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Question: msa package installation problem
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gravatar for branislav misovic
10 months ago by
Netherlands, Leiden
branislav misovic120 wrote:

hi MSA  devs ,all 

  I have  msa installation problem  (all dependent packages went fine  ).

biocLite ("msa")

...

 Welcome to Clustal Omega - version 1.2.0 (AndreaGiacomo)

                       +NMMMMMMMMMS=
                    MMMMM?      :MMMMM8
                  IMMMMS           MMMMM,
                ~MMMMN              ,MMMMM
               =MMMMM                 MMMMM
              ?MMMMM                  +MMMMM
              MMMMMS                   MMMMM
              MMMMM                    MMMMM:
              MMMMM                    MMMMM+
              MMMMM                    MMMMM~
              MMMMM                    MMMMM
              MMMMMZ                   MMMMM
               MMMMM                  ,MMMMZ
                MMMM8                 MMMM+
                 MMMMS               MMMM,
                   MMMMO           MMMM
            ,N       SMMM        MMM8       +8
            ,M7         M+       M+        :M8
            ,MMMMMMMMMMMMI       MMMMMMMMMMMM8
            ,MMMMMMMMMMMM8       MMMMMMMMMMMM8
            ,MMMMMMMMMMMMN       MMMMMMMMMMMM8

              
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 ...-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 `...': machine `...' not recognized
configure: error: /bin/bash ./config.sub ... failed
make[2]: Entering directory `/tmp/RtmpprcIG1/R.INSTALL43a16ade47f6/msa/src/ClustalOmega/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/bmisovic/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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"/home/bmisovic/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c argtable2/argtable2.c -o argtable2/argtable2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/bmisovic/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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"/home/bmisovic/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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"/home/bmisovic/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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"/home/bmisovic/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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:60:5: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration]
     while (isspace(*ptr))
     ^
argtable2/arg_int.c:89:4: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration]
    if (toupper(*ptr++)!=toupper(X))
    ^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/bmisovic/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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"/home/bmisovic/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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"/home/bmisovic/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c argtable2/arg_file.c -o argtable2/arg_file.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/bmisovic/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"    -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c kmpp/KMeans.cpp -o kmpp/KMeans.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/bmisovic/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"    -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c kmpp/KmTree.cpp -o kmpp/KmTree.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/bmisovic/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"    -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c kmpp/KmUtils.cpp -o kmpp/KmUtils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/bmisovic/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c clustal/hhalign_wrapper.c -o clustal/hhalign_wrapper.o
clustal/hhalign_wrapper.c:22:20: fatal error: config.h: No such file or directory
 #include "config.h"
                    ^
compilation terminated.
make[2]: *** [clustal/hhalign_wrapper.o] Error 1
make[2]: Leaving directory `/tmp/RtmpprcIG1/R.INSTALL43a16ade47f6/msa/src/ClustalOmega/src'
make[1]: *** [clustalomega] Error 1
make[1]: Leaving directory `/tmp/RtmpprcIG1/R.INSTALL43a16ade47f6/msa/src/ClustalOmega'
make: *** [build_clustalomega] Error 2
ERROR: compilation failed for package ‘msa’
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

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

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

other attached packages:
[1] BiocInstaller_1.24.0


any tips ?

 

msa
ADD COMMENTlink modified 9 months ago by Nam10 • written 10 months ago by branislav misovic120
1

Probably not enough info. Maybe ADD the output from the installation process from where it starts

    Welcome to Clustal Omega - version 1.2.0 (AndreaGiacomo)

and then post a comment indicating that you've updated your post.

ADD REPLYlink written 10 months ago by Martin Morgan ♦♦ 20k

Ok Martin just did what you asked.

ADD REPLYlink written 10 months ago by branislav misovic120
2
gravatar for UBodenhofer
10 months ago by
UBodenhofer200
Johannes Kepler University, Linz, Austria
UBodenhofer200 wrote:

Thanks for posting this issue, Branislav! Actually, this is not the first time that I am seeing this issue with config.h when compiling hhalign (shipped as part of ClustalOmega). We will try to deal with it soon. We still do not know what the reason is, since everything usually works fine on all Linux systems and we could not yet reproduce the error on any of our systems. We will keep you posted.

ADD COMMENTlink written 10 months ago by UBodenhofer200
1

Thank you  for quick response, no rush here ....   I just found your package and wanted to test it,  you made fantastic easy  MSA access!
Btw.  how can  i skip installation of  Clustal omega ?  I guess  other aligners  are  probably working  (i just noticed the  info in your  PDF demo about commenting some lines for MAC OS users ) .

 

 

ADD REPLYlink written 10 months ago by branislav misovic120
1

In case it's useful, it seems like the error comes from https://github.com/Bioconductor-mirror/msa/blob/master/src/ClustalOmega/configure#L4750 maybe because msa/src/ClustalOmega/config.guess returns '...' (branislav could test this by downloading the package source and tryint to run the config.guess command)? This is being generated by https://github.com/Bioconductor-mirror/msa/blob/master/src/ClustalOmega/configure.ac#L127 AC_CANONICAL_HOST.

ADD REPLYlink written 10 months ago by Martin Morgan ♦♦ 20k
thanx for the feedback gents ,  and sorry for the slow reply ... today i checked it and if i run :

> ./config.guess    

x86_64-unknown-linux-gnu

# If i check the config.guess  shell script my  box is 
UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
UNAME_SYSTEM=`(uname -s) 2>/dev/null`  || UNAME_SYSTEM=unknown
UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
> echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}"
x86_64:Linux:3.16.0-77-generic:#99~14.04.1-Ubuntu SMP Tue Jun 28 19:17:10 UTC 2016

the ./configure   gives no issues in terminal output but i see some errors in the  log
The config.log  file is  in gdir :

https://drive.google.com/drive/folders/0B4LuO2QQI4otQVNjWm0wQXVnRFk?usp=sharing

Ok hopefully you  can detect what is wrong …

ADD REPLYlink modified 10 months ago • written 10 months ago by branislav misovic120

Thanks for your detailed analysis, Branislav! I had a look at the config.log file and everything seems fine. Don't worry about the error messages. They come from compiler tests. What is important is the "configure: exit 0" in the end. Moreover, I see "config.status:1173: creating src/config.h" below. Can you please check whether the file is there and whether it was actually been created by the configure script. As far as I can interpret your original issue, this is the file that the compiler complains about. Thanks, Ulrich

ADD REPLYlink written 10 months ago by UBodenhofer200

ok thanx, i checked ,  it is created , i deleted the  ClustalOmega/src/config.h  file before runing the  ./configure ...

still if i run the install.packages  ("msa_1.6.0.tar.gz" ,  repos = NULL) i get the same error :

checking build system type... Invalid configuration `...': machine `...' not recognized
configure: error: /bin/bash ./config.sub ... failed

I'll send you an email ,  we can  post a fix here on forum when we find the bug.

ADD REPLYlink written 10 months ago by branislav misovic120
2
gravatar for branislav misovic
9 months ago by
Netherlands, Leiden
branislav misovic120 wrote:

    I  found an issue  ...   Year ago i added 2lines into  my Rprofile.site   : the    source("http://bioconductor.org/biocLite.R")   and  a line with   cat("some message") ,for some reminder  .  This cat was the hidden trouble maker ,  never had issue with it till now ...   I discovered by accident this week that  when installing new  shiny version  & its dependency on httpuv  package,  i got an error that had some pieces of my cat("some message") around error message, apparently during installation Rprofile.site is run as well.    So i decided for quick test to start R via    R --vanillla  (to  skip  Rprofile.site),  and i could install shiny and later your msa ... so i was the culprit :)   sorry for the confusion .


Now i should post to dev forums to ask why is this so, but not many people put reminders into  Rprofile.site  :)

ciao

Branko

ADD COMMENTlink written 9 months ago by branislav misovic120
1
gravatar for UBodenhofer
10 months ago by
UBodenhofer200
Johannes Kepler University, Linz, Austria
UBodenhofer200 wrote:

I now tried to dig deeper into this issue. I cannot reproduce the error, but I fully agree with Martin Morgan that something goes wrong with the configure script in 'src/ClustalOmega'. I suggest the following in line with Martin's suggestion:

  1. Download the package tarball and untar it to a temporary location.
  2. Change to 'msa/src/ClustalOmega' and run './configure' there.
  3. Let us know what happened (either by private message or, preferably by posting here):
    1. Show/send us 'msa/src/ClustalOmega/config.log'.
    2. Has 'msa/src/ClustalOmega/clustal/config.h' been created? I suppose no, otherwise you would not encounter the error.
    3. Also run 'msa/src/ClustalOmega/config.guess' as suggested by Martin to make sure whether the system type is correctly identified.

I hope that will bring us closer to the source of the problem. Sorry for asking such efforts from you!

ADD COMMENTlink modified 10 months ago • written 10 months ago by UBodenhofer200

I got the same problem when install msa.

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.10

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.20.3

loaded via a namespace (and not attached):
[1] tools_3.3.2

I followed your suggestion, and these are the results:

1. the config.log https://www.dropbox.com/s/4v6wenujzuryrgl/config.log?dl=0

2. The folder clustal has not been created in the ClustalOmega folder, so there is not config.h file

3. ./config.guess
x86_64-unknown-linux-gnu

 
ADD REPLYlink modified 9 months ago • written 9 months ago by Nam10
1
gravatar for Nam
9 months ago by
Nam10
Nam10 wrote:

I know the the solution!

After updating biocinstaller following the instruction here https://bioconductor.org/install/#troubleshoot-biocinstaller, I have successfully install msa!

ADD COMMENTlink modified 9 months ago • written 9 months ago by Nam10
0
gravatar for UBodenhofer
10 months ago by
UBodenhofer200
Johannes Kepler University, Linz, Austria
UBodenhofer200 wrote:

I tried to work on this issue in the last few days. I even resurrected a laptop running Ubuntu 14.04 in order to test whether I can reproduce the problem. I even switched to the 'nl_NL' locale. However, I did not succeed, all attempts to install the 'msa' package completed successfully without a single hint to the troubles experienced by Branko. So, the problem remains an enigma to me. 

Branko, I admit that this is no solution of the actual problem, but is it possible that you upgrade to a new R version and/or Ubuntu release? Would you also be willing to try the following: I could build a binary package on my Ubuntu 14.04 system and send it to you - hoping that you can install it on your system. What do you think?

ADD COMMENTlink written 10 months ago by UBodenhofer200

You can build the binary package on Ubuntu 16.10 and send it to me.

ADD REPLYlink written 9 months ago by Nam10
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