[Bioc-devel] erro in package build

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Tue Aug 13 21:56:20 CEST 2019

Hi Claudio,

As you can see on our build/check report, what is broken is 'R CMD
INSTALL Mulcom'. The problem is easy to reproduce:

   hpages using spectre:~$ git clone 
https://git.bioconductor.org/packages/MulcomCloning into 'Mulcom'...
   remote: Enumerating objects: 570, done.
   remote: Counting objects: 100% (570/570), done.
   remote: Compressing objects: 100% (555/555), done.
   remote: Total 570 (delta 343), reused 0 (delta 0)
   Receiving objects: 100% (570/570), 4.87 MiB | 2.03 MiB/s, done.
   Resolving deltas: 100% (343/343), done.
   Checking connectivity... done.

   hpages using spectre:~$ R CMD INSTALL Mulcom
   * installing to library ‘/home/hpages/R/R-3.6.r76454/library’
   * installing *source* package ‘Mulcom’ ...
   ** using staged installation
   ** libs
   ** R
   ** data
   ** inst
   ** byte-compile and prepare package for lazy loading
   ** help
   *** installing help indices
   ** building package indices
   ** installing vignettes
   Warning in file(con, "w") :
     cannot open file 
No such file or directory
   Error in file(con, "w") : cannot open the connection
   ERROR: installing vignettes failed
   * removing ‘/home/hpages/R/R-3.6.r76454/library/Mulcom’
   * restoring previous ‘/home/hpages/R/R-3.6.r76454/library/Mulcom’

What seems to cause this is the presence of things in your package
source tree that don't belong there. These things are the build/
folder and the src/symbols.rds file. Remove them and the problem will
go away.

Please refer to the "Package structure" subsection of the "Writing R
Extensions" manual 
for more information about how to maintain
a valid package source tree.

Hope this helps.


On 7/16/19 01:04, Claudio Isella wrote:
> dear all,
> I am experiencing problem in generating a packages suitable for bioconductor repositories.
> I checked locally and both build and check runs properly, however when the package is pushed on the git server I received this error.
> https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.9_bioc-2DLATEST_Mulcom_malbec2-2Dinstall.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fQ4-JqkOjn_u0m7mvGLwQi066aOuH10BLxJf-57chEI&s=1hd4QAH2fMt-gNr-Epi29tzpfOsGB-YvA0J-XXGU1lE&e=
> can you help me?
>> Claudio

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
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