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@3/3.0.5/lib/libssl.a
/opt/homebrew/Cellar/openssl@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-boun...@r-project.org> on behalf of Leonardo Collado
Torres <lcollado...@gmail.com>
Sent: Thursday, February 23, 2023 2:48 PM
To: Bioc-devel <bioc-devel@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
lcollado...@gmail.com
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