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 _______________________________________________ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=BRxpnUxOEpNwBnvNz7_tvWT-eQ3eQOVrI6k5vXKWROddWJMxFsDhKTp5JOelaIM_&s=zjoOkX2-XpaR-_jfe7tHgtDLKlyMDnfppaDy0EInzP4&e= [[alternative HTML version deleted]]
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