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

Goldfeld, Keith Ke|th@Go|d|e|d @end|ng |rom nyu|@ngone@org
Thu Feb 7 18:27:01 CET 2019


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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