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Question: Installation of MSA package fails
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gravatar for sean.pikosz
5 days ago by
sean.pikosz10
sean.pikosz10 wrote:

Hi,

I searched around but can't seem to locate a similar error -- I'm trying to install the MSA package using the standard installation procedure.  

source("https://bioconductor.org/biocLite.R")
biocLite("msa")

 

EDIT: Wanted to add that biocValid() returns TRUE

It looks like it correctly finishes the ClustalW component and then moves on to the Clustal Omega (version 1.2.0).  During this part an error occurs and the installation fails and exits.  Here is the installation text for Clustal Omega:


----------------------------------------
--------------- ClustalW ---------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile --directory=ClustalOmega
make[1]: Entering directory '/tmp/RtmplMhU6Z/R.INSTALL19ac1e0d4b3d/msa/src/ClustalOmega'
./configure `/usr/lib/R/bin/Rscript -e "if Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`; \
export PKG_LIBS=" "; \
export PKG_CXXFLAGS="  `/usr/lib/R/bin/Rscript -e "if Sys.info()['sysname'] == 'Darwin') cat('-DMATH_H_CLIB')"` -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
export PKG_CFLAGS="  -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
cd src; \
/usr/lib/R/bin/R CMD SHLIB -o libClustalOmega.so exceptions4c/e4c_lite.c argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c clustal/tree.c clustal/util.c clustal/weights.c squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c squid/types.c squid/vectorops.c squid/weight.c hhalign/hhalign.cpp RClustalOmega.cpp mymain.c clustal-omega.c && \
ar rcs libClustalOmega.a exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o && \
cp libClustalOmega.a ../../
configure: WARNING: you should use --build, --host, --target
configure: WARNING: you should use --build, --host, --target
configure: WARNING: you should use --build, --host, --target
configure: WARNING: invalid host type: R!
configure: WARNING: you should use --build, --host, --target
configure: WARNING: invalid host type: Goodbye!
configure:

    Welcome to Clustal Omega - version 1.2.0 (AndreaGiacomo)

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking for Welcome-gcc... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking build system type... Invalid configuration `Welcome': machine `Welcome' not recognized
configure: error: /bin/bash ./config.sub Welcome failed
make[2]: Entering directory '/tmp/RtmplMhU6Z/R.INSTALL19ac1e0d4b3d/msa/src/ClustalOmega/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"     -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c exceptions4c/e4c_lite.c -o exceptions4c/e4c_lite.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"     -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c argtable2/argtable2.c -o argtable2/argtable2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"     -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c argtable2/arg_end.c -o argtable2/arg_end.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"     -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c argtable2/arg_rem.c -o argtable2/arg_rem.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"     -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c argtable2/arg_lit.c -o argtable2/arg_lit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"     -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c argtable2/arg_int.c -o argtable2/arg_int.o
argtable2/arg_int.c: In function ‘strtol0X’:
argtable2/arg_int.c:60:12: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration]
     while (isspace(*ptr))
            ^
argtable2/arg_int.c:89:8: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration]
    if (toupper(*ptr++)!=toupper(X))
        ^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"     -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c argtable2/arg_dbl.c -o argtable2/arg_dbl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"     -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c argtable2/arg_str.c -o argtable2/arg_str.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"     -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c argtable2/arg_file.c -o argtable2/arg_file.o
g++  -I/usr/share/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"
g++: fatal error: no input files
compilation terminated.
/usr/lib/R/etc/Makeconf:168: recipe for target 'kmpp/KMeans.o' failed
make[2]: *** [kmpp/KMeans.o] Error 1
make[2]: Leaving directory '/tmp/RtmplMhU6Z/R.INSTALL19ac1e0d4b3d/msa/src/ClustalOmega/src'
msaMakefile:48: recipe for target 'clustalomega' failed
make[1]: *** [clustalomega] Error 1
make[1]: Leaving directory '/tmp/RtmplMhU6Z/R.INSTALL19ac1e0d4b3d/msa/src/ClustalOmega'
Makevars:36: recipe for target 'build_clustalomega' failed
make: *** [build_clustalomega] Error 2
ERROR: compilation failed for package ‘msa’
* removing ‘/usr/local/lib/R/site-library/msa’

The downloaded source packages are in
        ‘/tmp/Rtmp8bEkqI/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘msa’ had non-zero exit status

 


What jumps out is the part around 

g++  -I/usr/share/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"
g++: fatal error: no input files


And here is the session info:

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

other attached packages:
[1] Rcpp_0.12.14         BiocInstaller_1.28.0

loaded via a namespace (and not attached):
[1] compiler_3.4.2 tools_3.4.2

ADD COMMENTlink modified 5 days ago by UBodenhofer230 • written 5 days ago by sean.pikosz10
2
gravatar for sean.pikosz
5 days ago by
sean.pikosz10
sean.pikosz10 wrote:

Found the problem- all I needed to do is comment out the .First and .Last functions in my Rprofile.site file.  Apparently messages that use cat() were the issue. 

ADD COMMENTlink modified 5 days ago • written 5 days ago by sean.pikosz10
1
gravatar for UBodenhofer
5 days ago by
UBodenhofer230
Johannes Kepler University, Linz, Austria
UBodenhofer230 wrote:

I'm glad you fixed it yourself, thanks for letting us know! It seems this was the same issue as described in A: msa package installation problem. As an advice to everybody who reads this: if you have an Rprofile.site, check it carefully or install 'msa' in a vanilla R session.

ADD COMMENTlink written 5 days ago by UBodenhofer230
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