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Bioconductor / Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
https://bioconductor.org/packages/Rsamtools
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Compilation problem on macOS Sonoma 14.2.1 #62

Closed mohammedemamkhattabunipd closed 7 months ago

mohammedemamkhattabunipd commented 7 months ago

Describe the bug Trying to install Rsamtools through BiocManager, but im getting the following compilation error:

In file included from bam_mate_iter.cpp:2:
In file included from ./BamRangeIterator.h:7:
In file included from ./BamIterator.h:8:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/set:1761:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:526:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:321:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:32:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1313:15: error:
   expected ';' at end of declaration list
  int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const

To Reproduce Run BiocManager::install("Rsamtools").

Expected behavior The package should be compiled correctly.

sessionInfo Please report the output of sessionInfo() here.

R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin23.2.0 (64-bit)
Running under: macOS Sonoma 14.2.1

Matrix products: default
BLAS:   /opt/homebrew/Cellar/openblas/0.3.26/lib/libopenblasp-r0.3.26.dylib 
LAPACK: /opt/homebrew/Cellar/r/4.3.3/lib/R/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] C/UTF-8/C/C/C/C

time zone: Europe/Rome
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.22 compiler_4.3.3      tools_4.3.3
vjcitn commented 7 months ago

Hi, sorry to hear about this; does your R configuration give answers consistent with those at https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/kjohnson1-NodeInfo.html ?

hpages commented 7 months ago

Any reason you need to compile Rsamtools yourself?

Compilation problems on Mac can be easily avoided by installing the package binaries that we provide. Note that installing package binaries is actually the default if you use the R binary for Mac arm64 available at https://cran.r-project.org/bin/macosx/ (pick up R-4.3.3-arm64.pkg). In addition to solving compilation issues, this makes package installations much faster.

If for some reason using R-4.3.3-arm64.pkg is not an option for you, try BiocManager::install("Rsamtools", type="mac.binary.big-sur-arm64").

mohammedemamkhattabunipd commented 7 months ago

It worked with BiocManager::install("Rsamtools", type="mac.binary.big-sur-arm64") thanks a lot.