Tag the old lmds-0.1.0 release

[mmokrejs]

Hi,
I just realized the release tarball 0.1.0 is missing from github. That maybe also explains why the tarball is missing from CRAN mirrors. Please try to get it available although it is already several years ago. Thank you.

I could download the master.zip which unpacks into lmds-master/.

$ unzip master.zip
$ rm master.zip
$ mv lmds-master lmds-0.1.0
$ tar cvf - lmds-0.1.0 |  gzip -c > lmds-0.1.0.tar.gz
$ R CMD INSTALL lmds-0.1.0.tar.gz 
* installing to library ‘/home/bionic/R/x86_64-pc-linux-gnu-library/3.5’
* installing *source* package ‘lmds’ ...
** R
** byte-compile and prepare package for lazy loading
Error : object ‘partial_eigen’ is not exported by 'namespace:irlba'
ERROR: lazy loading failed for package ‘lmds’
* removing ‘/home/bionic/R/x86_64-pc-linux-gnu-library/3.5/lmds’
$

Seems irlba-2.0.0 is the minimum requirement.

[rcannood]

I'm a bit confused by this message.

Installing lmds from CRAN works fine for me:

>  install.packages("lmds")
Installing package into ‘/home/rcannood/R/x86_64-redhat-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/lmds_0.1.0.tar.gz'
Content type 'application/x-gzip' length 150427 bytes (146 KB)
==================================================
downloaded 146 KB

* installing *source* package ‘lmds’ ...
** package ‘lmds’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘lmds’
    finding HTML links ... done
    cmdscale_landmarks                      html  
    lmds                                    html  
    select_landmarks                        html  
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lmds)

The downloaded source packages are in
        ‘/tmp/RtmpPg4Ffj/downloaded_packages’

If you want to install lmds from source, please use a package like remotes to help you with this:

> remotes::install_github("dynverse/lmds")
Downloading GitHub repo dynverse/lmds@HEAD
── R CMD build ────────────────
✔  checking for file ‘/tmp/RtmpPg4Ffj/remotes6663975d5e7bf/dynverse-lmds-9b66a2c/DESCRIPTION’ ...
─  preparing ‘lmds’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Omitted ‘LazyData’ from DESCRIPTION
─  building ‘lmds_0.1.0.tar.gz’
   
Installing package into ‘/home/rcannood/R/x86_64-redhat-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
* installing *source* package ‘lmds’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘lmds’
    finding HTML links ... done
    cmdscale_landmarks                      html  
    lmds                                    html  
    select_landmarks                        html  
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lmds)

Error : object ‘partial_eigen’ is not exported by 'namespace:irlba'

If you are getting this error, it's likely the irlba you have installed is <2.0.0, which was released in 2015.

[mmokrejs]

Hi,
I was trying to install any version of a package which could be installed on R-3.5.5 although I needed initially R-3.4.4. Therefore, because remotes:: nor devtools:: do not provide any looping mechanism to install any older package version untill they succeed. They either succeed with the latest or exit.
I had to download the tarballs from CRAN archives a hack a shellscript to do the looping. And I could not find any lmds-0.1.0.tar.gz anywhere and on github I do not see "Tags" and therefore the are no released files for download.

I agree the remotes:: do get it from somewhere.

> remotes::install_github("dynverse/lmds")
Downloading GitHub repo dynverse/lmds@HEAD
Skipping 1 packages not available: irlba
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/Rtmpd6gkPh/remotes3fba1c5873cd/dynverse-lmds-8b67ce3/DESCRIPTION’ ... OK
─  preparing ‘lmds’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘lmds_0.1.0.tar.gz’
   
Installing package into ‘/home/bionic/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
* installing *source* package ‘lmds’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded
* DONE (lmds)
> 

Hmm, yeah, I had recent irlba isntalled so let's re-try.

$ R CMD INSTALL irlba_1.0.3.tar.gz
* installing to library ‘/home/bionic/R/x86_64-pc-linux-gnu-library/3.5’
* installing *source* package ‘irlba’ ...
** package ‘irlba’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (irlba)
$

> remotes::install_github("dynverse/lmds")
Skipping install of 'lmds' from a github remote, the SHA1 (8b67ce35) has not changed since last install.
  Use `force = TRUE` to force installation
> remotes::install_github("dynverse/lmds", force = TRUE)
Downloading GitHub repo dynverse/lmds@HEAD
Skipping 1 packages not available: irlba
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/Rtmp7xcFDx/remotes41b9599baf34/dynverse-lmds-8b67ce3/DESCRIPTION’ ...
─  preparing ‘lmds’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘lmds_0.1.0.tar.gz’
   
Installing package into ‘/home/bionic/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
* installing *source* package ‘lmds’ ...
** R
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace ‘irlba’ 1.0.3 is being loaded, but >= 2.0.0 is required
ERROR: lazy loading failed for package ‘lmds’
* removing ‘/home/bionic/R/x86_64-pc-linux-gnu-library/3.5/lmds’
* restoring previous ‘/home/bionic/R/x86_64-pc-linux-gnu-library/3.5/lmds’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/Rtmp7xcFDx/file41b95927f4cd/lmds_0.1.0.tar.gz’ had non-zero exit status
> 

OK, I agree the requirement checks work fine. I do not know how the releasing strategy is setup for R packages but I would assume that like other R projects on github that lmds has a tag for each release.