Documentation?
bpbond opened this issue · comments
Hi folks, is there documentation for getting started with recordr? I see the slides on figshare (http://figshare.com/articles/Reproducible_science_via_semantics_and_provenance_for_ecological_data/1512516) -- anything else available? Your README is sort of, um, minimal.
Thanks.
@bpbond Unfortunately, not much yet in the package. As we are implementing this both in R and Matlab, we are working against a language-neutral design document that provides a lot of the details, but isn't meant to be user-facing documentation. We plan on writing a vignette, in addition to the standard package, class, and methods docs. But haven't gotten there yet. We'll try to pull together a quick getting started in the README as a placeholder until we get the vignette written.
Thanks! Re bpbond/dataprov#2 I'd be happy to provide feedback on recordr, if given even a bare-bones getting started vignette.
@bpbond An intial version of a recordr intro vignette can be found here: https://github.com/NCEAS/recordr/blob/master/vignettes/intro_recordr.Rmd.
Note that this vignette still needs work as explained in #44
Thanks in advance for any feedback!
Thanks @sbpcs59 for putting the work in for a vignette. I tried to install recordr but hit mistakes in the README (easy to fix, see pull request #47 ), then errors as the redland libraries weren't installed, and THEN errors using MacPorts to install redland:
WE29152:~ d3x290$ sudo port install redland
Error: Port redland not found
WE29152:~ d3x290$ sudo port -v selfupdate
---> Updating MacPorts base sources using rsync
receiving file list ... done
sent 36 bytes received 69 bytes 70.00 bytes/sec
total size is 27013120 speedup is 257267.81
receiving file list ... done
sent 36 bytes received 76 bytes 74.67 bytes/sec
total size is 512 speedup is 4.57
Error: Failed to verify signature for MacPorts source!
To report a bug, follow the instructions in the guide:
http://guide.macports.org/#project.tickets
Error: /opt/local/bin/port: port selfupdate failed: Failed to verify signature for MacPorts source!
Sadly, my interest in recordr isn't so strong that I'm going to chase down port bugs. If there's something obvious I'm doing wrong, please let me know; otherwise, I'd respectfully suggest you work on reducing the friction for users trying to install your package. Thanks and kind regards.
Thanks for the input, @bpbond . We're aware of the installation issues, and are working on those -- which is why we haven't yet released the package. The redland package has proven difficult on Windows, although Mac installs have generally been fine. Not sure why your MacPorts install is horked.
That's good to know that MacPorts should have been smooth. I'll try to revisit that later -- sorry, the "my interest isn't so strong" above sounds snotty, didn't get much sleep -- and try to get it working. Thanks!
Un-borked my MacPorts, and did sudo port install redland without problems. Yay! Unfortunately, then got an error when trying to install this package (see long output below)--it doesn't seem to recognize that Redland is installed. Any suggestions? Thanks.
Also, note typo (extra parenthesis) in README line install.packages("drat")).
> install.packages("recordr")
Installing package into ‘/Users/d3x290/Library/R/3.2/library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘redland’, ‘dataone’, ‘datapackage’
There are binary versions available but the source versions are later:
binary source needs_compilation
redland 1.0.17 1.0.17-1 FALSE
datapackage 0.9.0.9002 0.9.0.9003 FALSE
installing the source packages ‘redland’, ‘dataone’, ‘datapackage’, ‘recordr’
trying URL 'http://NCEAS.github.io/drat/src/contrib/redland_1.0.17-1.tar.gz'
Content type 'application/octet-stream' length 271527 bytes (265 KB)
==================================================
downloaded 265 KB
trying URL 'http://NCEAS.github.io/drat/src/contrib/dataone_1.1.0.9005.tar.gz'
Content type 'application/octet-stream' length 89999 bytes (87 KB)
==================================================
downloaded 87 KB
trying URL 'http://NCEAS.github.io/drat/src/contrib/datapackage_0.9.0.9003.tar.gz'
Content type 'application/octet-stream' length 36058 bytes (35 KB)
==================================================
downloaded 35 KB
trying URL 'http://NCEAS.github.io/drat/src/contrib/recordr_0.9.0.9004.tar.gz'
Content type 'application/octet-stream' length 252244 bytes (246 KB)
==================================================
downloaded 246 KB
* installing *source* package ‘redland’ ...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... /bin/sh: /private/var/folders/jl/gn9f6wd95dd0s53s396fy9p86dyn5r/T/RtmpFaBDcb/R.INSTALL179381166efed/redland/tools/missing: No such file or directory
configure: WARNING: 'missing' script is too old or missing
yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... 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 whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... none
checking for R... R
checking for pkg-config... no
checking for redland... not found
./configure: line 3971: --exists: command not found
configure: error: Redland is not installed - Please see https://github.com/ropensci/redland-bindings/tree/master/R/redland/README.md
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c redland.c -o redland.o
redland.c:1254:10: fatal error: 'redland.h' file not found
#include <redland.h>
^
1 error generated.
make: *** [redland.o] Error 1
ERROR: compilation failed for package ‘redland’
* removing ‘/Users/d3x290/Library/R/3.2/library/redland’
ERROR: dependency ‘redland’ is not available for package ‘datapackage’
* removing ‘/Users/d3x290/Library/R/3.2/library/datapackage’
ERROR: dependency ‘datapackage’ is not available for package ‘dataone’
* removing ‘/Users/d3x290/Library/R/3.2/library/dataone’
ERROR: dependencies ‘dataone’, ‘datapackage’ are not available for package ‘recordr’
* removing ‘/Users/d3x290/Library/R/3.2/library/recordr’
The downloaded source packages are in
‘/private/var/folders/jl/gn9f6wd95dd0s53s396fy9p86dyn5r/T/RtmpvegDKG/downloaded_packages’
Warning messages:
1: In install.packages("recordr") :
installation of package ‘redland’ had non-zero exit status
2: In install.packages("recordr") :
installation of package ‘datapackage’ had non-zero exit status
3: In install.packages("recordr") :
installation of package ‘dataone’ had non-zero exit status
4: In install.packages("recordr") :
installation of package ‘recordr’ had non-zero exit status
@bpbond It appears newer 'source' versions of the packages were selected for installation
which required a local build, which was not our intention for Mac OS X. To resolve this I've updated the mac binary builds for recordr and dependent packages in our drat repo, and verified that these install correctly on a 'fresh' Mac OS X Mavericks system. All you should have to do at this point is
library(drat)
addRepo("NCEAS")
install.packages("recordr")Thanks for your patience. We are working to complete our automatic builds / testing so that
these kind of problems will be avoided.