[Phylobase-devl] CRAN submission phylobase 0.6.5
Ben Bolker
bbolker at gmail.com
Sat Nov 24 21:21:46 CET 2012
Version 0.6.5 (version bump) is in incoming.
Also fixed last bit (I hope) of check-mismatch notes output.
Maybe I'll get it right this time.
sincerely
Ben Bolker
On 12-11-24 12:54 PM, Prof Brian Ripley wrote:
> On 24/11/2012 15:31, Ben Bolker wrote:
>> On 12-11-23 09:46 AM, Kurt Hornik wrote:
>>>>>>>> Ben Bolker writes:
>>>
>>> Ben,
>>>
>>> Please see the CRAN Repository Policy for appropriate subject lines.
>
> And also note that we communicate only with a single maintainer, so
> don't Cc: a list.
>
>>>
>>> I get
>>>
>>> * checking CRAN incoming feasibility ... WARNING
>>> Maintainer: ‘Ben Bolker <bolker at mcmaster.ca>’
>>> Insufficient package version (submitted: 0.6.4, existing: 0.6.4)
>>> Days since last update: 3
>>>
>>> Did we ask for a same-version update?
>>
>> Uwe Ligges reported a required dependency on a recent version of Rcpp,
>> which I hadn't noticed when running it on any of my machines, so I
>> resubmitted.
>>
>>> Also I get lots differences in the test outputs: can these be
>>> eliminated?
>>
>> This was harder than I expected because it turns out that one of the
>> tests returns different output on different machines (I still don't
>> completely understand what's going on here, but I got rid of the
>> .Rout.save for that test). There are a few small test-output differences
>>
>> I have uploaded yet another version (still 0.6.4; I assumed you
>> didn't want a version bump every time I responded to a CRAN maintainer
>> query ... ?). Sorry for the hassle.
>
> We certainly do want it. The whole point of version numbers is that
> they identify versions uniquely: update.packages() relies on it .... The
> only time we can accept a same-version update is when we ask for it and
> we only do that if it affects only a small set of platforms on which the
> current version does not work.
>
> I still see
>
> Comparing ‘plottest.Rout’ to ‘plottest.Rout.save’ ...62,72c62,73
> < iter 5 value 3.201783
> < iter 10 value 1.432415
> < iter 15 value 1.217510
> < iter 20 value 1.069446
> < iter 25 value 0.662087
> < iter 30 value 0.237888
> < iter 35 value 0.106249
> < iter 40 value 0.045765
> < iter 45 value 0.020016
> < final value 0.007666
> < converged
> ---
>> iter 5 value 3.201793
>> iter 10 value 1.433796
>> iter 15 value 1.147120
>> iter 20 value 0.914894
>> iter 25 value 0.705057
>> iter 30 value 0.376895
>> iter 35 value 0.256479
>> iter 40 value 0.091883
>> iter 45 value 0.024262
>> iter 50 value 0.010918
>> final value 0.010918
>> stopped after 50 iterations
>
> Don't check tracing information, and especially do not have reference
> output which did not even converge!
>
>>
>>>
>>> Best
>>> -k
>>>
>>> * using log directory ‘/home/Hornik/tmp/CRAN/phylobase.Rcheck’
>>> * using R Under development (unstable) (2012-11-23 r61139)
>>> * using platform: x86_64-unknown-linux-gnu (64-bit)
>>> * using session charset: UTF-8
>>> * checking for file ‘phylobase/DESCRIPTION’ ... OK
>>> * checking extension type ... Package
>>> * this is package ‘phylobase’ version ‘0.6.4’
>>> * checking CRAN incoming feasibility ... WARNING
>>> Maintainer: ‘Ben Bolker <bolker at mcmaster.ca>’
>>> Insufficient package version (submitted: 0.6.4, existing: 0.6.4)
>>> Days since last update: 3
>>> Possibly mis-spelled words in DESCRIPTION:
>>> phylogenetic (3:25)
>>> * 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 whether package ‘phylobase’ can be installed ... [63s/63s] OK
>>> * checking installed package size ... NOTE
>>> installed size is 19.2Mb
>>> sub-directories of 1Mb or more:
>>> libs 17.8Mb
>>> * checking package directory ... OK
>>> * checking for portable file names ... OK
>>> * checking for sufficient/correct file permissions ... 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 for unstated 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 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 contents of ‘data’ directory ... OK
>>> * checking data for non-ASCII characters ... OK
>>> * checking data for ASCII and uncompressed saves ... OK
>>> * checking line endings in C/C++/Fortran sources/headers ... OK
>>> * checking line endings in Makefiles ... OK
>>> * checking for portable compilation flags in Makevars ... OK
>>> * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
>>> * checking compiled code ... OK
>>> * checking sizes of PDF files under ‘inst/doc’ ... OK
>>> * checking installed files from ‘inst/doc’ ... OK
>>> * checking examples ... [3s/3s] OK
>>> * checking for unstated dependencies in tests ... OK
>>> * checking tests ... [18s/18s] OK
>>> Running ‘doRUnit.R’
>>> Comparing ‘doRUnit.Rout’ to ‘doRUnit.Rout.save’ ...71c71
>>> < [1] "/home/Hornik/tmp/CRAN/phylobase.Rcheck/tests"
>>> ---
>>>> [1] "/mnt/hgfs/bolker/Documents/R/pkgs/phylobase/pkg/tests"
>>> 74c74
>>> < [1] "/tmp/RtmpHlp0r5/RLIBS_2dec3867b1c2/phylobase/unitTests"
>>> ---
>>>> [1]
>>>> "/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/phylobase/unitTests"
>>>>
>>> 93,110d92
>>> < Executing test function test.phylo4.matrix ... Error in
>>> .createLabels(value = tip.label, ntips = ntips, nnodes = nnodes, :
>>> < Number of labels does not match number of nodes.
>>> < Error in .createLabels(node.label, ntips = ntips, nnodes = nnodes,
>>> type = "internal") :
>>> < Number of labels does not match number of nodes.
>>> < Error in .local(x, ...) :
>>> < unknown order: allowed values are
>>> unknown,preorder,postorder,pruningwise,cladewise
>>> < Error in checkSlotAssignment(object, name, value) :
>>> < assignment of an object of class "character" is not valid for
>>> slot 'annote' in an object of class "phylo4"; is(value, "list") is
>>> not TRUE
>>> < done successfully.
>>> <
>>> <
>>> <
>>> < Executing test function test.phylo4.phylo ... Error in .local(x,
>>> ...) : Labels are not unique
>>> < Error in .local(x, ...) : Labels are not unique
>>> < done successfully.
>>> <
>>> <
>>> <
>>> 135a118,135
>>>> Executing test function test.phylo4.matrix ... Error in
>>>> .createLabels(value = tip.label, ntips = ntips, nnodes = nnodes, :
>>>> Number of labels does not match number of nodes.
>>>> Error in .createLabels(node.label, ntips = ntips, nnodes = nnodes,
>>>> type = "internal") :
>>>> Number of labels does not match number of nodes.
>>>> Error in .local(x, ...) :
>>>> unknown order: allowed values are
>>>> unknown,preorder,postorder,pruningwise,cladewise
>>>> Error in checkSlotAssignment(object, name, value) :
>>>> assignment of an object of class “character” is not valid for
>>>> slot 'annote' in an object of class “phylo4”; is(value, "list") is
>>>> not TRUE
>>>> done successfully.
>>>>
>>>>
>>>>
>>>> Executing test function test.phylo4.phylo ... Error in .local(x,
>>>> ...) : Labels are not unique
>>>> Error in .local(x, ...) : Labels are not unique
>>>> done successfully.
>>>>
>>>>
>>>>
>>> 193a194,241
>>>> Executing test function test.addData.phylo4 ... done successfully.
>>>>
>>>>
>>>>
>>>> Executing test function test.addData.phylo4d ... done successfully.
>>>>
>>>>
>>>>
>>>> Executing test function test.hasNodeData.phylo4d ... done
>>>> successfully.
>>>>
>>>>
>>>>
>>>> Executing test function test.na.omit.phylo4d ... done successfully.
>>>>
>>>>
>>>>
>>>> Executing test function test.nData ... done successfully.
>>>>
>>>>
>>>>
>>>> Executing test function test.nodeData.phylo4d ... done successfully.
>>>>
>>>>
>>>>
>>>> Executing test function test.Replace.nodeData.phylo4d ... done
>>>> successfully.
>>>>
>>>>
>>>>
>>>> Executing test function test.Replace.tdata.phylo4d ... done
>>>> successfully.
>>>>
>>>>
>>>>
>>>> Executing test function test.Replace.tipData.phylo4d ... done
>>>> successfully.
>>>>
>>>>
>>>>
>>>> Executing test function test.summary.phylo4d ... done successfully.
>>>>
>>>>
>>>>
>>>> Executing test function test.tdata.phylo4d ... done successfully.
>>>>
>>>>
>>>>
>>>> Executing test function test.tipData.phylo4d ... done successfully.
>>>>
>>>>
>>>>
>>> 360,407d407
>>> < Executing test function test.addData.phylo4 ... done successfully.
>>> <
>>> <
>>> <
>>> < Executing test function test.addData.phylo4d ... done successfully.
>>> <
>>> <
>>> <
>>> < Executing test function test.hasNodeData.phylo4d ... done
>>> successfully.
>>> <
>>> <
>>> <
>>> < Executing test function test.na.omit.phylo4d ... done successfully.
>>> <
>>> <
>>> <
>>> < Executing test function test.nData ... done successfully.
>>> <
>>> <
>>> <
>>> < Executing test function test.nodeData.phylo4d ... done successfully.
>>> <
>>> <
>>> <
>>> < Executing test function test.Replace.nodeData.phylo4d ... done
>>> successfully.
>>> <
>>> <
>>> <
>>> < Executing test function test.Replace.tdata.phylo4d ... done
>>> successfully.
>>> <
>>> <
>>> <
>>> < Executing test function test.Replace.tipData.phylo4d ... done
>>> successfully.
>>> <
>>> <
>>> <
>>> < Executing test function test.summary.phylo4d ... done successfully.
>>> <
>>> <
>>> <
>>> < Executing test function test.tdata.phylo4d ... done successfully.
>>> <
>>> <
>>> <
>>> < Executing test function test.tipData.phylo4d ... done successfully.
>>> <
>>> <
>>> <
>>> 433c433
>>> < 'arg' should be one of "warn", "fail", "ok"
>>> ---
>>>> 'arg' should be one of “warn”, “fail”, “ok”
>>> 957,960d956
>>> < Executing test function test.multiPhylo.As.multiPhylo4 ... done
>>> successfully.
>>> <
>>> <
>>> <
>>> 965,969c961
>>> < Executing test function test.phylo.As.phylo4 ... done successfully.
>>> <
>>> <
>>> <
>>> < Executing test function test.phylo.As.phylo4d ... done successfully.
>>> ---
>>>> Executing test function test.multiPhylo.As.multiPhylo4 ... done
>>>> successfully.
>>> 979,981c971,972
>>> < In addition: Warning messages:
>>> < 1: In rm(ExContDataFile) : object 'ExContDataFile' not found
>>> < 2: In asMethod(object) : losing data while coercing phylo4d to phylo
>>> ---
>>>> In addition: Warning message:
>>>> In rm(ExContDataFile) : object 'ExContDataFile' not found
>>> 1006a998,1005
>>>> Executing test function test.phylo.As.phylo4 ... done successfully.
>>>>
>>>>
>>>>
>>>> Executing test function test.phylo.As.phylo4d ... done successfully.
>>>>
>>>>
>>>>
>>> 1012,1013c1011,1013
>>> < In addition: Warning message:
>>> < In asMethod(object) : losing data while coercing phylo4d to phylo
>>> ---
>>>> In addition: Warning messages:
>>>> 1: In asMethod(object) : losing data while coercing phylo4d to phylo
>>>> 2: In asMethod(object) : losing data while coercing phylo4d to phylo
>>> 1058c1058
>>> < Executing test function test.plot.phylo4 ... done successfully.
>>> ---
>>>> Executing test function test.plotOneTree ... done successfully.
>>> 1062c1062
>>> < Executing test function test.plotOneTree ... done successfully.
>>> ---
>>>> Executing test function test.plot.phylo4 ... done successfully.
>>> 1142c1142
>>> < RUNIT TEST PROTOCOL -- Fri Nov 23 15:34:01 2012
>>> ---
>>>> RUNIT TEST PROTOCOL -- Wed Nov 21 17:55:51 2012
>>> Running ‘misctests.R’
>>> Comparing ‘misctests.Rout’ to ‘misctests.Rout.save’ ... OK
>>> Running ‘nexusdata.R’
>>> Comparing ‘nexusdata.Rout’ to ‘nexusdata.Rout.save’ ... OK
>>> Running ‘phylo4dtests.R’
>>> Comparing ‘phylo4dtests.Rout’ to ‘phylo4dtests.Rout.save’ ... OK
>>> Running ‘phylosubtest.R’
>>> Comparing ‘phylosubtest.Rout’ to ‘phylosubtest.Rout.save’ ... OK
>>> Running ‘phylotorture.R’
>>> Comparing ‘phylotorture.Rout’ to ‘phylotorture.Rout.save’ ... OK
>>> Running ‘plottest.R’
>>> Comparing ‘plottest.Rout’ to ‘plottest.Rout.save’ ...62,72c62,73
>>> < iter 5 value 3.201783
>>> < iter 10 value 1.432415
>>> < iter 15 value 1.217510
>>> < iter 20 value 1.069446
>>> < iter 25 value 0.662087
>>> < iter 30 value 0.237888
>>> < iter 35 value 0.106249
>>> < iter 40 value 0.045765
>>> < iter 45 value 0.020016
>>> < final value 0.007666
>>> < converged
>>> ---
>>>> iter 5 value 3.201793
>>>> iter 10 value 1.433796
>>>> iter 15 value 1.147120
>>>> iter 20 value 0.914894
>>>> iter 25 value 0.705057
>>>> iter 30 value 0.376895
>>>> iter 35 value 0.256479
>>>> iter 40 value 0.100497
>>>> iter 45 value 0.044026
>>>> iter 50 value 0.016151
>>>> final value 0.016151
>>>> stopped after 50 iterations
>>> Running ‘roundtrip.R’
>>> Comparing ‘roundtrip.Rout’ to ‘roundtrip.Rout.save’ ... OK
>>> Running ‘testprune.R’
>>> Comparing ‘testprune.Rout’ to ‘testprune.Rout.save’ ... OK
>>> * checking for unstated dependencies in vignettes ... OK
>>> * checking package vignettes in ‘inst/doc’ ... OK
>>> * checking running R code from vignettes ... [2s/2s] OK
>>> * checking re-building of vignette PDFs ... [3s/5s] OK
>>> * checking PDF version of manual ... OK
>>> WARNING: There was 1 warning.
>>> NOTE: There was 1 note.
>>> See
>>> ‘/home/Hornik/tmp/CRAN/phylobase.Rcheck/00check.log’
>>> for details.
>>>
>>>
>>>
>>> On 12-11-21 03:50 PM, Uwe Ligges wrote:
>>>>>> Dear maintainer,
>>>>>>
>>>>>> please see the ERRORs on
>>>>>> http://cran.r-project.org/web/checks/check_results_phylobase.html
>>>>>>
>>>>>> Particularly
>>>>>>
>>>>>> http://www.r-project.org/nosvn/R.check/r-oldrel-windows-ix86+x86_64/phylobase-00check.html
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> shows that you apparently need a newer version of Rcpp that you
>>>>>> failed to declare in your DESCRIPTION file.
>>>>>>
>>>>>> Plesse fiyx.
>>>>>>
>>>>>> Best, Uwe Ligges
>>>
>>> I fixed the Rcpp versioning issue (thanks).
>>> I must confess I'm totally baffled by the rest of the error output,
>>> which looks like it's based on the old version. I don't have any idea
>>> how I could have re-submitted an unchanged version (I'm tempted to
>>> blame it on R-forge, since I did an automated submission via R-forge,
>>> but ???)
>>>
>>> In any case, I have put an updated version on the FTP incoming site.
>>> There is still some false-positive "chatter" coming from differences
>>> with saved test files -- I am having a hard time figuring out how to
>>> suppress these reliably (the files are generated using RUnit, and seem
>>> to have some variation from machine to machine ...)
>>>
>>> thanks,
>>> Ben Bolker
>>>
>>>
>>>
>>>
>>
>
>
More information about the Phylobase-devl
mailing list