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

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Mon Jul 12 13:42:45 CEST 2021

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.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Fabricio de Almeida <fabricio_almeidasilva using hotmail.com>
Sent: Friday, July 9, 2021 11:17 AM
To: bioc-devel using r-project.org <bioc-devel using 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:

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

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