msa Installation failed - please help
0
0
Entering edit mode
Ido • 0
@bf6e46ea
Last seen 11 months ago
Israel

Hi everyone, Is there a problem in the current msa package installation? I did everything by the book.

> sessionInfo( )
R version 4.2.0 (2022-04-22)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS/LAPACK: /home/ido/miniconda3/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8  
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.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_1.30.20 compiler_4.2.0      tools_4.2.0

Thanks, Ido

Below are the relevant error messages from the output

mymain.c: In function 'ParseCommandLine':
mymain.c:565:34: error: 'PACKAGE_NAME' undeclared (first use in this function)
  565 |         printf("%s - %s (%s)\n", PACKAGE_NAME, PACKAGE_VERSION, PACKAGE_CODENAME);
      |                                  ^~~~~~~~~~~~
mymain.c:565:34: note: each undeclared identifier is reported only once for each function it appears in
mymain.c:565:48: error: 'PACKAGE_VERSION' undeclared (first use in this function)
  565 |         printf("%s - %s (%s)\n", PACKAGE_NAME, PACKAGE_VERSION, PACKAGE_CODENAME);
      |                                                ^~~~~~~~~~~~~~~
mymain.c:565:65: error: 'PACKAGE_CODENAME' undeclared (first use in this function)
  565 |         printf("%s - %s (%s)\n", PACKAGE_NAME, PACKAGE_VERSION, PACKAGE_CODENAME);
      |                                                                 ^~~~~~~~~~~~~~~~
mymain.c:610:43: error: 'PACKAGE' undeclared (first use in this function)
  610 |         arg_print_errors(stdout, opt_end, PACKAGE);
      |                                           ^~~~~~~
make[2]: *** [/home/ido/miniconda3/lib/R/etc/Makeconf:170: mymain.o] Error 1
make[2]: Leaving directory '/tmp/RtmpdwMi6o/R.INSTALL3c7fb81f9ea6c0/msa/src/ClustalOmega/src'
make[1]: *** [msaMakefile:48: clustalomega] Error 1
make[1]: Leaving directory '/tmp/RtmpdwMi6o/R.INSTALL3c7fb81f9ea6c0/msa/src/ClustalOmega'
make: *** [Makevars:36: build_clustalomega] Error 2
ERROR: compilation failed for package 'msa'
* removing '/home/ido/miniconda3/lib/R/library/msa'

The downloaded source packages are in
        '/tmp/RtmpHO4Mkq/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(...) :
  installation of package 'msa' had non-zero exit status
Install msa • 610 views
ADD COMMENT
0
Entering edit mode

What is the "problem" ? Provide what is the code you ran and what is the error you have

ADD REPLY
0
Entering edit mode

I have just added the relevant part from output. The code is:

BiocManager::install("msa")
ADD REPLY

Login before adding your answer.

Traffic: 373 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6