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Bioconductor / pwalign

Perform pairwise sequence alignments
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Got error when installing in M1 chip mac #1

Closed jianhong closed 4 months ago

jianhong commented 4 months ago

When I install the package, I got call to undeclared function 'get_XStringSet_width'.

Here is the details:

BiocManager::install('Bioconductor/pwalign')
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable)
  (2024-03-12 r86109)
Installing github package(s) 'Bioconductor/pwalign'
Downloading GitHub repo Bioconductor/pwalign@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/tz/xmhml8w1791c398plv8ztw0c0000gn/T/RtmpckwaDv/remotes1103e1ff27274/Bioconductor-pwalign-d0830ed/DESCRIPTION’ ...
─  preparing ‘pwalign’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘pwalign_0.99.0.tar.gz’

* installing *source* package ‘pwalign’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_pairwiseAlignment.c -o R_init_pairwiseAlignment.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c align_utils.c -o align_utils.o
align_utils.c:180:30: error: call to undeclared function 'get_XStringSet_width'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
        int numberOfChars = INTEGER(get_XStringSet_width(GET_SLOT(subject, install("unaligned"))))[0];
                                    ^
align_utils.c:180:30: note: did you mean 'get_XStringSet_length'?
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include/Biostrings_interface.h:140:5: note: 'get_XStringSet_length' declared here
int get_XStringSet_length(SEXP x);
    ^
align_utils.c:180:30: warning: incompatible integer to pointer conversion passing 'int' to parameter of type 'SEXP' (aka 'struct SEXPREC *') [-Wint-conversion]
        int numberOfChars = INTEGER(get_XStringSet_width(GET_SLOT(subject, install("unaligned"))))[0];
                                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:275:22: note: passing argument to parameter 'x' here
int  *(INTEGER)(SEXP x);
                     ^
1 warning and 1 error generated.
make: *** [align_utils.o] Error 1
ERROR: compilation failed for package ‘pwalign’

SessionInfo:

R Under development (unstable) (2024-03-12 r86109)
Platform: aarch64-apple-darwin20
Running under: macOS Ventura 13.3.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

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

time zone: America/New_York
tzcode source: internal

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

loaded via a namespace (and not attached):
 [1] processx_3.8.4      BiocManager_1.30.22 compiler_4.4.0      R6_2.5.1            cli_3.6.2          
 [6] tools_4.4.0         rstudioapi_0.15.0   curl_5.2.1          remotes_2.5.0       desc_1.4.3         
[11] callr_3.7.5         ps_1.7.6            pkgbuild_1.4.4
hpages commented 4 months ago

Make sure you have the latest Biostrings i.e. version 2.71.5. Note that pwalign requires Biostrings >= 2.71.5. However, a serious design flaw in R CMD INSTALL is that it checks for version requirements after compilation, when it should actually do this before doing anything else.

jianhong commented 4 months ago

Thanks! It works!