getBioC(relLevel="devel") fails under r-devel
1
0
Entering edit mode
Douglas Bates ▴ 180
@douglas-bates-5
Last seen 9.6 years ago
Using a current version of r-devel on a Debian GNU/Linux system I encounter an error in getBioC(relLevel="devel"). The part of the transcript after creating the reposTools package is ... winConvertSourceRepos text html latex example * DONE (reposTools) Loading required package: reposTools Loading required package: Biobase Error in bindingIsLocked(m2, where) : not an environment Creating a new generic function for "summary" in "reposTools" There were 29 warnings (use warnings() to see them) Error in "[<-.data.frame"(`*tmp*`, , fields[i], value = I(strsplit(df[, : replacement element 2 has 2 rows, need 33 In addition: Warning message: provided 33 variables to replace 1 variables in: "[<-.data.frame"(`*tmp*`, , fields[i], value = I(strsplit(df[,
reposTools reposTools • 1.1k views
ADD COMMENT
0
Entering edit mode
Jeff Gentry ★ 3.9k
@jeff-gentry-12
Last seen 9.6 years ago
> Using a current version of r-devel on a Debian GNU/Linux system I > encounter an error in getBioC(relLevel="devel"). Is this happening to you on R-release? Is it possible that something has changed in the time between R-release and now in the R-devel branch that would be causing this? I'm downloading R-devel now, will see what is going on. I can't replicate this using R-1.8 (which for about a week longer is what the BioC-devel is going to be tracking instead of R-devel)
ADD COMMENT
0
Entering edit mode
Jeff Gentry <jgentry@jimmy.harvard.edu> writes: > > Using a current version of r-devel on a Debian GNU/Linux system I > > encounter an error in getBioC(relLevel="devel"). > > Is this happening to you on R-release? Is it possible that something has > changed in the time between R-release and now in the R-devel branch that > would be causing this? > > I'm downloading R-devel now, will see what is going on. I can't replicate > this using R-1.8 (which for about a week longer is what the BioC- devel is > going to be tracking instead of R-devel) The problem existed only in my modified version of R-devel. I had made a modification so that assignment of an attribute did not copy the value if NAMED(val) == 0. Up until now we thought that this modification would be benign and would give a performance boost to packages that use S4 classes and methods, which means most of Bioconductor. However, it seems this change is not benign. In a sense this is good news because it will allow us to isolate where the problem lies. I have not committed this change to r-devel so others need not worry about the use of a current r-devel breaking Bioconductor. -- Douglas Bates bates@stat.wisc.edu Statistics Department 608/262-2598 University of Wisconsin - Madison http://www.stat.wisc.edu/~bates/
ADD REPLY

Login before adding your answer.

Traffic: 933 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6