Hi all, I am getting a warning message when I create my contrast matrix (for a six-membered loop design experiment) that I can't find any previous threads about. The message reads: Warning message: use of NULL environment is deprecated Here is a log of how it is generated, starting with a list of my targets file: > targetsB SlideNumber Name FileName Cy3 Cy5 2005-11-18_B130high 1 B130 2005-11-18_B130high.gpr A B 2005-11-16_B121high 2 B121 2005-11-16_B121high.gpr B C 2005-11-15_B117high 3 B117 2005-11-15_B117high.gpr C D 2005-11-16_B119high 4 B119 2005-11-16_B119high.gpr D E 2005-11-18_B122high 5 B122 2005-11-18_B122high.gpr E RC 2005-11-17_B128high 6 B128 2005-11-17_B128high.gpr RC A 2005-11-17_B129high 7 B129 2005-11-17_B129high.gpr A C 2005-11-18_B131high 8 B131 2005-11-18_B131high.gpr B D 2005-11-16_B120high 9 B120 2005-11-16_B120high.gpr C E 2005-11-15_B118high 10 B118 2005-11-15_B118high.gpr D RC 2005-11-22_B137high 11 B137 2005-11-22_B137high.gpr E A 2005-11-18_B136high 12 B136 2005-11-18_B136high.gpr RC B > designmatrix <- modelMatrix(targetsB, ref="RC") Found unique target names: A B C D E RC > designmatrix A B C D E 2005-11-18_B130high -1 1 0 0 0 2005-11-16_B121high 0 -1 1 0 0 2005-11-15_B117high 0 0 -1 1 0 2005-11-16_B119high 0 0 0 -1 1 2005-11-18_B122high 0 0 0 0 -1 2005-11-17_B128high 1 0 0 0 0 2005-11-17_B129high -1 0 1 0 0 2005-11-18_B131high 0 -1 0 1 0 2005-11-16_B120high 0 0 -1 0 1 2005-11-15_B118high 0 0 0 -1 0 2005-11-22_B137high 1 0 0 0 -1 2005-11-18_B136high 0 1 0 0 0 > contrast.matrix = makeContrasts(A, A-B, A-C, A-E, B, B-C, B-E, C-E, C-D, E, levels=designmatrix) Warning message: use of NULL environment is deprecated > contrast.matrix A A - B A - C A - E B B - C B - E C - E C - D E A 1 1 1 1 0 0 0 0 0 0 B 0 -1 0 0 1 1 1 0 0 0 C 0 0 -1 0 0 -1 0 1 1 0 D 0 0 0 0 0 0 0 0 -1 0 E 0 0 0 -1 0 0 -1 -1 0 1 What am I screwing up? Thanks in advance. Matt --------------------------------------------- College of Agriculture and Life Sciences Web Mail. http://ag.arizona.edu

Hi Matt, On 9 Jan 2006, scholz at ag.arizona.edu wrote: > Hi all, > > I am getting a warning message when I create my contrast matrix (for > a six-membered loop design experiment) that I can't find any > previous threads about. The message reads: > > Warning message: > use of NULL environment is deprecated What version of R are you using? My guess is a recent R-devel. The NEWS file says: o Changed environment tree to be rooted in an empty environment, available as emptyenv(). baseenv() modified to return an environment with emptyenv() as parent, rather than NULL. o Use of NULL as an environment is deprecated and gives a warning. You will, at least, see this message any time you load an annotation data package (that is, until we rebuilt the annotation packages with the latest R-devel). + seth

Hi Seth, Thanks for your response. Given my Cro-Magnon-level computing skills, though, I'm not quite sure what this all means. You are correct that I'm using the recent R-devel, and if I understand you correctly, I shouldn't worry about the message? Thanks, Matt Hi Matt, On 9 Jan 2006, scholz at ag.arizona.edu wrote: > Hi all, > > I am getting a warning message when I create my contrast matrix (for > a six-membered loop design experiment) that I can't find any > previous threads about. The message reads: > > Warning message: > use of NULL environment is deprecated What version of R are you using? My guess is a recent R-devel. The NEWS file says: o Changed environment tree to be rooted in an empty environment, available as emptyenv(). baseenv() modified to return an environment with emptyenv() as parent, rather than NULL. o Use of NULL as an environment is deprecated and gives a warning. You will, at least, see this message any time you load an annotation data package (that is, until we rebuilt the annotation packages with the latest R-devel). + seth --------------------------------------------- College of Agriculture and Life Sciences Web Mail. http://ag.arizona.edu

On 10 Jan 2006, scholz at ag.arizona.edu wrote: > Hi Seth, > > Thanks for your response. Given my Cro-Magnon-level computing > skills, though, I'm not quite sure what this all means. You are > correct that I'm using the recent R-devel, and if I understand you > correctly, I shouldn't worry about the message? Yes, the executive summary (is that Cro-Magnon-level?) is: don't worry about. If you are writing code that uses environments (e.g. new.env()), then it would be a good idea to modify the code to eliminate the warning. If the message is coming from someone else's code, expect it to get fixed in the next few months and don't worry: this warning message does not indicate a fault in computation. + seth