[Phylobase-devl] CRAN submission phylobase 0.6.4
Ben Bolker
bbolker at gmail.com
Sat Nov 24 16:31:57 CET 2012
On 12-11-23 09:46 AM, Kurt Hornik wrote:
>>>>>> Ben Bolker writes:
>
> Ben,
>
> Please see the CRAN Repository Policy for appropriate subject lines.
>
> 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.
>
> 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
>
>
>
>
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