- using R Under development (unstable) (2024-12-21 r87453 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
- checking for file 'SFSI/DESCRIPTION' ... OK
- this is package 'SFSI' version '1.4.1'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'SFSI' can be installed ... OK
See the install log for details.
- used C compiler: 'gcc.exe (GCC) 13.3.0'
- checking installed package size ... OK
- checking package directory ... OK
- checking 'build' directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [58s] OK
- checking whether the package can be loaded with stated dependencies ... [56s] OK
- checking whether the package can be unloaded cleanly ... [54s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s] OK
- checking loading without being on the library search path ... [2s] OK
- checking whether startup messages can be suppressed ... [54s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [11s] OK
- checking Rd files ... [1s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of 'data' directory ... OK
- checking data for non-ASCII characters ... [1s] OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compiled code ... OK
- checking installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ... [16s] ERROR
Running examples in 'SFSI-Ex.R' failed
The error most likely occurred in:
> ### Name: Reading and combining SGP outputs
> ### Title: Read and combine SGP outputs
> ### Aliases: read_SGP read_summary
>
> ### ** Examples
>
> require(SFSI)
> data(wheatHTP)
>
> index = which(Y$trial %in% 1:10) # Use only a subset of data
> Y = Y[index,]
> M = scale(M[index,])/sqrt(ncol(M)) # Subset and scale markers
> G = tcrossprod(M) # Genomic relationship matrix
> y = as.vector(scale(Y[,"E1"])) # Scale response variable
>
> # Training and testing sets
> tst = which(Y$trial %in% 1:3)
> trn = seq_along(y)[-tst]
>
> path = paste0(tempdir(),"/testSGP_")
>
> # Run the analysis into 4 subsets and save them at a given path
> SGP(y, K=G, trn=trn, tst=tst, subset=c(1,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 1/4) of 84 and nTRN = 194 records
|
| | 0%
|
|=== | 5%
|
|======= | 10%
|
|========== | 14%
|
|============= | 19%
|
|================= | 24%
|
|==================== | 29%
|
|======================= | 33%
|
|=========================== | 38%
|
|============================== | 43%
|
|================================= | 48%
|
|===================================== | 52%
|
|======================================== | 57%
|
|=========================================== | 62%
|
|=============================================== | 67%
|
|================================================== | 71%
|
|===================================================== | 76%
|
|========================================================= | 81%
|
|============================================================ | 86%
|
|=============================================================== | 90%
|
|=================================================================== | 95%
|
|======================================================================| 100%
Results were saved at file:
'D:\temp\2024_12_22_01_50_00_26287\RtmpCoWcid\testSGP_subset_1_of_4_SGP.RData'
> SGP(y, K=G, trn=trn, tst=tst, subset=c(2,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 2/4) of 84 and nTRN = 194 records
|
| | 0%
|
|=== | 5%
|
|======= | 10%
|
|========== | 14%
|
|============= | 19%
|
|================= | 24%
|
|==================== | 29%
|
|======================= | 33%
|
|=========================== | 38%
|
|============================== | 43%
|
|================================= | 48%
|
|===================================== | 52%
|
|======================================== | 57%
|
|=========================================== | 62%
|
|=============================================== | 67%
|
|================================================== | 71%
|
|===================================================== | 76%
|
|========================================================= | 81%
|
|============================================================ | 86%
|
|=============================================================== | 90%
|
|=================================================================== | 95%
|
|======================================================================| 100%
Results were saved at file:
'D:\temp\2024_12_22_01_50_00_26287\RtmpCoWcid\testSGP_subset_2_of_4_SGP.RData'
> SGP(y, K=G, trn=trn, tst=tst, subset=c(3,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 3/4) of 84 and nTRN = 194 records
|
| | 0%
|
|=== | 5%
|
|======= | 10%
|
|========== | 14%
|
|============= | 19%
|
|================= | 24%
|
|==================== | 29%
|
|======================= | 33%
|
|=========================== | 38%
|
|============================== | 43%
|
|================================= | 48%
|
|===================================== | 52%
|
|======================================== | 57%
|
|=========================================== | 62%
|
|=============================================== | 67%
|
|================================================== | 71%
|
|===================================================== | 76%
|
|========================================================= | 81%
|
|============================================================ | 86%
|
|=============================================================== | 90%
|
|=================================================================== | 95%
|
|======================================================================| 100%
Results were saved at file:
'D:\temp\2024_12_22_01_50_00_26287\RtmpCoWcid\testSGP_subset_3_of_4_SGP.RData'
> SGP(y, K=G, trn=trn, tst=tst, subset=c(4,4), save.at=path)
Parameter estimation from a LMM within training data (nTRN = 194)
Variance components:
varU varE
1.5145659 0.1149247
Fixed effects:
(Intercept)
0.0009088514
Fitting a SGP model using nTST = 21 (subset 4/4) of 84 and nTRN = 194 records
|
| | 0%
|
|=== | 5%
|
|======= | 10%
|
|========== | 14%
|
|============= | 19%
|
|================= | 24%
|
|==================== | 29%
|
|======================= | 33%
|
|=========================== | 38%
|
|============================== | 43%
|
|================================= | 48%
|
|===================================== | 52%
|
|======================================== | 57%
|
|=========================================== | 62%
|
|=============================================== | 67%
|
|================================================== | 71%
|
|===================================================== | 76%
|
|========================================================= | 81%
|
|============================================================ | 86%
|
|=============================================================== | 90%
|
|=================================================================== | 95%
|
|======================================================================| 100%
Results were saved at file:
'D:\temp\2024_12_22_01_50_00_26287\RtmpCoWcid\testSGP_subset_4_of_4_SGP.RData'
>
> # Collect all results after completion
> fm = read_SGP(path)
Warning in grep(pattern = paste0(fullpath, "$"), value = TRUE, x = list.files(infolder, :
TRE pattern compilation error 'Invalid back reference'
Error in grep(pattern = paste0(fullpath, "$"), value = TRUE, x = list.files(infolder, :
invalid regular expression 'D:\temp\2024_12_22_01_50_00_26287\RtmpCoWcid\testSGP_.*SGP.RData$', reason 'Invalid back reference'
Calls: read_SGP -> lapply -> FUN -> basename -> grep
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [6s] OK
- checking PDF version of manual ... [23s] OK
- checking HTML version of manual ... [5s] OK
- DONE
Status: 1 ERROR