[Bioc-devel] Package build error for windows system
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 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. Cheers, H.
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
Herv? Pag?s 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 at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319