sos4R archived on CRAN - Githubissues

edzer commented 5 years ago

sos4R is no longer available on CRAN: https://cran.r-project.org/package=sos4R

The master branch checks without NOTES for me, is there a particular reason to not submit it to CRAN?

nuest commented 5 years ago

Thanks for the poke, @BenGraeler also made some considerable contributions recently, so sos4R should be back on CRAN soon.

The check results shows some problems with vignettes, which will be fixed as part of #31 :+1:

https://cran.r-project.org/web/checks/check_results_sos4R.html

Check Details

Version: 0.2-11
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘rgdal’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    Package in Depends field not imported from: ‘methods’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.2-11
Check: R code for possible problems
Result: NOTE
    .getObservation_1.0.0: no visible global function definition for
     ‘object.size’
    .getObservation_1.0.0: no visible global function definition for
     ‘write.csv’
    .kvpKeyAndValues: no visible global function definition for ‘is’
    .sosRequest_1.0.0: no visible global function definition for
     ‘functionBody’
    .toString.OwsGetCapabilities: no visible global function definition for
     ‘is’
    GmlDirectPosition: no visible global function definition for ‘new’
    GmlDirectPositionLatLon: no visible global function definition for
     ‘new’
    GmlEnvelope: no visible global function definition for ‘new’
    GmlFeatureCollection: no visible global function definition for ‘new’
    GmlFeatureProperty: no visible global function definition for ‘new’
    GmlMeasure: no visible global function definition for ‘new’
    GmlPoint: no visible global function definition for ‘new’
    GmlPointProperty: no visible global function definition for ‘new’
    GmlTimeInstant: no visible global function definition for ‘new’
    GmlTimeInstantProperty: no visible global function definition for ‘new’
    GmlTimeInterval: no visible global function definition for ‘new’
    GmlTimePeriod: no visible global function definition for ‘new’
    GmlTimePosition: no visible global function definition for ‘new’
    OgcBBOX: no visible global function definition for ‘new’
    OgcContains: no visible global function definition for ‘new’
    OgcIntersects: no visible global function definition for ‘new’
    OgcOverlaps: no visible global function definition for ‘new’
    OmMeasurement: no visible global function definition for ‘new’
    OmObservation: no visible global function definition for ‘new’
    OmObservationCollection: no visible global function definition for
     ‘new’
    OmObservationProperty: no visible global function definition for ‘new’
    OwsCapabilities: no visible global function definition for ‘new’
    OwsContents: no visible global function definition for ‘new’
    OwsException: no visible global function definition for ‘new’
    OwsExceptionReport: no visible global function definition for ‘new’
    OwsGetCapabilities: no visible global function definition for ‘new’
    OwsOperation: no visible global function definition for ‘new’
    OwsOperationsMetadata: no visible global function definition for ‘new’
    OwsRange: no visible global function definition for ‘new’
    OwsServiceIdentification: no visible global function definition for
     ‘new’
    OwsServiceProvider: no visible global function definition for ‘new’
    SOS: no visible global function definition for ‘getCurlHandle’
    SOS: no visible global function definition for ‘new’
    SOS: no visible global function definition for ‘is’
    SaSamplingPoint: no visible global function definition for ‘new’
    SaSamplingSurface: no visible global function definition for ‘new’
    SensorML: no visible global function definition for ‘new’
    SosCapabilities: no visible global function definition for ‘new’
    SosContents: no visible global function definition for ‘new’
    SosDescribeSensor: no visible global function definition for ‘new’
    SosEventTime: no visible global function definition for ‘new’
    SosEventTimeLatest: no visible global function definition for ‘new’
    SosFeatureOfInterest: no visible global function definition for ‘new’
    SosFilter_Capabilities: no visible global function definition for ‘new’
    SosGetObservation: no visible global function definition for ‘new’
    SosGetObservationById: no visible global function definition for ‘new’
    SosObservationOffering: no visible global function definition for ‘new’
    SweCompositePhenomenon: no visible global function definition for ‘new’
    SwePhenomenon: no visible global function definition for ‘new’
    SwePhenomenonProperty: no visible global function definition for ‘new’
    SweTextBlock: no visible global function definition for ‘new’
    TM_After: no visible global function definition for ‘new’
    TM_Before: no visible global function definition for ‘new’
    TM_During: no visible global function definition for ‘new’
    TM_Equals: no visible global function definition for ‘new’
    parseSosObservationOffering: no visible global function definition for
     ‘extends’
    parseValues: no visible global function definition for ‘str’
    plot.SensorML: no visible global function definition for ‘as’
    plot.SosObservationOffering: no visible global function definition for
     ‘as’
    plot,SensorML-missing: no visible global function definition for ‘as’
    plot,SosObservationOffering-missing: no visible global function
     definition for ‘as’
    sosCoordinates,SosObservationOffering: no visible global function
     definition for ‘as’
    sosFeaturesOfInterest,SOS: no visible binding for global variable
     ‘slot’
    sosTime,SosObservationOffering: no visible global function definition
     for ‘is’
    Undefined global functions or variables:
     as extends functionBody getCurlHandle is new object.size slot str
     write.csv
    Consider adding
     importFrom("methods", "as", "extends", "functionBody", "is", "new",
     "slot")
     importFrom("utils", "object.size", "str", "write.csv")
    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
    contains 'methods').
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.2-11
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘rgdal’
Flavor: r-oldrel-osx-x86_64

Version: 0.2-11
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Warning in FUN(X[[i]], ...) :
     swe:Quantity given without unit of measurement: Salinity

    Attaching package: ‘xtable’

    The following object is masked from ‘package:maptools’:

     label

    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'sos4R.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `csquotes.sty' not found.

    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)

    ! Emergency stop.
    <read *>

    l.19 ^^M

    ! ==> Fatal error occurred, no output PDF file produced!
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted

nuest commented 5 years ago

Short update: code in my forks dev branch is in principle ready for CRAN:

$ R CMD build sos4R; R CMD check --as-cran sos4R_0.3.0.9002.tar.gz
* checking for file ‘sos4R/DESCRIPTION’ ... OK
* preparing ‘sos4R’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘sos4R_0.3.0.9002.tar.gz’

* using log directory ‘/home/daniel/git/sos4R.Rcheck’
* using R version 3.5.2 (2018-12-20)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘sos4R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sos4R’ version ‘0.3.0.9002’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Daniel Nuest <daniel.nuest@uni-muenster.de>’

New submission

Package was archived on CRAN

Version contains large components (0.3.0.9002)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2018-06-17 as check problems were not
    corrected despite reminders.

Found the following (possibly) invalid URLs:
  URL: doi:%5B10.1007/978-3-642-19789-5_12%5D(https://doi.org/10.1007/978-3-642-19789-5_12)
    From: inst/doc/sos4R-vignette-01-quickstart.html
    Message: Invalid URI scheme (use \doi for DOIs in Rd markup)
  URL: https://52north.github.io/sos4R
    From: inst/doc/sos4R-vignette-01-quickstart.html
    Status: 404
    Message: Not Found
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘sos4R’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/daniel/git/sos4R.Rcheck/00check.log’
for details.

nuest commented 5 years ago

New website is online at https://52north.github.io/sos4R/ and version 0.3.0 is submitted to CRAN.

There is an error, so the problem on Travis is explained:

* installing *source* package ‘sos4R’ ...
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses,  : 
  The prototype for class “OwsCapabilities_2.0.0” has undefined slot(s): ''
Error: unable to load R code in package ‘sos4R’
Execution halted
ERROR: lazy loading failed for package ‘sos4R’
* removing ‘/tmp/RtmpED93Wp/Rinst6d3435881153/sos4R’

In the changelog

In the definition of an S4 class, prototype elements are checked against the slots of the class, with giving a prototype for an undefined slot now being an error. (Reported by Bill Dunlap.)

nuest commented 5 years ago

Testing now locally with container:

$ docker run --rm -it -v $(pwd)/sos4R:/home/sos4R rocker/geospatial:devel bash
root@efd9c9d665ec:/# cd home/
root@efd9c9d665ec:/# install2.r cshapes
root@efd9c9d665ec:/home# R CMD build sos4R; R CMD check --as-cran sos4R_0.3.0.tar.gz

See #118

nuest commented 5 years ago

Re-subbmitted.

nuest commented 5 years ago

sos4R is not in the submission queue:

> library("foghorn")
> foghorn::cran_incoming()
# A tibble: 113 x 4
   package   version cran_folder time               
   <chr>     <chr>   <fct>       <dttm>             
 1 gexp      0.1-0   publish     2019-04-04 17:55:00
 2 waiter    0.0.4   publish     2019-04-09 16:21:00
 3 CaPO4Sim  0.1.0   newbies     2019-04-11 00:11:00
 4 CoSMoS    0.4.1   newbies     2019-04-09 19:17:00
 5 HDMT      1.0     newbies     2019-04-11 02:33:00
 6 Irescale  0.1.4   newbies     2019-04-10 22:00:00
 7 MLRShiny  0.1.0   newbies     2019-04-11 07:35:00
 8 PLNmodels 0.9.1   newbies     2019-03-18 17:31:00
 9 R2MLwiN   0.8-6   newbies     2019-04-09 08:04:00
10 RSCAT     1.0.0   newbies     2019-04-11 05:53:00
# … with 103 more rows
> foghorn::cran_incoming(pkg = "sos4R")
# A tibble: 0 x 4
# … with 4 variables: pa

Making a further submission now...

nuest commented 5 years ago

> foghorn::cran_incoming(pkg = "sos4R")
# A tibble: 1 x 4
  package version cran_folder time               
  <chr>   <chr>   <fct>       <dttm>             
1 sos4R   0.3.0   pretest     2019-04-11 12:29:00

nuest commented 5 years ago

One more fix, see #123

nuest commented 5 years ago

Pretests passed

Dear maintainer,

package sos4R_0.3.0.tar.gz has been auto-processed and is pending a manual inspection of this new CRAN submission. A CRAN team member will typically respond to you within the next 10 working days. For technical reasons you may receive a second copy of this message when a team member triggers a new check.

Log dir: <https://win-builder.r-project.org/incoming_pretest/sos4R_0.3.0_20190411_141944/>
The files will be removed after roughly 7 days.
Installation time in seconds: 38
Check time in seconds: 217 
R version 3.6.0 alpha (2019-04-09 r76362)

Pretests results:
Windows: <https://win-builder.r-project.org/incoming_pretest/sos4R_0.3.0_20190411_141944/Windows/00check.log>
Status: 1 NOTE
Debian: <https://win-builder.r-project.org/incoming_pretest/sos4R_0.3.0_20190411_141944/Debian/00check.log>
Status: 1 NOTE

Same note in both logs: package is "new"/"archived":

* using log directory ‘/srv/hornik/tmp/CRAN/sos4R.Rcheck’
* using R Under development (unstable) (2019-04-10 r76363)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘sos4R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sos4R’ version ‘0.3.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Daniel Nuest <daniel.nuest@uni-muenster.de>’

New submission

Package was archived on CRAN

Possibly mis-spelled words in DESCRIPTION:
  Geospatial (22:31)
  OGC (3:28, 22:54)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2018-06-17 as check problems were not
    corrected despite reminders.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘sos4R’ can be installed ... [14s/14s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [17s/17s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [3s/3s] OK
  Running ‘testthat.R’ [3s/3s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [11s/53s] OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE

* using log directory 'd:/RCompile/CRANincoming/R-devel/sos4R.Rcheck'
* using R version 3.6.0 alpha (2019-04-09 r76362)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'sos4R/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sos4R' version '0.3.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Daniel Nuest <daniel.nuest@uni-muenster.de>'

New submission

Package was archived on CRAN

Possibly mis-spelled words in DESCRIPTION:
  Geospatial (22:31)
  OGC (3:28, 22:54)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2018-06-17 as check problems were not
    corrected despite reminders.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'sos4R' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
** checking use of S3 registration ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
** checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [27s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [5s] OK
** running examples for arch 'x64' ... [5s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ... [6s] OK
  Running 'testthat.R' [6s]
** running tests for arch 'x64' ... [7s] OK
  Running 'testthat.R' [6s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [37s] OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE

nuest commented 5 years ago

@BenGraeler @pokulo FYI, hope to get to CRAN some time next week, pending a manual inspection.

nuest commented 5 years ago

Addressed the comments and corrections after CRAN team inspection, #127

> foghorn::cran_incoming(pkg = "sos4R")
# A tibble: 2 x 4
  package version cran_folder time               
  <chr>   <chr>   <fct>       <dttm>             
1 sos4R   0.3.0   pretest     2019-04-13 16:12:00

nuest commented 5 years ago

Sorry @pokulo - I intended to notify @EHJ-52n !

nuest commented 5 years ago

It's back: https://cran.r-project.org/web/packages/sos4R/index.html

Binaries are still missing, should come within the next days.

52North / sos4R

sos4R archived on CRAN #54