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

[Jennifer Wokaty]

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

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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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