Hi Gang - we have been getting some weird and inconsistent errors with 3dMEMA recently. These errors happen for new analyses and old scripts that previously worked (and nothing was changed). Sometimes the program seems to work fine, however, many more times we are halted by random errors. I have tried to find a pattern and cannot. I can run the same code on the same data multiple times in a row and sometimes it will give a random error (possibly different errors even though the same code was run) and sometimes it will work.
Here are some examples of the errors we have received:
Error in gzfile(file, "rb") : invalid 'compress' argument
Execution halted
Error in dim(rs2$brk) <- ddb : dims do not match the length of object
Calls: process.MEMA.opts -> lapply -> FUN -> read.c.AFNI
Execution halted
Error in routines[[103]] : subscript out of bounds
Execution halted
Warning in read.MEMA.opts.batch(args, verb = 0) :
You must have either one or two groups
Error: Error parsing input
Execution halted
During startup - Warning message:
package "methods" in options("defaultPackages") was not found
** Error:
Expecting 101 parameters for option "-prefix".
Have 1 parameter(s) in string "VSppi.agree.peer-comp" instead.
NULL options
** Error:
Error parsing arguments. See 3dMEMA -help for details.
During startup - Warning messages:
1: package "methods" in options("defaultPackages") was not found
2: package 'datasets' in options("defaultPackages") was not found
3: package 'utils' in options("defaultPackages") was not found
4: package 'grDevices' in options("defaultPackages") was not found
5: package 'graphics' in options("defaultPackages") was not found
6: package 'stats' in options("defaultPackages") was not found
7: package 'methods' in options("defaultPackages") was not found
Error in strsplit(Sys.getenv("PATH"), ":")[[101]] :
subscript out of bounds
Calls: source -> first.in.path -> paste
Execution halted
Error in lop$subjLab[[ii]] : subscript out of bounds
Calls: process.MEMA.opts
Execution halted
Here are some other errors we have received from another bit of code that used to work:
Writing xMat to copyASDvTD_11_Age+meanFD_P-C_G.RxMat
Error in array(apply(comArr[, , kk, ], 3, function(x) x * (abs(lop$maskData[, :
negative length vectors are not allowed
In addition: Warning message:
In array(apply(comArr[, , kk, ], 3, function(x) x * (abs(lop$maskData[, :
NAs introduced by coercion to integer range
Execution halted
Error in dim(rs2$brk) <- ddb : the dims contain missing values
Calls: process.MEMA.opts -> lapply -> FUN -> read.c.AFNI
In addition: Warning messages:
1: In get.c.AFNI.attribute(hatr, "DATASET_DIMENSIONS") :
NAs introduced by coercion to integer range
2: In get.c.AFNI.attribute(hatr, "DATASET_RANK") :
NAs introduced by coercion to integer range
Execution halted
We are using Precompiled binary linux_xorg7_64: Feb 21 2018 (Version AFNI_18.0.18) and R 3.2.2.
Running afni_system_check is all fine except that I don’t have the R library ‘psych’ installed. However, I haven’t needed it for MEMA or LME previously.
We are also running a lot of analysis on our server: multiple 3dDeconvolve and 3dMEMA commands, each of which with multiple -jobs. Do you think this could get in the way?