MSA package fails to be installed - installation of package ‘msa’ had non-zero exit status
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Entering edit mode
@user-25080
Last seen 8 weeks ago

Hi there, These last days I'm trying to install the msa package to perform a multiple sequence alignment on my computer. I use my Rstudio on Uduntu linux. I had some issues too on windows enviroment but I managed to resolve these. Any ideas why this happens?

BiocManager::install("msa")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'msa'
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/msa_1.22.0.tar.gz'
Content type 'application/x-gzip' length 3767128 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

* installing *source* package ‘msa’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/doctoras/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include'   -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-PsrVor/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_msa.cpp -o R_init_msa.o
In file included from ./Muscle/RMuscle.h:4,
                 from R_init_msa.cpp:3:
./Muscle/muscle.h:54: warning: "assert" redefined
   54 | #define assert(exp)     ((void)0)
      | 
In file included from /usr/include/c++/10/cassert:44,
                 from /home/doctoras/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:137,
                 from /home/doctoras/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/utils/tinyformat.h:40,
                 from /home/doctoras/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:70,
                 from /home/doctoras/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
                 from ./ClustalOmega/src/RClustalOmega.h:4,
                 from R_init_msa.cpp:1:
/usr/include/assert.h:50: note: this is the location of the previous definition
   50 | # define assert(expr)  (__ASSERT_VOID_CAST (0))
      | 
.
.
.
.
Everything goes well until this point........
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.
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libs/allchblk.o:/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/pthread_stop_world.o:/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
/usr/bin/ld: .libs/mach_dep.o:/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'; .libs/allchblk.o:/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:1180: libgc.la] Error 1
make[3]: Leaving directory '/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2'
make[2]: *** [Makefile:1517: all-recursive] Error 1
make[2]: Leaving directory '/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2'
make[1]: *** [msaMakefile:5: build_gc] Error 2
make[1]: Leaving directory '/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2'
make: *** [Makevars:12: build_gc] Error 2
ERROR: compilation failed for package ‘msa’
* removing ‘/home/doctoras/R/x86_64-pc-linux-gnu-library/4.0/msa’

The downloaded source packages are in
    ‘/tmp/RtmpvRTKyX/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘msa’ had non-zero exit status

# include your problematic code here with any corresponding output 
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:1180: libgc.la] Error 1
make[3]: Leaving directory '/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2'
make[2]: *** [Makefile:1517: all-recursive] Error 1
make[2]: Leaving directory '/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2'
make[1]: *** [msaMakefile:5: build_gc] Error 2
make[1]: Leaving directory '/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2'
make: *** [Makevars:12: build_gc] Error 2
ERROR: compilation failed for package ‘msa’
* removing ‘/home/doctoras/R/x86_64-pc-linux-gnu-library/4.0/msa’

The downloaded source packages are in
    ‘/tmp/RtmpvRTKyX/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘msa’ had non-zero exit status

# please also include the results of running the following in an R session 

sessionInfo( )
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.10

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8   
 [6] LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.2      rsconnect_0.8.16    tools_4.0.2         yaml_2.2.1
msa MultipleSequenceAlignment • 98 views
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Entering edit mode
UBodenhofer ▴ 250
@ubodenhofer-5425
Last seen 17 days ago
University of Applied Sciences Upper Au…

I am sorry that you are encountering problems installing 'msa'! Unfortunately, the package is known to have some installation problems on more exotic platforms, but yours seems quite standard and not exotic at all. Do you have a non-standard gcc compiler or anything like that? I am afraid I cannot help much at this point. If you want, you can send the entire output by posting it here or sending it to me by e-mail, maybe I can spot a pecularity. Otherwise I'd recommend you to wait for the upcoming BioC 3.13 release - hoping that it would solve your issues.

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