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Installation #2

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wenbostar opened this issue Feb 27, 2019 · 3 comments
Closed

Installation #2

wenbostar opened this issue Feb 27, 2019 · 3 comments

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@wenbostar
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When I tried to install this package, I got the following error:

> BiocManager::install("LTLA/BiocSingular")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing github package(s) 'LTLA/BiocSingular'
Downloading GitHub repo LTLA/BiocSingular@master
Installing 1 packages: rsvd
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/rsvd_1.0.0.tgz'
Content type 'application/x-gzip' length 6130139 bytes (5.8 MB)
==================================================
downloaded 5.8 MB


The downloaded binary packages are in
	/var/folders/11/zcb2x4g97c92gr68fsd15k6c0000gn/T//RtmpHcxZv1/downloaded_packages
✔  checking for file ‘/private/var/folders/11/zcb2x4g97c92gr68fsd15k6c0000gn/T/RtmpHcxZv1/remotesa673acb6ec9/LTLA-BiocSingular-cfaba17/DESCRIPTION’ ...
─  preparing ‘BiocSingular’:
✔  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
─  building ‘BiocSingular_0.99.12.tar.gz’
   
* installing *source* package ‘BiocSingular’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/r/headers.h:59:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/unordered_map:369:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/__hash_table:16:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:653:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/typeinfo:61:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/exception:82:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/cstdlib:86:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/stdlib.h:94:
In file included from /usr/include/stdlib.h:65:
In file included from /usr/include/sys/wait.h:110:
In file included from /usr/include/sys/resource.h:72:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/stdint.h:119:
In file included from /usr/local/include/stdint.h:82:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/inttypes.h:247:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/10.0.0/include/inttypes.h:30:
/usr/include/inttypes.h:235:8: error: unknown type name 'intmax_t'
extern intmax_t
       ^
/usr/include/inttypes.h:236:9: error: unknown type name 'intmax_t'
imaxabs(intmax_t j);
        ^
/usr/include/inttypes.h:240:2: error: unknown type name 'intmax_t'
        intmax_t quot;
        ^
/usr/include/inttypes.h:241:2: error: unknown type name 'intmax_t'
        intmax_t rem;
        ^
/usr/include/inttypes.h:246:9: error: unknown type name 'intmax_t'
imaxdiv(intmax_t __numer, intmax_t __denom);
        ^
/usr/include/inttypes.h:246:27: error: unknown type name 'intmax_t'
imaxdiv(intmax_t __numer, intmax_t __denom);
                          ^
/usr/include/inttypes.h:250:8: error: unknown type name 'intmax_t'
extern intmax_t
       ^
/usr/include/inttypes.h:256:8: error: unknown type name 'uintmax_t'; did you mean 'uintptr_t'?
extern uintmax_t
       ^
/usr/include/sys/_types/_uintptr_t.h:30:24: note: 'uintptr_t' declared here
typedef unsigned long           uintptr_t;
                                ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/r/headers.h:59:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/unordered_map:369:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/__hash_table:16:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:653:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/typeinfo:61:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/exception:82:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/cstdlib:86:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/stdlib.h:94:
In file included from /usr/include/stdlib.h:65:
In file included from /usr/include/sys/wait.h:110:
In file included from /usr/include/sys/resource.h:72:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/stdint.h:119:
In file included from /usr/local/include/stdint.h:82:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/inttypes.h:247:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/10.0.0/include/inttypes.h:30:
/usr/include/inttypes.h:263:8: error: unknown type name 'intmax_t'
extern intmax_t
       ^
/usr/include/inttypes.h:269:8: error: unknown type name 'uintmax_t'; did you mean 'uintptr_t'?
extern uintmax_t
       ^
/usr/include/sys/_types/_uintptr_t.h:30:24: note: 'uintptr_t' declared here
typedef unsigned long           uintptr_t;
                                ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/r/headers.h:59:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/unordered_map:369:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/__hash_table:16:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:653:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/typeinfo:61:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/exception:82:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/cstdlib:86:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/stdlib.h:94:
In file included from /usr/include/stdlib.h:65:
In file included from /usr/include/sys/wait.h:110:
/usr/include/sys/resource.h:197:2: error: unknown type name 'uint64_t'
        uint64_t ri_user_time;
        ^
/usr/include/sys/resource.h:198:2: error: unknown type name 'uint64_t'
        uint64_t ri_system_time;
        ^
/usr/include/sys/resource.h:199:2: error: unknown type name 'uint64_t'
        uint64_t ri_pkg_idle_wkups;
        ^
/usr/include/sys/resource.h:200:2: error: unknown type name 'uint64_t'
        uint64_t ri_interrupt_wkups;
        ^
/usr/include/sys/resource.h:201:2: error: unknown type name 'uint64_t'
        uint64_t ri_pageins;
        ^
/usr/include/sys/resource.h:202:2: error: unknown type name 'uint64_t'
        uint64_t ri_wired_size;
        ^
/usr/include/sys/resource.h:203:2: error: unknown type name 'uint64_t'
        uint64_t ri_resident_size;
        ^
/usr/include/sys/resource.h:204:2: error: unknown type name 'uint64_t'
        uint64_t ri_phys_footprint;
        ^
/usr/include/sys/resource.h:205:2: error: unknown type name 'uint64_t'
        uint64_t ri_proc_start_abstime;
        ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘BiocSingular’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BiocSingular’
Error in i.p(...) : 
  (converted from warning) installation of package ‘/var/folders/11/zcb2x4g97c92gr68fsd15k6c0000gn/T//RtmpHcxZv1/filea674473df68/BiocSingular_0.99.12.tar.gz’ had non-zero exit status
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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

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

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0         rstudioapi_0.9.0   knitr_1.21         magrittr_1.5       R6_2.4.0           tools_3.5.1        pkgbuild_1.0.2     xfun_0.5          
 [9] cli_1.0.1          withr_2.1.2        htmltools_0.3.6    remotes_2.0.2      yaml_2.2.0         digest_0.6.18      assertthat_0.2.0   rprojroot_1.3-2   
[17] crayon_1.3.4       processx_3.2.1     BiocManager_1.30.4 callr_3.1.1        ps_1.3.0           curl_3.3           evaluate_0.13      rmarkdown_1.11    
[25] compiler_3.5.1     backports_1.1.3    prettyunits_1.0.2  BiocStyle_2.10.0
@LTLA
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LTLA commented Feb 27, 2019

I've never seen this before. Can you compile other Rcpp-dependent packages? I suspect it's a problem with your system libraries or headers, probably need to update Xcode or something.

@wenbostar
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Author

Thanks. The Xcode installed is the latest version. It works in Linux so I will use it on Linux system.

@LTLA
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Owner

LTLA commented Feb 27, 2019

Okay. BiocSingular is now in Bioconductor, so there will be Mac OSX binaries available soon-ish.

@LTLA LTLA closed this as completed Feb 27, 2019
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@wenbostar @LTLA