Issue with warnings about 'memory.size()'

[zjwinn]

Hi,

I am using GAPIT for a study and I am reciving the following information from my log:

[1] "--------------------- Welcome to GAPIT ----------------------------"
[1] "MLM"
[1] "--------------------Processing traits----------------------------------"
[1] "Phenotype provided!"
[1] "The 1 model in all."
[1] "MLM"
[1] "GAPIT.DP in process..."
[1] "GAPIT will filter marker with MAF setting !!"
[1] "The markers will be filtered by SNP.MAF: 0.05"
maf_index
TRUE 
 600 
[1] "Calculating kinship..."
[1] "Number of individuals and SNPs are  1000  and  600"
[1] "Calculating ZHANG relationship defined by Zhiwu Zhang..."
[1] "substracting mean..."
[1] "Getting X'X..."
[1] "Adjusting..."
[1] "Calculating kinship with Zhang method: done"
[1] "kinship calculated"
[1] "Adding IDs to kinship..."
[1] "Writing kinship to file..."
[1] "Kinship save as file"
[1] "Kinship created!"
NULL
[1] "GAPIT.DP accomplished successfully for multiple traits. Results are saved"
[1] "Processing trait: Two_Gene:genotypic_value"
[1] "--------------------Phenotype and Genotype ----------------------------------"
[1] "Zhang"
[1] TRUE
[1] "There are  1  traits in phenotype data."
[1] "There are  1000  individuals in phenotype data."
[1] "There are  600  markers in genotype data."
[1] "Phenotype and Genotype are test OK !!"
[1] "--------------------GAPIT Logical Done----------------------------------"
[1] "GAPIT.IC in process..."
[1] "There is 0 Covarinces."
[1] "There are 1000 common individuals in genotype , phenotype and CV files."
[1] "The dimension of total CV is "
[1] 1000    2
[1] "GAPIT.IC accomplished successfully for multiple traits. Results are saved"
[1] "GAPIT.SS in process..."
[1] "GAPIT will be into GWAS approach..."
[1] "Zhang"
[1] "The GAPIT would go into Main..."
[1] "------------Examining data (QC)------------------------------------------"
[1] "Try to group from and to were set to 1"
[1] "------------Examining data (QC) done-------------------------------------"
[1] "-------------------Sandwich burger and dressing------------------------"
The upper bound of groups is too high. It was set to the size of kinship!
The lower bound of groups is too high. It was set to the size of kinship!
[1] "-------------------------Iteration in process--------------------------"
[1] "Total iterations: 1"
[1] "Compressing and Genome screening..."
[1] "-------Mixed model with Kinship-----------------------------"
[1] "1 of 1 -- Vg= 11.9898 VE= 0.4783 -2LL= 3318.82   Clustering= average   Group number= 1000   Group kinship= Mean"
[1] "---------------------Sandwich bottom bun-------------------------------"
[1] "--------------------Final results presentations------------------------"
[1] "Generating summary"
[1] "Genomic Breeding Values (GBV) ..."
[1] "GAPIT.GS accomplished successfully!"
[1] "Writing GBV and Acc..."
[1] "GBV and accuracy distribution..."
[1] "Compression portfolios..."
[1] "Compression Visualization done"
     Type   Cluster   Group  REML               VA                 VE                
[1,] "Mean" "average" "1000" "3318.81952484662" "11.9897712527485" "0.47825123729183"
[1] "p3d objects transfered"
[1] "Merge BLUP and BLUE"
[1] "GAPIT before BLUP and BLUE"
[1] "GAPIT after BLUP and BLUE"
[1] "MLM.Two_Gene:genotypic_value has been analyzed successfully!"
[1] "The results are saved in the directory of  C:/Users/zwinn/OneDrive/GitHub/GWAS-Simulation-Study/Minimum_Reproducible_Code"
[1] "before ending GAPIT.Main"
[1] "GAPIT accomplished successfully for multiple traits. Result are saved"
[1] "GAPIT has done all analysis!!!"
There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: 'memory.size()' is no longer supported
2: 'memory.size()' is no longer supported
3: 'memory.size()' is no longer supported
4: 'memory.size()' is no longer supported
5: 'memory.size()' is no longer supported
6: 'memory.size()' is no longer supported
7: 'memory.size()' is no longer supported
8: 'memory.size()' is no longer supported
9: 'memory.size()' is no longer supported
10: 'memory.size()' is no longer supported
11: 'memory.size()' is no longer supported
12: 'memory.size()' is no longer supported
13: 'memory.size()' is no longer supported
14: 'memory.size()' is no longer supported
15: 'memory.size()' is no longer supported
16: 'memory.size()' is no longer supported
17: 'memory.size()' is no longer supported
18: 'memory.size()' is no longer supported
19: 'memory.size()' is no longer supported
20: 'memory.size()' is no longer supported
21: 'memory.size()' is no longer supported
22: 'memory.size()' is no longer supported
23: 'memory.size()' is no longer supported
24: 'memory.size()' is no longer supported
25: 'memory.size()' is no longer supported
26: 'memory.size()' is no longer supported
27: 'memory.size()' is no longer supported
28: 'memory.size()' is no longer supported
29: 'memory.size()' is no longer supported
30: 'memory.size()' is no longer supported
31: 'memory.size()' is no longer supported
32: 'memory.size()' is no longer supported
33: 'memory.size()' is no longer supported
34: 'memory.size()' is no longer supported
35: 'memory.size()' is no longer supported
36: 'memory.size()' is no longer supported
37: 'memory.size()' is no longer supported
38: 'memory.size()' is no longer supported
39: 'memory.size()' is no longer supported
40: 'memory.size()' is no longer supported
41: 'memory.size()' is no longer supported
42: 'memory.size()' is no longer supported
43: 'memory.size()' is no longer supported
44: 'memory.size()' is no longer supported
45: 'memory.size()' is no longer supported
46: 'memory.size()' is no longer supported
47: 'memory.size()' is no longer supported
48: 'memory.size()' is no longer supported
49: 'memory.size()' is no longer supported
50: 'memory.size()' is no longer supported

It appears that there is a package being called upon internally that has updated so the argument "memory.size()" is no longer supported.

[Gpolizel]

I think you do not need to concern about it. Your analysis was done. These messages are just "warnings".

[Samrath0402]

@Gpolizel : i am getting the following error and analysis is not performed
Error in file(filename, "r", encoding = encoding) : cannot open the connection to 'http://zzlab.net/GAPIT/GAPIT.library.R' In addition: Warning message: In file(filename, "r", encoding = encoding) : URL 'https://zzlab.net/GAPIT/GAPIT.library.R': status was 'SSL connect error