't test a lot of things at once...
conda-build r-mytaiERROR: dependency ‘RcppArmadillo’ is not available for package ‘myTAI’Regarding the error, Error in library("myTAI") : there is no package called ‘myTAI’, my first guess is that it could be related to this commit? Let me know if it is related.
Apologies in advance for I haven't been able to solve it today.
Best, Sodai
LotharukpongJS
commented
1 year ago Hi @gallardoalba,
After adding - r-rcpparmadillo to host and run, I tried to build the conda package again using
conda-build r-mytaiIt finished with
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library('myTAI')
>
>
+ exit 0
Resource usage statistics from testing r-mytai:
Process count: 2
CPU time: Sys=0:00:00.1, User=0:00:00.1
Memory: 16.2M
Disk usage: 12B
Time elapsed: 0:00:04.1
TEST END: /ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/linux-64/r-mytai-0.9.3-r42h3fd9d12_0.tar.bz2
Renaming work directory '/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work' to '/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop'
INFO:conda_build.utils:Renaming work directory '/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work' to '/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop'
shutil.move(work)=/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work, dest=/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop)
INFO:conda_build.utils:shutil.move(work)=/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work, dest=/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/r-mytai_1688054674046/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop)
# Automatic uploading is disabled
# If you want to upload package(s) to anaconda.org later, type:
# To have conda build upload to anaconda.org automatically, use
# conda config --set anaconda_upload yes
anaconda upload \
/ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld/linux-64/r-mytai-0.9.3-r42h3fd9d12_0.tar.bz2
anaconda_upload is not set. Not uploading wheels: []
INFO :: The inputs making up the hashes for the built packages are as follows:
{
"r-mytai-0.9.3-r42h3fd9d12_0": {
"recipe": {
"c_compiler": "gcc",
"cxx_compiler": "gxx",
"target_platform": "linux-64"
}
}
}
####################################################################################
Resource usage summary:
Total time: 0:14:07.3
CPU usage: sys=0:00:32.4, user=0:00:07.6
Maximum memory usage observed: 706.0M
Total disk usage observed (not including envs): 9.2K
####################################################################################
Source and build intermediates have been left in /ebio/abt5_projects/small_projects/jlotharukpong/miniconda3/envs/r4-base/conda-bld.
There are currently 2 accumulated.
To remove them, you can run the ```conda build purge``` commandIs this the behaviour you expected?
I tried doing the same using on another VM and got something similar
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library('myTAI')
>
>
+ exit 0
Resource usage statistics from testing r-mytai:
Process count: 2
CPU time: Sys=-, User=0:00:00.0
Memory: 14.3M
Disk usage: 16B
Time elapsed: 0:00:02.0
TEST END: /home/ubuntu/miniconda3/envs/pkgtest/conda-bld/linux-64/r-mytai-0.9.3-r42h3fd9d12_0.tar.bz2
Renaming work directory '/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work' to '/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop'
INFO:conda_build.utils:Renaming work directory '/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work' to '/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop'
shutil.move(work)=/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work, dest=/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop)
INFO:conda_build.utils:shutil.move(work)=/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work, dest=/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/r-mytai_1688122267558/work_moved_r-mytai-0.9.3-r>=31h3fd9d12_0_linux-64_main_build_loop)
# Automatic uploading is disabled
# If you want to upload package(s) to anaconda.org later, type:
# To have conda build upload to anaconda.org automatically, use
# conda config --set anaconda_upload yes
anaconda upload \
/home/ubuntu/miniconda3/envs/pkgtest/conda-bld/linux-64/r-mytai-0.9.3-r42h3fd9d12_0.tar.bz2
anaconda_upload is not set. Not uploading wheels: []
INFO :: The inputs making up the hashes for the built packages are as follows:
{
"r-mytai-0.9.3-r42h3fd9d12_0": {
"recipe": {
"c_compiler": "gcc",
"cxx_compiler": "gxx",
"target_platform": "linux-64"
}
}
}
####################################################################################
Resource usage summary:
Total time: 0:13:42.1
CPU usage: sys=0:00:05.7, user=0:00:09.7
Maximum memory usage observed: 700.3M
Total disk usage observed (not including envs): 8.0K
####################################################################################
Source and build intermediates have been left in /home/ubuntu/miniconda3/envs/pkgtest/conda-bld.
There are currently 6 accumulated.
To remove them, you can run the ```conda build purge``` commandBest, Sodai
HajkD
commented
1 year ago Dear @LotharukpongJS
Thank you very much for pushing this forward! I think you solved it!
@gallardoalba Does the installation work for you now?
With very best wishes, Hajk
gallardoalba
commented
1 year ago Yes, I think so. Thanks a lot!
gallardoalba
commented
1 year ago Sorry for bothering you again. I tried to include the dependency, but I'm still not able to build the package locally. When I try to install myTAI locally, I get this dependency problem:
* installing *source* package ‘textshaping’ ...
** package ‘textshaping’ successfully unpacked and MD5 sums checked
** using staged installation
Inconsistency detected by ld.so: dl-call-libc-early-init.c: 37: _dl_call_libc_early_init: Assertion `sym != NULL' failed!
Inconsistency detected by ld.so: dl-call-libc-early-init.c: 37: _dl_call_libc_early_init: Assertion `sym != NULL' failed!
Using PKG_CFLAGS=
Using PKG_LIBS=-lfreetype -lharfbuzz -lfribidi -lpng
--------------------------- [ANTICONF] --------------------------------
Configuration failed to find the harfbuzz freetype2 fribidi library. Try installing:
* deb: libharfbuzz-dev libfribidi-dev (Debian, Ubuntu, etc)
* rpm: harfbuzz-devel fribidi-devel (Fedora, EPEL)
* csw: libharfbuzz_dev libfribidi_dev (Solaris)
* brew: harfbuzz fribidi (OSX)
If harfbuzz freetype2 fribidi is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a harfbuzz freetype2 fribidi.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 MESSAGE] ---------------------------
<stdin>:1:10: fatal error: hb-ft.h: No such file or directory
compilation terminated.Do you think it could be related with the error?
Regards
HajkD
commented
1 year ago Hi @gallardoalba
Did you have a chance to try following the error message and install the suggested libraries?
Configuration failed to find the harfbuzz freetype2 fribidi library. Try installing:
* deb: libharfbuzz-dev libfribidi-dev (Debian, Ubuntu, etc)
* rpm: harfbuzz-devel fribidi-devel (Fedora, EPEL)
* csw: libharfbuzz_dev libfribidi_dev (Solaris)
* brew: harfbuzz fribidi (OSX)Configuration failed to find the harfbuzz freetype2 fribidi library
Let me know if this helps.
LotharukpongJS
commented
1 year ago Hi @gallardoalba
Could you also let us know about your sessionInfo()?
Perhaps you can also add fribidi and harfbuzz via conda (perhaps with -c anaconda). Please double-check the link though.
However, I don't think these packages are typically required for users outside of Hebrew and Arabic languages - perhaps these are packages that should ideally be installed by individual users from these regions.
Description for fribidi:
One of the missing links stopping the penetration of free software in Middle East is the lack of support for the Arabic and Hebrew alphabets. In order to have proper Arabic and Hebrew support, the bidi algorithm needs to be implemented. It is our hope that this library will stimulate more free software in the Middle Eastern countries.
Description for harfbuzz:
HarfBuzz is a text shaping library. New Harbuzz targets various font technologies while Old HarfBuzz targets only OpenType fonts.
Also, see the Wikipedia article for harfbuzz.
A possible solution may be to indicate the channels when using conda-build, i.e.
conda-build r-mytai -c conda-forge -c bioconda -c anacondawhich I used with micromamba. Or perhaps it would help if you can install the packages prior to the build.
Let me know if this helps.
Best, Sodai
LotharukpongJS
commented
1 year ago Hi again @gallardoalba ,
When making the conda recipe, could you change the package description as to satisfy the updates to the DESCRIPTION file in R? The exact change can be found here #15
Description: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2018) <doi:10.1093/bioinformatics/btx835>). This package aims to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest.
Many thanks in advance, Sodai
bgruening
commented
1 year ago myTAI is now available as conda package from Bioconda https://anaconda.org/bioconda/r-mytai
HajkD
commented
1 year ago Wonderful!!! Thank you so much!
gallardoalba
commented
1 year ago
myTAIis now available as conda package from Bioconda https://anaconda.org/bioconda/r-mytai
Thanks a lot.
LotharukpongJS
commented
1 year ago Dear @gallardoalba and @bgruening ,
Would it be possible for you to update the conda package description to the one provided here?
When making the conda recipe, could you change the package description as to satisfy the updates to the DESCRIPTION file in R? The exact change can be found here #15
Description: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2018) doi:10.1093/bioinformatics/btx835). This package aims to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest.
Best, Sodai
gallardoalba
commented
1 year ago HajkD
commented
1 year ago Wonderful, thank you so much for pushing this forward!
With very best wishes, Hajk
Hi,
I'm trying to create the Bioconda package, but not sure why it not working. Have you experience on that? Here is the PR https://github.com/bioconda/bioconda-recipes/pull/41628
Regards