[R-pkg-devel] Ubuntu Linux: Package suggested but not available

[Goldfeld, Keith]

Interestingly, when I removed the code related to package ordinal (and hence package ucminf), I got the same error from another package (gee) that I suggested in the description file. So, the issue is not with package ucfminf and probably not package gee, but something else.

My solution for now is to pare down my vignette so that I am not referencing this or any other extraneous packages for illustrative purposes. Gábor - thanks for your help.

- Keith

On 2/7/19, 12:34 PM, "R-package-devel on behalf of Goldfeld, Keith" <r-package-devel-bounces using r-project.org on behalf of Keith.Goldfeld using nyulangone.org> wrote:

    It appears that the ucminf package was installed properly:
    
    #> * installing *binary* package ‘ucminf’ ...
    #> * ‘ucminf’ was already a binary package and will not be rebuilt
    #> * creating tarball
    #> packaged installation of ‘ucminf’ as ‘ucminf_1.1-4_R_x86_64-pc-linux-gnu.tar.gz’
    #> * DONE (ucminf)
    
    On 2/7/19, 12:18 PM, "Gábor Csárdi" <csardi.gabor using gmail.com> wrote:
    
        I think this means that the ucminf package was not installed properly.
        There is probably something about it in the log....
        
        G.
        
        On Thu, Feb 7, 2019 at 5:15 PM Goldfeld, Keith
        <Keith.Goldfeld using nyulangone.org> wrote:
        >
        > I did just take a look at the log, which may provide some insight, though not to me.
        >
        > This is the key part of the message where things go awry:
        >
        > #> Error in dyn.load(file, DLLpath = DLLpath, ...) :
        > #> unable to load shared object '/home/docker/R/ucminf/libs/ucminf.so':
        > #>      : cannot open shared object file: No such file or directory
        > #> ERROR: lazy loading failed for package ‘ordinal’
        >
        > Does this pinpoint the problem? If so, what can I do about it?
        >
        >
        >
        > And here is the full log from the attempt to install ordinal.
        >
        > #> * installing *source* package ‘ordinal’ ...
        > #> ** package ‘ordinal’ successfully unpacked and MD5 sums checked
        > #> ** libs
        > #> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c get_fitted.c -o get_fitted.o
        > #> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
        > #> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c links.c -o links.o
        > #> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utilityFuns.c -o utilityFuns.o
        > #> g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ordinal.so get_fitted.o init.o links.o utilityFuns.o -L/usr/lib/R/lib -lR
        > #> installing to /home/docker/R/ordinal/libs
        > #> ** R
        > #> ** data
        > #> *** moving datasets to lazyload DB
        > #> ** inst
        > #> ** byte-compile and prepare package for lazy loading
        > #> Error in dyn.load(file, DLLpath = DLLpath, ...) :
        > #> unable to load shared object '/home/docker/R/ucminf/libs/ucminf.so':
        > #> libRblas.so: cannot open shared object file: No such file or directory
        > #> ERROR: lazy loading failed for package ‘ordinal’
        > #> * removing ‘/home/docker/R/ordinal’
        >
        > On 2/7/19, 11:56 AM, "Gábor Csárdi" <csardi.gabor using gmail.com> wrote:
        >
        >     You probably have an error earlier in the R-hub build log that
        >     explains why ordinal failed to install.
        >
        >     Gabor
        >
        >     On Thu, Feb 7, 2019 at 4:44 PM Goldfeld, Keith
        >     <Keith.Goldfeld using nyulangone.org> wrote:
        >     >
        >     > I am using devtools::check_rhub() before submitting a new version of my package simstudy to CRAN. I am getting an error message about a package I use in the vignette from the Ubuntu Linux platform:
        >     >
        >     > * checking package dependencies ... ERROR
        >     > Package suggested but not available: ‘ordinal’
        >     >
        >     > The suggested packages are required for a complete check.
        >     > Checking can be attempted without them by setting the environment
        >     > variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
        >     >
        >     >
        >     > This is not an issue for any of the other platforms. Any thoughts about how I can address this?
        >     >
        >     > Thanks - Keith
        >     >
        >     >
        >     >
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