[Bioc-devel] Openssl is not available in netConnectHttps for importing remote BigWig files

[Leonardo Collado Torres]

Awesome, thanks to both of you for checking this!

Best,
Leo


On Thu, Mar 2, 2023 at 2:36 PM Hervé Pagès <hpages.on.github using gmail.com> wrote:
>
> and also:
>
>    kjohnson:~ biocbuild$ curl -O
> https://bioconductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/rtracklayer_1.58.0.tgz
>
>    kjohnson:~ biocbuild$ tar zxf rtracklayer_1.58.0.tgz
>
>    kjohnson:~ biocbuild$ nm rtracklayer/libs/rtracklayer.so | grep
> _ssl_security
>    0000000000059aa8 T _ssl_security
>    000000000006dda0 T _ssl_security_cert
>    000000000006df38 T _ssl_security_cert_chain
>    000000000006deb8 t _ssl_security_cert_key
>    000000000005800c t _ssl_security_default_callback
>
> which confirms that the Mac arm64 binary currently available in release
> got linked to openssl.
>
> H.
>
> On 02/03/2023 10:52, Jennifer Wokaty wrote:
> > Hi Leo,
> >
> > I discussed this with Herve who noticed that you're running rtracklayer on an M1 Mac, so he looked at https://bioconductor.org/checkResults/3.16/bioc-mac-arm64-LATEST/rtracklayer/kjohnson-buildbin.html. It's linking to the static libraries for libssl.a and libcrypto.a so that it can be used on machine without these libraries according to the following line
> >
> > clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/aliType.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/hex.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread /opt/homebrew/Cellar/openssl using 3/3.0.5/lib/libssl.a /opt/homebrew/Cellar/openssl using 3/3.0.5/lib/libcrypto.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
> >
> >
> > We have not made any recent changes to these binaries but these are the first ones we made available for M1 Macs.
> >
> > Jennifer Wokaty (they/them)
> >
> > Waldron Lab at CUNY SPH
> > Bioconductor Core Team
> > ________________________________
> > From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Leonardo Collado Torres <lcolladotor using gmail.com>
> > Sent: Thursday, February 23, 2023 2:48 PM
> > To: Bioc-devel <bioc-devel using r-project.org>
> > Subject: [Bioc-devel] Openssl is not available in netConnectHttps for importing remote BigWig files
> >
> > ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.***
> >
> >
> > Hi Bioc-devel,
> >
> > recount had been failing in recent months at bioc-release and
> > bioc-devel. I finally had the time to dive into it, and eventually
> > that led to an error on rtracklayer that I reported at
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lawremi_rtracklayer_issues_83&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=BRxpnUxOEpNwBnvNz7_tvWT-eQ3eQOVrI6k5vXKWROddWJMxFsDhKTp5JOelaIM_&s=B-a7fuBFTYUWc0FdqCGxVp5IX_asMYsRZ1BAQeYsXmI&e= . Michael Lawrence
> > noticed that my R session information didn't show openssl being
> > loaded. In a message there, Michael speculated that maybe a change in
> > how the rtracklayer binaries were being built by Bioconductor could be
> > the source of the issue.
> >
> > Here's a small reprex for the error:
> >
> > library("GenomicRanges")
> > library("rtracklayer")
> > range <- GRanges(seqnames = "chrY", ranges = IRanges(1, 57227415))
> > rtracklayer::import("https://urldefense.proofpoint.com/v2/url?u=http-3A__sciserver.org_public-2Ddata_recount2_data_SRP002001_bw_mean-5FSRP002001.bw&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=BRxpnUxOEpNwBnvNz7_tvWT-eQ3eQOVrI6k5vXKWROddWJMxFsDhKTp5JOelaIM_&s=F0oFWXFFxsylMq6666c00YZ05rFgLzkkocPevscWyQc&e= ",
> > selection = reduce(range), as = "RleList")
> >
> > And here's the error output:
> >
> > Error in seqinfo(con) : UCSC library operation failed
> > In addition: Warning message:
> > In seqinfo(con) :
> >    No openssl available in netConnectHttps for sciserver.org : 443
> >> traceback()
> > 7: seqinfo(con)
> > 6: seqinfo(con)
> > 5: .local(con, format, text, ...)
> > 4: import(FileForFormat(con), ...)
> > 3: import(FileForFormat(con), ...)
> > 2: rtracklayer::import("https://urldefense.proofpoint.com/v2/url?u=http-3A__sciserver.org_public-2Ddata_recount2_data_SRP002001_bw_mean-5FSRP002001.bw&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=BRxpnUxOEpNwBnvNz7_tvWT-eQ3eQOVrI6k5vXKWROddWJMxFsDhKTp5JOelaIM_&s=F0oFWXFFxsylMq6666c00YZ05rFgLzkkocPevscWyQc&e= ",
> >         selection = reduce(range), as = "RleList")
> > 1: rtracklayer::import("https://urldefense.proofpoint.com/v2/url?u=http-3A__sciserver.org_public-2Ddata_recount2_data_SRP002001_bw_mean-5FSRP002001.bw&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=BRxpnUxOEpNwBnvNz7_tvWT-eQ3eQOVrI6k5vXKWROddWJMxFsDhKTp5JOelaIM_&s=F0oFWXFFxsylMq6666c00YZ05rFgLzkkocPevscWyQc&e= ",
> >         selection = reduce(range), as = "RleList")
> >> packageVersion("rtracklayer")
> > [1] �1.58.0�
> >
> >
> > I'm not sure what else I can do to help. As noted at
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lawremi_rtracklayer_issues_83-23issuecomment-2D1437585161&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=BRxpnUxOEpNwBnvNz7_tvWT-eQ3eQOVrI6k5vXKWROddWJMxFsDhKTp5JOelaIM_&s=fZTgbHR5Wn0VJkseyYfOtokJM5Xe__FMapkwjbUze04&e= ,
> > recount / rtracklayer versions from BioC 3.11 do work with the same
> > links.
> >
> > Thanks in advance.
> >
> > Best,
> > Leo
> >
> >
> > Leonardo Collado Torres, Ph. D.
> > Investigator
> >
> > LIEBER INSTITUTE for BRAIN DEVELOPMENT
> > 855 N. Wolfe St., Suite 300
> > Baltimore, MD 21205
> > lcolladotor.github.io
> > lcolladotor using gmail.com
> >
> > _______________________________________________
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> >
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> >
> >
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>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>