[Bioc-devel] Errors in Building AssessORF

Hervé Pagès hp@ge@ @ending from fredhutch@org
Tue Sep 11 00:57:16 CEST 2018

Hi Deepank,

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


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 
   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
file. But the inst/extdata/ folder doesn't contain such file:

   hpages using spectre:~/AssessORF$ ls inst/extdata/

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).


On 09/10/2018 02:57 PM, Deepank Korandla wrote:
> 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]]
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Hervé Pagès

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 using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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