Re: [Bioc-devel] Getting ready for package submission, running into a couple of errors/warnings that I can't figure out

[Nitesh Turaga]

Hi,

I will try to answer a couple of the questions you asked. I am not able to help 
with your question on ‘qpdf'. 

> On Jul 12, 2021, at 5:58 PM, Wight, Andrew E. 
>  wrote:
> 
> Good evening all - I'm getting my first package ready for submission to 
> Bioconductor, and I'm running into a couple of errors/warnings when I run R 
> CMD CHECK or BiocCheck. All of my current troubleshooting on these errors has 
> come up blank, so I'm hoping someone here can point me in the right direction.
> 
> I'm running R4.1 on Ubuntu 20.04, Bioconductor 3.13, and BiocCheck 1.28
> 
> 
>  1.  R CMD check warning: �qpdf� is needed for checks on size reduction of 
> PDFs
> 
> I am getting this warning with R CMD check despite the fact that I have 
> installed qpdf and it is visible to my R session. Stack Exchange suggested a 
> couple of fixes in .Renviron, none of which helped. This seems like a new 
> problem in R4.x, and possibly is only a problem with packages intended for 
> CRAN, but I wanted to make sure it wouldn't cause headaches during review.
> 
> 
>  1.  BiocCheck error: Maintainer must register at the support site; visit 
> https://support.bioconductor.org/accounts/signup/
> 
> I am registered on the support site as andrewe_wi...@dfci.harvard.edu, which 
> is the same email address as listed in my package's DESCRIPTION, so I'm not 
> sure what else to do here. I've been registered on the support site for 7 
> months now and have a verified email address.
> 

I don’t **think** local installation of BiocCheck has the ability to cross 
check the support site database of registered users. If you are registered, 
trust that once submitted this issue will not show up.  

>  1.  BiocCheckGitClone error: System Files found that should not be git 
> tracked:
>flowGate.Rproj
>.Rhistory
> 
> I accidentally tracked these two files ages past, but have long since added 
> them to .gitignore and deleted them with git rm --cached . I can 
> confirm that they are gone with git ls-files and git ls-files --cache; they 
> appear in neither of these lists when I run the command. To be certain, I 
> made a fresh clone of the repo on a new computer and ran BiocCheckGitClone, 
> but still got this error despite neither of these files showing up anywhere 
> in the git as far as I can tell.
> 

You would need to “purge” the file from your repository history. There is good 
documentation in a couple of places, for the tool called BFG repo cleaner.

- 
https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/removing-sensitive-data-from-a-repository#purging-a-file-from-your-repositorys-history

- https://rtyley.github.io/bfg-repo-cleaner/


> 
> My apologies for what seem like basic problems - these look like they should 
> be straightforward fixes (install qpdf, register for the site, and remove the 
> offending files), but none of those fixes worked and I'm not sure where to go 
> from here. Any insight anyone can give on how to fix these errors is greatly 
> appreciated!
> 
> Thanks,
> 
> -Andrew
> 
> 
> 
> 
> The information in this e-mail is intended only for th...{{dropped:17}}

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[Bioc-devel] reacVcf(remoteFile, "hg19", region) fails in VariantAnnotation 1.39.0 (and friends), works with 1.38.0

[Paul Shannon]

The problem is described in full here, with 4 lines of code to reproduce.

 https://support.bioconductor.org/p/9138262/ 


James MacDonald pointed out that my initial analysis is wrong. (Thank you, 
Jim!)  I claimed this works on macOS, fails on linux, and he shows in the 
support thread that readVcf(remoteFile) worked find for him on linux.

So maybe, as Jim suggests, there is a problem with the latest version of 
VariantAnnotation or packages it depends upon:?

Jim’s linux run, and my MacOD run, both used VariantAnnotation_1.38.0, 
My docker (Docker devel) has VariantAnnotation_1.39.0.

However, I installed  1.38.0 on the docker image, and the problem persisted.  
Leading me to think that the problem may be one of the packages (zlib, httr?) 
which VariantAnnotation uses?

One strategy we could employ is to expand the error message to tell us more.  
It currently reports

*[E::hts_open_format] Failed to open file
 https://igv-data.systemsbiology.net/static/ampad/test/chr2.vcf.gz
Error in open.BcfFile(BcfFile(file, character(0), ...)) :
  ‘open'  VCF/BCF failed
  filename: https://igv-data.systemsbiology.net/static/ampad/test/chr2.vcf.gz*

Maybe  more information is available at the point of failure which, if 
reported, might clarify the problem?

 - Paul





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[Bioc-devel] Getting ready for package submission, running into a couple of errors/warnings that I can't figure out

[Wight, Andrew E.]

Good evening all - I'm getting my first package ready for submission to 
Bioconductor, and I'm running into a couple of errors/warnings when I run R CMD 
CHECK or BiocCheck. All of my current troubleshooting on these errors has come 
up blank, so I'm hoping someone here can point me in the right direction.

I'm running R4.1 on Ubuntu 20.04, Bioconductor 3.13, and BiocCheck 1.28


  1.  R CMD check warning: �qpdf� is needed for checks on size reduction of PDFs

I am getting this warning with R CMD check despite the fact that I have 
installed qpdf and it is visible to my R session. Stack Exchange suggested a 
couple of fixes in .Renviron, none of which helped. This seems like a new 
problem in R4.x, and possibly is only a problem with packages intended for 
CRAN, but I wanted to make sure it wouldn't cause headaches during review.


  1.  BiocCheck error: Maintainer must register at the support site; visit 
https://support.bioconductor.org/accounts/signup/

I am registered on the support site as andrewe_wi...@dfci.harvard.edu, which is 
the same email address as listed in my package's DESCRIPTION, so I'm not sure 
what else to do here. I've been registered on the support site for 7 months now 
and have a verified email address.


  1.  BiocCheckGitClone error: System Files found that should not be git 
tracked:
flowGate.Rproj
.Rhistory

I accidentally tracked these two files ages past, but have long since added 
them to .gitignore and deleted them with git rm --cached . I can 
confirm that they are gone with git ls-files and git ls-files --cache; they 
appear in neither of these lists when I run the command. To be certain, I made 
a fresh clone of the repo on a new computer and ran BiocCheckGitClone, but 
still got this error despite neither of these files showing up anywhere in the 
git as far as I can tell.


My apologies for what seem like basic problems - these look like they should be 
straightforward fixes (install qpdf, register for the site, and remove the 
offending files), but none of those fixes worked and I'm not sure where to go 
from here. Any insight anyone can give on how to fix these errors is greatly 
appreciated!

Thanks,

-Andrew




The information in this e-mail is intended only for the ...{{dropped:15}}

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[Bioc-devel] Call for Community Volunteered Package Reviewers

[Kern, Lori]

Bioconductor is pleased to announce a call for community volunteers to
assist with Bioconductor Package Reviews.  This is an excellent way to get
involved with and give back to the Bioconductor Community. The minimum
requirement to volunteer is to be actively maintaining an existing Bioconductor
package. Please read Review Expectations for full details and information.

https://contributions.bioconductor.org/review-expectation.html


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] Usage of donttest{} in examples

[Kern, Lori]

We will look into the calculations for percentage to see if there is a bug in 
the reporting.


We encourage all functions to be adequately testing and run in actively 
executed code. Is it possible to scale down the example data set?  Often times 
it is feasible to show functionality of a function/package using a small or 
truncated data set rather than a complete set.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Fabricio de 
Almeida 
Sent: Friday, July 9, 2021 11:17 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Usage of donttest{} in examples

Dear Bioc developers,


I submitted a package 3 days ago and the build report returned TIMEOUT for 
Windows and macOS.

Then I included donttest{} in the example for a function that was taking too 
long to run, but now it is returning ERROR 
(http://secure-web.cisco.com/1rQq0oNkwIaLKFAZeRljuk8lUMFgoLyfO7bNl1XhyIUc077iFKXTXX-RPc4WuNbr_FqRMyJqt0mNU3avrFQj7YzwpN5_p1yhD0MvoB360Ky_iTjahbcidxWpn8yodiAP95SOF1iQ3VtscyqjCTbz6Uk09vivvjpDzcJOWPQn26Vgui3UU82ycvuq10emYaja4l9MiukDWdpft08s8h4fi5LBVJRGSljq0m8oyl10ssxxOMPlgT8tBkK_p8e5dQ9LLBGC-xM5YEnvbmaZmuvXQbOkiSC9YoMJPhEhSV2eGX3Wrs75aMP54XXjdUsQfo3b4p6e0gXNkt3kwuBJ6rmB-rQ/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2Fcageminer_buildreport_20210709105948.html
 See below:

* ERROR: At least 80% of man pages documenting exported objects
  must have runnable examples. The following pages do not:
  mine_candidates.Rd, score_genes.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
  14% of man pages use one of these cases.
  Found in the following files:
mine_candidates.Rd
score_genes.Rd


As you can see in the NOTE, these 2 functions represent 14% of the exported 
functions. Thus, 86% of the functions have runnable examples. Why is the build 
report saying that <80% have runnable examples?


Best regards,


=


Fabr�o de Almeida Silva

Undergraduate degree in Biological Sciences (UENF)

MSc. candidate in Plant Biotechnology (PGBV/UENF - RJ/Brazil)

Laborat� de Qu�ca e Fun� de Prote�s e Pept�os (LQFPP/CBB/UENF - RJ/Brazil)

Lattes CNPq: 
http://secure-web.cisco.com/1M5N1XqL9Gf2taYzE2xHpO00NrOVZ3shgElEM2e32_TDJUjrITnF1K3I60s_6lgAodcf7R7VP5y3afsRf9YNWcCjosBICID1ZAcdCr73zp01AGREskKzP6CPgjYS6aSXJos4I_pXY6Z12TYhX2Jsao5xQ2VcWq52D99_mL2ChnhiyNgpVXb5agTlSq3qhj7s1WQrq0KT_YMRdHolhQhfg9ykvjkz-ZurVHlhjQm7ah3vcKi0m4PQJPXLyXbMxMlSiy9QSoEJ0DfYe5bPjgLcr3NrlpaTPt3STwulCtXZvQFEEv6Dap9Ef6t8BJUeVtL2fGyaTBS_zAxUEy8z22ycnnw/http%3A%2F%2Flattes.cnpq.br%2F3119358824056108

Personal website: 
https://secure-web.cisco.com/1E-fYKalq79JpVgZI2j6bPW2RHyPlDhPB3wHUU8Qd5oXDG8bxB6juv4-Et_cv17A42WkVSFkn4pE43C5JTnMmHu8RNeWKRJh8PoTwB8V-UjGRUUaeTjxulZLb5XUu-915d0s0RRGpEmgZuJGdrgzznn_HGCBOEBicVB1Co7NSqj6Q4S2uv4RYvaG-l86U9GLelrQRe4XfO-F8y4y-nEOTPRulPM55o2-r2Dd27NHOCN54jwb5LmI-A06TZASi5MqEib5A15d1HsEHAElD3HY51FoOT8yLh2RvUGTcE3nz6OBS0ZxjkdckEHB2ebcLkpSg/https%3A%2F%2Falmeidasilvaf.github.io%2Fhome%2F


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