"R CMD check sos" with R 3.3.0 under Mac OS X 10.11.5 ends as
follows:
>* checking package dependencies ... ERROR
>Package suggested but not available: ?RODBC?
>
>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.
Unfortunately, "install.packages('RODBC')" says
it's only
available in source form. When I attempt to install from sources, it
fails as follows:
>checking for sqlext.h... no
>configure: error: "ODBC headers sql.h and sqlext.h not found"
>ERROR: configuration failed for package ?RODBC?
>* removing
?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RODBC?
>Warning in install.packages :
> installation of package ?RODBC? had non-zero exit status
The CRAN checks for RODBC also failed for the same reason
(https://cloud.r-project.org/web/checks/check_results_RODBC.html).
I'm not sure how to set "the environment variable
_R_CHECK_FORCE_SUGGESTS_ to a false value" on my Mac, and I'd rather
not
do it permanently. I tried various versions of "R CMD check
_R_CHECK_FORCE_SUGGESTS_=FALSE sos_1.3-9.tar.gz" and "R CMD check
_R_CHECK_FORCE_SUGGESTS_=0 sos_1.3-9.tar.gz", none of which worked.
Somewhere I found a suggestion to try, "R CMD check --as-cran
sos_1.3-9.tar.gz". That also failed for me.
Suggestions?
Thanks,
Spencer Graves
On Mon, Jun 20, 2016 at 9:19 AM, Spencer Graves <spencer.graves at prodsyse.com> wrote:> "R CMD check sos" with R 3.3.0 under Mac OS X 10.11.5 ends as > follows: > > > >* checking package dependencies ... ERROR > >Package suggested but not available: ?RODBC? > > > >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. > > > Unfortunately, "install.packages('RODBC')" says it's only available > in source form. When I attempt to install from sources, it fails as > follows: > > > >checking for sqlext.h... no > >configure: error: "ODBC headers sql.h and sqlext.h not found" > >ERROR: configuration failed for package ?RODBC? > >* removing > ?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RODBC? > >Warning in install.packages : > > installation of package ?RODBC? had non-zero exit status > > > The CRAN checks for RODBC also failed for the same reason > (https://cloud.r-project.org/web/checks/check_results_RODBC.html). > > > > I'm not sure how to set "the environment variable > _R_CHECK_FORCE_SUGGESTS_ to a false value" on my Mac, and I'd rather not do > it permanently. I tried various versions of "R CMD check > _R_CHECK_FORCE_SUGGESTS_=FALSE sos_1.3-9.tar.gz" and "R CMD check > _R_CHECK_FORCE_SUGGESTS_=0 sos_1.3-9.tar.gz", none of which worked. > Somewhere I found a suggestion to try, "R CMD check --as-cran > sos_1.3-9.tar.gz". That also failed for me. >_R_CHECK_FORCE_SUGGESTS_=FALSE R CMD check sos_1.3-9.tar.gz> > Suggestions? > Thanks, > Spencer Graves > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel-- Joshua Ulrich | about.me/joshuaulrich FOSS Trading | www.fosstrading.com R/Finance 2016 | www.rinfinance.com
> On Jun 20, 2016, at 9:19 AM, Spencer Graves <spencer.graves at prodsyse.com> wrote: > > "R CMD check sos" with R 3.3.0 under Mac OS X 10.11.5 ends as follows: > > > >* checking package dependencies ... ERROR > >Package suggested but not available: ?RODBC? > > > >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. > > > Unfortunately, "install.packages('RODBC')" says it's only available in source form. When I attempt to install from sources, it fails as follows: > > > >checking for sqlext.h... no > >configure: error: "ODBC headers sql.h and sqlext.h not found" > >ERROR: configuration failed for package ?RODBC? > >* removing ?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RODBC? > >Warning in install.packages : > > installation of package ?RODBC? had non-zero exit status > > > The CRAN checks for RODBC also failed for the same reason (https://cloud.r-project.org/web/checks/check_results_RODBC.html). > > > > I'm not sure how to set "the environment variable _R_CHECK_FORCE_SUGGESTS_ to a false value" on my Mac, and I'd rather not do it permanently. I tried various versions of "R CMD check _R_CHECK_FORCE_SUGGESTS_=FALSE sos_1.3-9.tar.gz" and "R CMD check _R_CHECK_FORCE_SUGGESTS_=0 sos_1.3-9.tar.gz", none of which worked. Somewhere I found a suggestion to try, "R CMD check --as-cran sos_1.3-9.tar.gz". That also failed for me. > > > Suggestions? > Thanks, > Spencer GravesSpencer, The RODBC related error is a common issue and is covered in the vignette for the RODBC package in Appendix A "Installation": https://cran.r-project.org/web/packages/RODBC/vignettes/RODBC.pdf You are missing the two iODBC header files that are required to compile the RODBC package from source code. When I install RODBC on my Mac running 10.11.5 (El Capitan), I use: install.packages("RODBC", type = "source", configure.args = "--with-odbc-include=/Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Tools/iODBC/libiodbc-3.52.10/include/") where I have placed the extracted iODBC source tarball in: /Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Tools/iODBC The: configure.args = "--with-odbc-include=..." part of the function call points to where the header files are located after extraction from the tarball as per the vignette. The iODBC source tarball can be downloaded from: http://www.iodbc.org/dataspace/iodbc/wiki/iODBC/Downloads If you want to temporarily set the OS X environment variable, you can open an OS X Terminal and in the console, use: export _R_CHECK_FORCE_SUGGESTS_=FALSE You can then check to see if it is set by using: env in the Terminal and/or with the following in an R console run from within that same Terminal session:> Sys.getenv("_R_CHECK_FORCE_SUGGESTS_")[1] "FALSE" Once you close that Terminal session, that modified environment is lost. Also, at least the RODBC part of the issue should have been posted to R-SIG-DB (https://stat.ethz.ch/mailman/listinfo/r-sig-db), since it is DB interface specific. Most queries about RODBC are there in the archives, including those covering the missing headers. The part that covers issues vis-a-vis checking your own package should go to R-Package-Devel: https://stat.ethz.ch/mailman/listinfo/r-package-devel rather than R-Devel. Regards, Marc Schwartz
Hi, Joshua et al.:
Could someone add Joshua's fix to "Writing R Extensions"?
This seems like a problem that could affect others, and it would
be great to have this documented there. (It worked for me!)
Thanks,
Spencer
On 6/20/2016 9:56 AM, Joshua Ulrich wrote:> On Mon, Jun 20, 2016 at 9:19 AM, Spencer Graves
> <spencer.graves at prodsyse.com> wrote:
>> "R CMD check sos" with R 3.3.0 under Mac OS X 10.11.5
ends as
>> follows:
>>
>>
>> >* checking package dependencies ... ERROR
>> >Package suggested but not available: ?RODBC?
>> >
>> <snip>
>>
> _R_CHECK_FORCE_SUGGESTS_=FALSE R CMD check sos_1.3-9.tar.gz
>
>> Suggestions?
>> Thanks,
>> Spencer Graves
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
Hi, Marc:
Thanks very much. Your instructions provided the keys required
to unlock the door. Since I had to read your email several times before
I got it to work, I will summarize here what I think were the crucial
steps:
1. I went to
"http://www.iodbc.org/dataspace/iodbc/wiki/iODBC/Downloads", as you
suggested, and clicked on "tarball from Sourceforge". That downloaded
"libiodbc-3.52.10.tar.gz". (Before I did that, I found "Mac OS
X" on
that page and dowloaded and installed "mxkozzzz.dmg". That was not
enough to install RODBC.)
2. I created a directory similar to what you described
(/Users/sbgraves/R.Files/SourceAndBinaries/OSX-Tools/iODBC/libiodbc-3.52.10/include/)
and moved "libiodbc-3.52.10.tar.gz" into it. Then I extracted a
folder
"libiodbc-3.52.10" from it in the aforementioned directory.
3. In R, I then tried the following:
install.packages("RODBC", type = "source", configure.args
"--with-odbc-include=/Users/sbgraves/R.Files/SourceAndBinaries/OSX-Tools/iODBC/libiodbc-3.52.10/include/")
It worked.
Thanks,
sg
On 6/20/2016 10:00 AM, Marc Schwartz wrote:>> On Jun 20, 2016, at 9:19 AM, Spencer Graves <spencer.graves at
prodsyse.com> wrote:
>>
>> "R CMD check sos" with R 3.3.0 under Mac OS X 10.11.5
ends as follows:
>>
>>
>>> * checking package dependencies ... ERROR
>>> Package suggested but not available: ?RODBC?
>>>
>>> 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.
>>
>> Unfortunately, "install.packages('RODBC')"
says it's only available in source form. When I attempt to install from
sources, it fails as follows:
>>
>>
>>> checking for sqlext.h... no
>>> configure: error: "ODBC headers sql.h and sqlext.h not
found"
>>> ERROR: configuration failed for package ?RODBC?
>>> * removing
?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RODBC?
>>> Warning in install.packages :
>>> installation of package ?RODBC? had non-zero exit status
>>
>> The CRAN checks for RODBC also failed for the same reason
(https://cloud.r-project.org/web/checks/check_results_RODBC.html).
>>
>>
>>
>> I'm not sure how to set "the environment variable
_R_CHECK_FORCE_SUGGESTS_ to a false value" on my Mac, and I'd rather
not do it permanently. I tried various versions of "R CMD check
_R_CHECK_FORCE_SUGGESTS_=FALSE sos_1.3-9.tar.gz" and "R CMD check
_R_CHECK_FORCE_SUGGESTS_=0 sos_1.3-9.tar.gz", none of which worked.
Somewhere I found a suggestion to try, "R CMD check --as-cran
sos_1.3-9.tar.gz". That also failed for me.
>>
>>
>> Suggestions?
>> Thanks,
>> Spencer Graves
>
> Spencer,
>
> The RODBC related error is a common issue and is covered in the vignette
for the RODBC package in Appendix A "Installation":
>
> https://cran.r-project.org/web/packages/RODBC/vignettes/RODBC.pdf
>
> You are missing the two iODBC header files that are required to compile the
RODBC package from source code.
>
> When I install RODBC on my Mac running 10.11.5 (El Capitan), I use:
>
> install.packages("RODBC", type = "source",
> configure.args =
"--with-odbc-include=/Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Tools/iODBC/libiodbc-3.52.10/include/")
>
> where I have placed the extracted iODBC source tarball in:
>
> /Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Tools/iODBC
>
> The:
>
> configure.args = "--with-odbc-include=..."
>
> part of the function call points to where the header files are located
after extraction from the tarball as per the vignette.
>
> The iODBC source tarball can be downloaded from:
>
> http://www.iodbc.org/dataspace/iodbc/wiki/iODBC/Downloads
>
>
> If you want to temporarily set the OS X environment variable, you can open
an OS X Terminal and in the console, use:
>
> export _R_CHECK_FORCE_SUGGESTS_=FALSE
>
> You can then check to see if it is set by using:
>
> env
>
> in the Terminal and/or with the following in an R console run from within
that same Terminal session:
>
>> Sys.getenv("_R_CHECK_FORCE_SUGGESTS_")
> [1] "FALSE"
>
>
> Once you close that Terminal session, that modified environment is lost.
>
> Also, at least the RODBC part of the issue should have been posted to
R-SIG-DB (https://stat.ethz.ch/mailman/listinfo/r-sig-db), since it is DB
interface specific. Most queries about RODBC are there in the archives,
including those covering the missing headers.
>
> The part that covers issues vis-a-vis checking your own package should go
to R-Package-Devel:
>
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> rather than R-Devel.
>
> Regards,
>
> Marc Schwartz
>
>