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AlexsLemonade / refinebio

Refine.bio harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists.
https://www.refine.bio/
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refine.bio R dependencies #3133

Closed arkid15r closed 1 year ago

arkid15r commented 1 year ago

Context

While working on Docker images building I got stuck with R dependencies related problem. I'd like some ideas on how to approach the issue

Problem or idea

The issue affects illumina and affymetrix images and is mostly about BiocGenerics and AnnotationDbi packages versions.

A default run with no illumina_dependencies.R modifications:

#0 120.9 make[1]: Leaving directory '/tmp/RtmpO3dUvL/R.INSTALL43b568cdc5c/RSQLite/src'
#0 120.9 installing to /usr/local/lib/R/site-library/RSQLite/libs
#0 120.9 ** R
#0 120.9 ** inst
#0 120.9 ** preparing package for lazy loading
#0 120.9 ** help
#0 120.9 *** installing help indices
#0 120.9 ** building package indices
#0 120.9 ** installing vignettes
#0 120.9 ** testing if installed package can be loaded
#0 120.9 * DONE (RSQLite)
#0 120.9
#0 120.9 The downloaded source packages are in
#0 120.9        ‘/tmp/RtmpBmipJX/make_packages’
✔  checking for file ‘/tmp/RtmpBmipJX/remotes7722350ac/oligoClasses/DESCRIPTION’ ...
─  preparing ‘oligoClasses’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
#0 121.2 ─  looking to see if a ‘data/datalist’ file should be added
#0 121.2 ─  building ‘oligoClasses_1.50.4.tar.gz’
   121.2
Installing package into ‘/usr/local/lib/R/site-library’
#0 121.3 (as ‘lib’ is unspecified)
#0 121.4 * installing *source* package ‘oligoClasses’ ...
#0 121.5 ** R
#0 121.5 ** data
#0 121.5 ** inst
#0 121.5 ** preparing package for lazy loading
#0 121.5 Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
#0 121.5   namespace ‘BiocGenerics’ 0.24.0 is being loaded, but >= 0.27.1 is required
#0 121.5 ERROR: lazy loading failed for package ‘oligoClasses’
#0 121.5 * removing ‘/usr/local/lib/R/site-library/oligoClasses’
#0 121.5 Error: Failed to install 'unknown package' from URL:
#0 121.5   (converted from warning) installation of package ‘/tmp/RtmpBmipJX/file772b9a1cb/oligoClasses_1.50.4.tar.gz’ had non-zero exit status
#0 121.5 Execution halted

‘BiocGenerics’ 0.24.0 is being loaded, but >= 0.27.1 is required

After adding 3.11 BiocGenerics package (3.11 seems to be the preferred version currently): 3.11 - 'https://bioconductor.org/packages/3.11/bioc/src/contrib/BiocGenerics_0.34.0.tar.gz',

#0 33.90 Downloading package from url: https://bioconductor.org/packages/3.11/bioc/src/contrib/BiocGenerics_0.34.0.tar.gz
✔  checking for file ‘/tmp/RtmpWkCb9r/remotes8578ed98f/BiocGenerics/DESCRIPTION’ ...
─  preparing ‘BiocGenerics’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
#0 38.90 ─  building ‘BiocGenerics_0.34.0.tar.gz’
   38.90
Installing package into ‘/usr/local/lib/R/site-library’
#0 38.96 (as ‘lib’ is unspecified)
**#0 39.10 ERROR: this R is version 3.4.4, package 'BiocGenerics' requires R >=  3.6.0**
#0 39.12 Error: Failed to install 'unknown package' from URL:
#0 39.12   (converted from warning) installation of package ‘/tmp/RtmpWkCb9r/file85d4b486/BiocGenerics_0.34.0.tar.gz’ had non-zero exit status
#0 39.12 Execution halted

this R is version 3.4.4, package 'BiocGenerics' requires R >= 3.6.0

Then I tried older versions:

3.10 - 'https://bioconductor.org/packages/3.10/bioc/src/contrib/BiocGenerics_0.32.0.tar.gz'

✔  checking for file ‘/tmp/RtmpRErF1i/remotes85c724f8f/BiocGenerics/DESCRIPTION’
─  preparing ‘BiocGenerics’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
#0 43.95 ─  building ‘BiocGenerics_0.32.0.tar.gz’
   43.95
Installing package into ‘/usr/local/lib/R/site-library’
#0 44.01 (as ‘lib’ is unspecified)
#0 44.16 ERROR: this R is version 3.4.4, package 'BiocGenerics' requires R >=  3.6.0
#0 44.17 Error: Failed to install 'unknown package' from URL:
#0 44.17   (converted from warning) installation of package ‘/tmp/RtmpRErF1i/file86d8c6250/BiocGenerics_0.32.0.tar.gz’ had non-zero exit status
#0 44.17 Execution halted

this R is version 3.4.4, package 'BiocGenerics' requires R >= 3.6.0

3.9 - 'https://bioconductor.org/packages/3.9/bioc/src/contrib/BiocGenerics_0.30.0.tar.gz',

#0 34.19 Downloading package from url: https://bioconductor.org/packages/3.9/bioc/src/contrib/BiocGenerics_0.30.0.tar.gz
✔  checking for file ‘/tmp/RtmpdA2WHn/remotes76c1c5d26/BiocGenerics/DESCRIPTION’ ...
─  preparing ‘BiocGenerics’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
#0 38.58 ─  building ‘BiocGenerics_0.30.0.tar.gz’
   38.58
Installing package into ‘/usr/local/lib/R/site-library’
#0 38.64 (as ‘lib’ is unspecified)
#0 38.78 ERROR: this R is version 3.4.4, package 'BiocGenerics' requires R >=  3.6.0
#0 38.79 Error: Failed to install 'unknown package' from URL:
#0 38.79   (converted from warning) installation of package ‘/tmp/RtmpdA2WHn/file72816e392/BiocGenerics_0.30.0.tar.gz’ had non-zero exit status
#0 38.79 Execution halted

this R is version 3.4.4, package 'BiocGenerics' requires R >= 3.6.0

3.8 'https://bioconductor.org/packages/3.8/bioc/src/contrib/BiocGenerics_0.28.0.tar.gz',

✔  checking for file ‘/tmp/RtmpHyVCiL/remotes8380399c4/AnnotationDbi/DESCRIPTION’ ...
─  preparing ‘AnnotationDbi’:
✔  checking DESCRIPTION meta-information ...
✔  checking vignette meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
#0 190.4 ─  building ‘AnnotationDbi_1.50.3.tar.gz’
   190.4
Installing package into ‘/usr/local/lib/R/site-library’
#0 191.7 (as ‘lib’ is unspecified)
#0 192.0 * installing *source* package ‘AnnotationDbi’ ...
#0 192.0 ** R
#0 192.0 ** inst
#0 192.0 ** preparing package for lazy loading
#0 192.0 Error : package ‘BiocGenerics’ 0.28.0 was found, but >= 0.29.2 is required by ‘AnnotationDbi’
#0 192.0 ERROR: lazy loading failed for package ‘AnnotationDbi’
#0 192.0 * removing ‘/usr/local/lib/R/site-library/AnnotationDbi’
#0 192.1 Error: Failed to install 'unknown package' from URL:
#0 192.1   (converted from warning) installation of package ‘/tmp/RtmpHyVCiL/file8cd04b09/AnnotationDbi_1.50.3.tar.gz’ had non-zero exit status
#0 192.1 Execution halted

package ‘BiocGenerics’ 0.28.0 was found, but >= 0.29.2 is required by ‘AnnotationDbi’

Any suggestions?

arkid15r commented 1 year ago

While affymetrix image still requires attention in terms of building time optimization the dependencies issue isn't a blocker anymore. The amd64 images build process is more simple and straightforward.

Closing this out for now.