[Bioc-devel] Errors in Building AssessORF

Hi Deepank,

Just to clarify, this is about a new submission and the build
you're referring to is:

 
http://bioconductor.org/spb_reports/AssessORF_buildreport_20180910173835.html

Note that I can reproduce this error on my laptop with:

   git clone https://github.com/DRK248/AssessORF
   git clone https://github.com/DRK248/AssessORFData
   R CMD INSTALL AssessORF AssessORFData
   R CMD build AssessORF
   R CMD check AssessORF_0.99.9.tar.gz

The last command (R CMD check) produces:

   ...
   * checking examples ... ERROR
   Running examples in ?AssessORF-Ex.R? failed
   The error most likely occurred in:

   > ### Name: ScoreAssesmentResults
   > ### Title: Score Gene Assessment Results
   > ### Aliases: ScoreAssesmentResults
   >
   > ### ** Examples
   >
   >
   > ScoreAssessmentResults(readRDS(system.file("extdata", 
"ATCC17978_PreSaved_ResultsObj_Prodigal.rds", package = "AssessORF")), "a")
   Warning in gzfile(file, "rb") :
     cannot open compressed file '', probable reason 'No such file or 
directory'
   Error in gzfile(file, "rb") : cannot open the connection
   Calls: ScoreAssessmentResults -> readRDS -> gzfile
   Execution halted
   ...

I cloned the 2 packages less than 30 min ago so I have the most current
versions. Also since this was the first time I cloned and installed
AssessORF and AssessORFData on my machine, I shouldn't have any stale
files or stale versions of the packages. So this error actually looks
like a true positive to me and not an error due to some caching or other
dysfunction of the SPB (Single Package Builder).

The problem is that the package contains an example (in the
ScoreAssesmentResults.Rd) man page that tries to read the
inst/extdata/ATCC17978_PreSaved_ResultsObj_Prodigal.rds
file. But the inst/extdata/ folder doesn't contain such file:

   hpages at spectre:~/AssessORF$ ls inst/extdata/
   Adenoviridae.sqlite
   MGAS5005_PreSaved_ResultsObj_Prodigal.rds
   MGAS5005_PreSaved_DataMapObj.rds
   MGAS5005_Prodigal.sco

You should be able to reproduce this error on your machine too by
using the standard 'R CMD build' + 'R CMD check' sequence.

Finally note that AssessORFData Suggests AssessORF even though it
looks like it should be the other way around (AssesORF uses
AssessORFData but AssessORFData has no mention of AssessORF and
doesn't seem to make any use of it).

Cheers,
H.

Hi,

I'm the developer of the AssessORF package. For the last couple of valid
builds that I pushed (each with an appropriate version bump), I am getting
the same error from the automated package builder involving code that is no
longer part of my package. Specifically, the automated package builder is
trying to run an outdated example for one of the functions in my package
and failing because the name of the function has changed and because the
data files used in the old example are no longer part of my package. I am
not sure how to resolve this issue on my end as I have pushed multiple
valid builds since I started seeing this error and nothing has changed. Can
anyone help me with this?

Thanks,
Deepank Korandla
Wright Lab, University of Pittsburgh

	[[alternative HTML version deleted]]

_______________________________________________
Bioc-devel at r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=tS_aEsUJun1qA9WO0HWeyiqKt8zalnNiL3cp0BZVtKQ&s=oWrN9I53U5I1BDWdLuzccCO_uWnj1E5Hj2rTpn0ss1g&e=

Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319