ERROR: dependencies ‘mnormt’, ‘pbivnorm’, ‘quadprog’, ‘numDeriv’ are not available for package ‘lava

[R McLaren]

Hi

I have been rebuilding my setup for R and this error message appears. 

ERROR: dependencies ‘mnormt’, ‘pbivnorm’, ‘quadprog’, ‘numDeriv’ are not available for package ‘lavaan’

* removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.3/lavaan’

My question is, Is there a solution path or will this require another uninstall/reinstall? 

Thanks,  

Rick

[kma...@aol.com]

Rick,
Thanks for posting this question.  I am a Linux newbie encountering the same problem under Mint 18.  The error that I am getting is that R cannot find gfortran when it attempts to build these packages.  One person got around the problem by copying gfortran to where R was looking but I have not located gfortran to copy from.  So, I do not have an answer but I can confirm that the problem is not unique to your machine.  If you scroll up through the error messages, does your problem also trace to not finding gfortran?

Keith
------------------------
Keith A. Markus
John Jay College of Criminal Justice, CUNY
http://jjcweb.jjay.cuny.edu/kmarkus
Frontiers of Test Validity Theory: Measurement, Causation and Meaning.
http://www.routledge.com/books/details/9781841692203/

[R MacLaren]

Hi Keith and thanks for the note. Unfortunately after I successfully uninstalled R (i.e., after considerable grief), given Ubuntu was nagging me for updates, I rebooted and the error messages were lost. I did read the error messages and I didn't encode whether or not gfortran was implicated. 

Of the error messages I remember, the 'car' file was holding fast and was resistant to extinction, and out of date. The continual message I kept getting was (to my amusement) kind of a scolding reminder to me that I'd neglected to accept updates. 

Presently I'm hoping to install R again, and I'll wait for folks to possibly reply to another thread just in case the standard R package is not the preferred package for using lavaan, sem, and EGA/MGM tools. 

I'll keep my eyes peeled, during the install process, for signs of fortran issues and I'll post here if I find any that may be relevant to your situation.

Good luck with your research. 

Rick 

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[R McLaren]

btw I don't think the message I reported on in my last note was from lavaan, I believe it came from the R/linux programming sphere.  

[Yves Rosseel]

I sounds like you need to install gcc-gfortran. One would think that a
distro like Mint would do that out of the box (or at least when R is
installed).

As a long-term linux user (using Arch linux), I prefer to install R from
source. This is the script I use for the current version of R:

#!/bin/sh
VERSION=3.3.2
cd /tmp
wget http://cran.at.r-project.org/src/base/R-3/R-$VERSION.tar.gz
tar xfz R-$VERSION.tar.gz
cd R-$VERSION
./configure --enable-memory-profiling --enable-R-shlib
make
make install


You need to install the basic compilation tools (make, gcc,
gcc-gfortran, ...) first, but once this is in place, it is bullet-proof.

Yves.

[R MacLaren]

Thanks Yves I wasn't aware my installation was mint - I don't recall if I mentioned the OS is Ubuntu 16.04 LTS. 

I'll follow up with the script you sent me. 

It seems when Ubuntu requests updates, it doesn't appear to tell or warn me in perhaps harsh enough terms (i.e., like !!!) that my system is upgrading to a new name like frosty flakes rotton turnip or mint (or whatever is the new name) for upgrades. When prompted by Ubuntu for these revisions, I'm averse to accepting them for fear that they'll blow up a perfectly functioning OS and stats gear, but I think I've accepted upgrades that don't jive with my older versions. 

My hypothesis is that I accidentally accepted the rotton turnip upgrade, when what I really need is mint. 

[R McLaren]

I just got an error message - my system is not accepting updates. And it is asking me to accept untrusted packages, which I also don't wish to do if I don't know they're safe. Are these usually or most always safe? 

Rick 

[kma...@aol.com]

Rick and Yves,
Rick, I am the one using Mint.  However, it is based on Ubuntu, which you are apparently using.

I tried this:
sudo apt-get install gfortran

It solved 3/4 of the problem but quadprog is still not working:

>>>

/usr/share/R/share/make/shlib.mk:6: recipe for target 'quadprog.so' failed

make: *** [quadprog.so] Error 1

ERROR: compilation failed for package ‘quadprog’

* removing ‘/home/kmarkus/.rkward/library/quadprog’

ERROR: dependency ‘quadprog’ is not available for package ‘lavaan’

* removing ‘/home/kmarkus/.rkward/library/lavaan’

>>>

Yves, can you point me to more specific instructions about what other tools I need to install and how to install them?  This is literally my 4th day using Linux.  So, I'm sorry that I do not have much background knowledge to work with.  I'm sure this must be a pretty basic question.

Thanks,

[kma...@aol.com]

Actually, I missed an earlier message that seems informative:

/usr/bin/ld: cannot find -lblas

collect2: error: ld returned 1 exit status

Is lblas something that I also need to install?

[R McLaren]

I will mirror your method presently, thanks.  

Rick 

[R MacLaren]

Keith did you install fortran from root? 

[R MacLaren]

The reason I ask is because I found files accessible only through root, that were blocking my uninstall, so I sent the commands from root #. The same command executed outside of the # environment were of no effect in my uninstall - reinstall instance.  

[R McLaren]

Ok so just to confirm, you performed the command sudo apt-get install gfortran from which directory and did you have a $ > or # prompt? 

Rick 

[R McLaren]

sudo apt-get install gfortran

from $

gets me 

ubuntu@ubuntu-Satellite-L775D:~$ sudo apt-get install gfortran

[sudo] password for ubuntu: 

Reading package lists... Done

Building dependency tree       

Reading state information... Done

gfortran is already the newest version (4:5.3.1-1ubuntu1).

gfortran set to manually installed.

0 upgraded, 0 newly installed, 0 to remove and 113 not upgraded.

ubuntu@ubuntu-Satellite-L775D:~$ ^C

ubuntu@ubuntu-Satellite-L775D:~$ 

R

[R MacLaren]

And it is reversible without grief:

ubuntu@ubuntu-Satellite-L775D:~$ sudo apt-get remove gfortran

Reading package lists... Done

Building dependency tree       

Reading state information... Done

The following packages will be REMOVED:

  gfortran

0 upgraded, 0 newly installed, 1 to remove and 113 not upgraded.

After this operation, 15.4 kB disk space will be freed.

Do you want to continue? [Y/n] y

(Reading database ... 472032 files and directories currently installed.)

Removing gfortran (4:5.3.1-1ubuntu1) ...

Processing triggers for man-db (2.7.5-1) ...

ubuntu@ubuntu-Satellite-L775D:~$ ^C

ubuntu@ubuntu-Satellite-L775D:~$ ^C

ubuntu@ubuntu-Satellite-L775D:~$ 

[R MacLaren]

Hi Yves I thought I followed your script but I got this reply: 

2017-01-28 20:08:17 (481 KB/s) - ‘R-3.3.2.tar.gz.1’ saved [29440670/29440670]

ubuntu@ubuntu-Satellite-L775D:/tmp$ tar xfz R-$VERSION.tar.gz

ubuntu@ubuntu-Satellite-L775D:/tmp$ cd R-$VERSION

ubuntu@ubuntu-Satellite-L775D:/tmp/R-3.3.2$ ./configure --enable-memory-profiling --enable-R-shlib

checking build system type... x86_64-pc-linux-gnu

checking host system type... x86_64-pc-linux-gnu

loading site script './config.site'

loading build-specific script './config.site'

checking for pwd... /bin/pwd

checking whether builddir is srcdir... yes

checking for working aclocal... found

checking for working autoconf... found

checking for working automake... found

checking for working autoheader... found

checking whether ln -s works... yes

checking for bison... no

checking for byacc... no

checking for ar... ar

checking for a BSD-compatible install... /usr/bin/install -c

checking for sed... /bin/sed

checking for which... /usr/bin/which

checking for less... /usr/bin/less

checking for gtar... no

checking for gnutar... no

checking for tar... /bin/tar

checking for tex... /usr/bin/tex

checking for pdftex... /usr/bin/pdftex

checking for pdflatex... /usr/bin/pdflatex

checking for makeindex... /usr/bin/makeindex

checking for texi2any... no

configure: WARNING: you cannot build info or HTML versions of the R manuals

checking for texi2dvi... no

checking for kpsewhich... /usr/bin/kpsewhich

checking for latex inconsolata package... missing

configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally

checking for unzip... /usr/bin/unzip

checking for zip... /usr/bin/zip

checking for gzip... /bin/gzip

checking for bzip2... /bin/bzip2

checking for firefox... no

checking for mozilla... no

checking for galeon... no

checking for opera... /usr/bin/opera

using default browser ... /usr/bin/opera

checking for acroread... no

checking for acroread4... no

checking for xdg-open... /usr/bin/xdg-open

checking for notangle... false

checking for realpath... /usr/bin/realpath

checking for pkg-config... /usr/bin/pkg-config

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 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 whether gcc needs -traditional... no

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 how to run the C preprocessor... gcc -E

checking for f95... f95

checking whether we are using the GNU Fortran 77 compiler... yes

checking whether f95 accepts -g... yes

checking for g++... g++

checking whether we are using the GNU C++ compiler... yes

checking whether g++ accepts -g... yes

checking how to run the C++ preprocessor... g++ -E

checking whether __attribute__((visibility())) is supported... yes

checking whether gcc accepts -fvisibility... yes

checking whether f95 accepts -fvisibility... yes

checking for gcc... gcc

checking whether we are using the GNU Objective C compiler... no

checking whether gcc accepts -g... no

checking for Objective C++ compiler... trying some possibilities

checking whether g++ can compile ObjC++... no

checking whether  can compile ObjC++... no

no working ObjC++ compiler found

checking how to print strings... printf

checking for a sed that does not truncate output... (cached) /bin/sed

checking for fgrep... /bin/grep -F

checking for ld used by gcc... /usr/bin/ld

checking if the linker (/usr/bin/ld) is GNU ld... yes

checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B

checking the name lister (/usr/bin/nm -B) interface... BSD nm

checking the maximum length of command line arguments... 1572864

checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop

checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop

checking for /usr/bin/ld option to reload object files... -r

checking for objdump... objdump

checking how to recognize dependent libraries... pass_all

checking for dlltool... no

checking how to associate runtime and link libraries... printf %s\n

checking for archiver @FILE support... @

checking for strip... strip

checking for ranlib... ranlib

checking for gawk... gawk

checking command to parse /usr/bin/nm -B output from gcc object... ok

checking for sysroot... no

checking for a working dd... /bin/dd

checking how to truncate binary pipes... /bin/dd bs=4096 count=1

checking for mt... mt

checking if mt is a manifest tool... no

checking for dlfcn.h... yes

checking for objdir... .libs

checking if gcc supports -fno-rtti -fno-exceptions... no

checking for gcc option to produce PIC... -fPIC -DPIC

checking if gcc PIC flag -fPIC -DPIC works... yes

checking if gcc static flag -static works... yes

checking if gcc supports -c -o file.o... yes

checking if gcc supports -c -o file.o... (cached) yes

checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking whether -lc should be explicitly linked in... no

checking dynamic linker characteristics... GNU/Linux ld.so

checking how to hardcode library paths into programs... immediate

checking whether stripping libraries is possible... yes

checking if libtool supports shared libraries... yes

checking whether to build shared libraries... yes

checking whether to build static libraries... no

checking how to run the C++ preprocessor... g++ -E

checking for ld used by g++... /usr/bin/ld -m elf_x86_64

checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes

checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking for g++ option to produce PIC... -fPIC -DPIC

checking if g++ PIC flag -fPIC -DPIC works... yes

checking if g++ static flag -static works... yes

checking if g++ supports -c -o file.o... yes

checking if g++ supports -c -o file.o... (cached) yes

checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking dynamic linker characteristics... (cached) GNU/Linux ld.so

checking how to hardcode library paths into programs... immediate

checking if libtool supports shared libraries... yes

checking whether to build shared libraries... yes

checking whether to build static libraries... no

checking for f95 option to produce PIC... -fPIC

checking if f95 PIC flag -fPIC works... yes

checking if f95 static flag -static works... yes

checking if f95 supports -c -o file.o... yes

checking if f95 supports -c -o file.o... (cached) yes

checking whether the f95 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking dynamic linker characteristics... (cached) GNU/Linux ld.so

checking how to hardcode library paths into programs... immediate

checking for cos in -lm... yes

checking for sin in -lm... yes

checking for dlopen in -ldl... yes

checking readline/history.h usability... no

checking readline/history.h presence... no

checking for readline/history.h... no

checking readline/readline.h usability... no

checking readline/readline.h presence... no

checking for readline/readline.h... no

checking for rl_callback_read_char in -lreadline... no

checking for main in -lncurses... no

checking for main in -ltermcap... no

checking for main in -ltermlib... no

checking for rl_callback_read_char in -lreadline... no

checking for history_truncate_file... no

configure: error: --with-readline=yes (default) and headers/libs are not available

ubuntu@ubuntu-Satellite-L775D:/tmp/R-3.3.2$ make

make: *** No targets specified and no makefile found.  Stop.

ubuntu@ubuntu-Satellite-L775D:/tmp/R-3.3.2$ make install

make: *** No rule to make target 'install'.  Stop.

ubuntu@ubuntu-Satellite-L775D:/tmp/R-3.3.2$ make install gcc

make: *** No rule to make target 'install'.  Stop.

I suspect make is installed but I'm not specifying the target, which I thought would be gcc. 

Is this printout as you would expect Yves? 

I'm concerned I didn't get the sequencing correct. 

Rick 

On Sat, Jan 28, 2017 at 3:14 PM, Yves Rosseel <yros...@gmail.com> wrote:

[R MacLaren]

I erred in the sequencing of gfortran, gcc, gcc-fortran, and the script - though the syntax make and make install didn't lead to success in this instance. I'll uninstall. 

R

On Sat, Jan 28, 2017 at 3:14 PM, Yves Rosseel <yros...@gmail.com> wrote:

[Yves Rosseel]

On 01/29/2017 02:39 AM, R MacLaren wrote:
> checking for texi2any... no
> configure: WARNING: you cannot build info or HTML versions of the R manuals
> checking for texi2dvi... no
> checking for kpsewhich... /usr/bin/kpsewhich
> checking for latex inconsolata package... missing
> configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF
> vignettes and package manuals will not be rendered optimally

> configure: error: --with-readline=yes (default) and headers/libs are not
> available

The last error is fatal: your linux system does not have the readline
libraries installed. You need to install this first.

Also (although not fatal), other missing parts are: texinfo, and some
extra fonts needed for the PDF manual (usually part of
texlive-fonts-extra or something similar).

How to install these components depends on your distribution. To get an
overview of *all* components you may ever need in the R system, see:

https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Essential-and-useful-other-programs-under-a-Unix_002dalike

Yves.

[Yves Rosseel]

On 01/29/2017 12:16 AM, kmarkus via lavaan wrote:
> Actually, I missed an earlier message that seems informative:
>
>
> /usr/bin/ld: cannot find -lblas

The source code of R includes blas, so if you are installing from
source, you should not need it. If you installed a binary version of R,
it may have omitted blas (because it want to give you options: there are
several blas libraries to choose from).

I am most familiar with installing everything from source (which is the
same procedure for all distributions). The necessary components are
listed here:

https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Installing-R-under-Unix_002dalikes

Yves.

[kma...@aol.com]

Yves, Thanks.  That helps me get my bearings.

Rick, I used the $ prompt.  Here is the page from which I copied the command.

http://askubuntu.com/questions/837364/usr-local-bin-gfortran-command-not-found

[R MacLaren]

Yves thank you for your assistance.

I read the 'installing under the Unix look alike' as you suggested and using grep found 3 versions of gfortran. I ran these grep commands in sequence as the instructions require, and gfortran comes up first. However, because there exist 3 gfortrans, including one 'gfortran-5', does this pose a problem for the installation? I searched and found no explicit Ubuntu gcc-fortran on the Ubuntu boards. I concluded the installation could go ahead with the caveat that I add the libraries you suggested in sequence, and the problem appears to be gone. 

Thanks 

Rick

[R McLaren]

Hi Keith and thanks for the link. I tried it and things are good here. I'm testing the system out presently. It is possible I'll still take my computer to my linux pro and reinstall the Ubuntu package or upgrate, and then do a complete reinstall of R. But if I can get through today without having R crash on me, I'll reconsider.  

Best Rick 

[kma...@aol.com]

As a follow-up to this thread, I found a front-door path to installing lavaan as an alternative to the back-door path suggested by Yves.  I can only confirm this worked for me using Linux Mint.  However, I would expect it to work for any Debian branch distribution, including Ubuntu.  I am assuming that R base is already installed.

1. Use your package manager to install the following in Linux:
libssl-dev
libssh2-1-dev
Libclblas-dev (I cannot confirm that this one is necessary.)
Libblas-devs


2. Use R to install the following package:
devtools

3. Use R to install lavaan.