[Bioc-devel] Package build error for windows system

Hervé Pagès hpages at fredhutch.org
Wed Mar 11 02:00:16 CET 2015

Hi Liu,

On 03/10/2015 10:08 AM, Liu, Yuanhang wrote:
> Hello, everyone,
> I recently submitted my first R package. Everything checks fine on my
> local machine. However, when I upload the tarball to the single package
> builder at bioconductor.org, it gave me the following error on windows
> system:
> * creating vignettes ...Warning: running command
> '"E:/packagebuilder/R/bin/x64/Rscript" --vanilla --default-packages= -e
> "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 5
> Error in withCallingHandlers(tryCatch(evalq((function (i) :
> object '.rcpp_warning_recorder' not found

Don't worry about this one. The problem is probably on the build machine
side (in the R it uses). Please ignore.

> The name of the windows build system is :
> moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit)/x64​
> What does this mean? I would really appreciate it if someone can help me
> with this.
> I also got a warning on one linux system (morelia Mac OS X Mavericks
> (10.9.5)/x86_64):
> * checking loading without being on the library search path ... WARNING
> Loading required package: IRanges
> Error: package BiocGenerics 0.13.4 is loaded, but >= 0.13.6 is required by IRanges
> In addition: Warning message:
> version 0.13.6 of BiocGenerics masked by 0.13.4 in /private/tmp/Rtmp8nLYMq/RLIBS_9d027c2fae3
> Execution halted

mmh... again something doesn't look quite right on this build machine. 
Please ignore.

> Then I checked my version of BiocGenerics, which is 0.12.1, the latest version.

This is the current release version. However remember that for testing
before package submission you should be using BioC devel (BioC 3.1, 
which requires R 3.2), not BioC release (BioC 3.0). That's what the
automatic single package builder uses.
The latest version of BiocGenerics in devel is 0.13.6.


> How come the system require 0.13.6? I also checked IRanges manual, which it says it depends on BiocGenerics(>= 0.11.3). Would anybody tell me what does this mean? Thanks in advance!
> Regards
> Yuanhang Liu
> PhD Candidate
> Bioinformatics and Computational Biology laboratory
> Cellular & Structural Biology, Department of Epidemiology & Biostatistics
> UT Health Science Center at San Antonio
> email: liuy12 at uthscsa.edu    cel: 210-784-082​8

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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