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 <bioc-devel-boun...@r-project.org> on behalf of Fabricio de
Almeida <fabricio_almeidasi...@hotmail.com>
Sent: Friday, July 9, 2021 11:17 AM
To: bioc-devel@r-project.org <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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