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vjcitn / CDNMscrna

materials for single-cell RNA-seq workshop at Channing
https://vjcitn.github.io/CDNMscrna/
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libPaths and version #1

Closed mikecho95 closed 4 months ago

mikecho95 commented 4 months ago

Vince, do you think sharing a libpaths might be better? I'm using the latest version on RStudio which is 4.3. Getting this error which is probably temporary, but...

Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TENxPBMCData_1.18.0.tar.gz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.17/data/experiment/src/contrib/TENxPBMCData_1.18.0.tar.gz': status was 'SSL connect error' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package ‘TENxPBMCData’ failed

vjcitn commented 4 months ago

really sorry u r running into this this is on ride?

On Mon, May 13, 2024 at 7:43 AM Michael Cho @.***> wrote:

Vince, do you think sharing a libpaths might be better? I'm using the latest version on RStudio which is 4.3. Getting this error which is probably temporary, but...

Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL ' https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TENxPBMCData_1.18.0.tar.gz ' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : URL ' https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.17/data/experiment/src/contrib/TENxPBMCData_1.18.0.tar.gz': status was 'SSL connect error' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package ‘TENxPBMCData’ failed

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vjcitn commented 4 months ago

I'd say hold off for now. I did not test on ride. It is currently using Bioc 3.17, not recommended. One reason to go with the workshop concept is that it is containerized. The software is validated. But to work on ride I need to jump on there and get organized. You may be right that shared library will have to be used if we are on ride.

mikecho95 commented 4 months ago

I'm happy to not be on ride if that is better!

vjcitn commented 4 months ago

Not clear to me why I don't see this (I got an email about SingleR) in the issues tracker. Anyway, I feel you are in a firewall/certificate situation. It might improve things to use

BiocManager::install(version="3.19") and deal with the upgrade effort if you are running R 4.4, or you could use the obsolete "3.18" and might get the resources from a more agreeable host. But 3.17 is too old -- those URLs are good but the certificate checking you are dealing with (on ride? cluster?) is too severe.

On Wed, May 15, 2024 at 10:08 AM Michael Cho @.***> wrote:

Issue I'm seeing Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL ' https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scRNAseq_2.14.0.tar.gz ' but then: trying URL ' https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scRNAseq_2.14.0.tar.gz ' Content type 'application/gzip' length 349394 bytes (341 KB)

downloaded 341 KB

Trying the same thing with SingleR but wonder if there are latency issues from our side that are causing problems.

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mikecho95 commented 4 months ago

Actually, persistence works. Trying again does the trick. Can't use a newer R on ride AFAIK?

Now I'm getting : g++: error: unrecognized command line option ‘-std=gnu++17’ using C++ compiler: ‘g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)’ using C++17 g++ -std=gnu++17 -I"/app/R-4.3.0@i86-rhel7.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I'/app/R-4.3.0@i86-rhel7.0/lib64/R/library/Rcpp/include' -I'/app/R-4.3.0@i86-rhel7.0/lib64/R/library/beachmat/include' -I'/app/R-4.3.0@i86-rhel7.0/lib64/R/library/BiocNeighbors/include' -I/usr/local/include -I/app/SQLite-3.33.0@i86-rhel7.0/include -I/app/mpfr-4.0.1@i86-rhel7.0/include -I/app/gcc-11.2.0@i86-rhel7.0/include -I/app/tcltk-8.6.8@i86-rhel7.0/include -I/app/curl-7.82.0@i86-rhel7.0/include -I/app/zlib-1.2.11@i86-rhel7.0/include -I/app/pcre2-10.39@i86-rhel7.0/include -I/app/bzip2-1.0.6@i86-rhel7.0/include -I/app/bzip2-1.0.6@i86-rhel7.0/lib -I/app/bzip2-1.0.6@i86-rhel7.0 -I/app/xz-5.2.4@i86-rhel7.0/include -I/app/openssl-1.1.1h@i86-rhel7.0/include -I/app/proj-7.1.0@i86-rhel7.0/include -I/usr/lib/jvm/java-1.8.0-openjdk/include -std=c99 -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++: error: unrecognized command line option ‘-std=gnu++17’ make: *** [RcppExports.o] Error 1 ERROR: compilation failed for package ‘SingleR’

mikecho95 commented 4 months ago

Alternative (which I'm fine with) is to use VS Code or my laptop (since it's all public data)...

vjcitn commented 4 months ago

OK -- when you run into compilation problems in Rstudio, you can usually get around them by working in a pure shell. You start by module load gcc/13.1 or some really recent gcc that they have. Then you start the version of R you want to use in Rstudio, I'd suggest 4.3. module load R/4.3.0 ... start R. Then do BiocManager::install("SingleR") -- the error will go away because you are using a modern compiler. The package will be usable from the R 4.3 in Rstudio

mikecho95 commented 4 months ago

Thanks! Worked.