Last updated on 2018-05-03 10:50:04 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1 | 9.48 | 90.23 | 99.71 | WARN | |
| r-devel-linux-x86_64-debian-gcc | 1.1 | 6.22 | 77.31 | 83.53 | WARN | |
| r-devel-linux-x86_64-fedora-clang | 1.1 | 129.65 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1 | 122.80 | WARN | |||
| r-devel-windows-ix86+x86_64 | 1.1 | 15.00 | 83.00 | 98.00 | ERROR | |
| r-patched-linux-x86_64 | 1.1 | 6.82 | 85.75 | 92.57 | WARN | |
| r-patched-solaris-x86 | 1.1 | 168.50 | WARN | |||
| r-release-linux-x86_64 | 1.1 | 5.72 | 85.45 | 91.17 | WARN | |
| r-release-windows-ix86+x86_64 | 1.1 | 15.00 | 83.00 | 98.00 | ERROR | |
| r-release-osx-x86_64 | 1.1 | WARN | ||||
| r-oldrel-windows-ix86+x86_64 | 1.1 | 10.00 | 135.00 | 145.00 | OK | |
| r-oldrel-osx-x86_64 | 1.1 | OK |
Version: 1.1
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bigpca.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bigpca.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/data/gannet/ripley/R/packages/tests-clang/bigpca.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/data/gannet/ripley/R/packages/tests-devel/bigpca.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.1
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See 'd:/Rcompile/CRANpkg/local/3.5/bigpca.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64
Version: 1.1
Check: examples
Result: ERROR
Running examples in 'bigpca-Ex.R' failed
The error most likely occurred in:
> ### Name: big.PCA
> ### Title: PCA/Singular Value Decomposition for big.matrix
> ### Aliases: big.PCA
>
> ### ** Examples
>
> # create an example matrix and its transpose
> min.dim <- 200; nvar <- 500; subset.size <- 50
> mat <- matrix(rnorm(min.dim*nvar),ncol=min.dim)
> prv.large(mat)
Warning in check.bio() :
bioconductor does not appear to be installed - this function works better if it is
col#
row# 1 2 ..... 200
1 -0.6265 0.0773 ... 0.0374
2 0.1836 -0.2969 ... -1.6128
3 -0.8356 -1.1832 ... 0.7146
... ... ... ... ...
500 -0.8733 -0.6973 ... 0.7118
> t.mat <- t(mat)
> # create two alternative covariance matrices
> MMs <- t.mat %*% mat
> MsM <- mat %*% t.mat
> # run singular value decomposition
> pca <- svd(mat)
> D <- pca$d # singular values (=sqrt(eigenvalues))
> V <- pca$v # right singular vector
> U <- pca$u # left singular vector
> sig <- mat-mat; diag(sig) <- D;
> MMs2 <- V %*% (t(sig) %*% sig) %*% t(V)
> sig <- t.mat-t.mat; diag(sig) <- D;
> MsM2 <- U %*% (sig %*% t(sig)) %*% t(U)
> # show that the covariance matrices are equal to the functions of
> # the left and right singular vectors
> prv(MMs,MsM); prv(MMs2,MsM2)
MMs (matrix, 200*200)
col#
row# 1 2 ..... 200
1 511.2318 -22.5321 ... -22.6612
2 -22.5321 558.8836 ... 12.462
3 -14.5398 -40.9556 ... -32.9189
... ... ... ... ...
200 -22.6612 12.462 ... 568.2967
MsM (matrix, 500*500)
col#
row# 1 2 ..... 500
1 198.2148 -1.7057 ... 16.2122
2 -1.7057 241.7104 ... 0.4053
3 -14.7584 12.003 ... 4.6714
... ... ... ... ...
500 16.2122 0.4053 ... 191.1251
Warning messages:
1: In check.bio() :
bioconductor does not appear to be installed - this function works better if it is
2: In check.bio() :
bioconductor does not appear to be installed - this function works better if it is
3: In check.bio() :
bioconductor does not appear to be installed - this function works better if it is
4: In check.bio() :
bioconductor does not appear to be installed - this function works better if it is
MMs2 (matrix, 200*200)
col#
row# 1 2 ..... 200
1 511.2318 -22.5321 ... -22.6612
2 -22.5321 558.8836 ... 12.462
3 -14.5398 -40.9556 ... -32.9189
... ... ... ... ...
200 -22.6612 12.462 ... 568.2967
MsM2 (matrix, 500*500)
col#
row# 1 2 ..... 500
1 198.2148 -1.7057 ... 16.2122
2 -1.7057 241.7104 ... 0.4053
3 -14.7584 12.003 ... 4.6714
... ... ... ... ...
500 16.2122 0.4053 ... 191.1251
Warning messages:
1: In check.bio() :
bioconductor does not appear to be installed - this function works better if it is
2: In check.bio() :
bioconductor does not appear to be installed - this function works better if it is
3: In check.bio() :
bioconductor does not appear to be installed - this function works better if it is
4: In check.bio() :
bioconductor does not appear to be installed - this function works better if it is
> pr <- princomp(mat) # PCA using eigendecomposition of cov matrix
> L <- matrix(rep(0,40000),ncol=200); diag(L) <- pr[[1]]^2 # eigenvalues as diag
> mat2 <- (pr[[2]]) %*% L %*% solve(pr[[2]]) # = eigenvectors * eigenvalues * inv(eigenvectors)
> prv.large(cov(mat)); prv.large(mat2) # == COVmat (may be slight tolerance differences)
col#
row# 1 2 ..... 200
1 1.024 -0.0441 ... -0.045
2 -0.0441 1.1179 ... 0.024
3 -0.0291 -0.0822 ... -0.066
... ... ... ... ...
200 -0.045 0.024 ... 1.1385
Warning message:
In check.bio() :
bioconductor does not appear to be installed - this function works better if it is
col#
row# 1 2 ..... 200
1 1.022 -0.044 ... -0.0449
2 -0.044 1.1157 ... 0.024
3 -0.029 -0.082 ... -0.0659
... ... ... ... ...
200 -0.0449 0.024 ... 1.1362
Warning message:
In check.bio() :
bioconductor does not appear to be installed - this function works better if it is
> ## Now demonstrate the correlation between SVD and PCA ##
> # the right singular vector is highly correlated with the pca loadings:
> median(abs(diag(cor(V,pr[["loadings"]]))))
[1] 0.9834328
> # the left singular vector is highly correlated with the pca scores (eigenvectors):
> median(abs(diag(cor(U,pr[["scores"]]))))
[1] 0.9835682
> cor(pr$sdev,D) # the singular values are equivalent to the eigenvalues
[1] 0.9999933
>
> ## MAIN EXAMPLES ##
> orig.dir <- getwd(); setwd(tempdir()); # move to temporary dir
> if(file.exists("testMyBig.bck")) { unlink(c("testMyBig.bck","testMyBig.dsc")) }
> bmat <- as.big.matrix(mat,backingfile="testMyBig.bck",
+ descriptorfile="testMyBig.dsc", backingpath = getwd())
Error in filebacked.big.matrix(nrow = nrow, ncol = ncol, type = type, :
Backing file already exists! Either remove or specify
different backing file
Calls: as.big.matrix ... as.big.matrix -> big.matrix -> filebacked.big.matrix
Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64
Version: 1.1
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bigpca.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-patched-linux-x86_64
Version: 1.1
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/home/ripley/R/packages/tests32/bigpca.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-patched-solaris-x86
Version: 1.1
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bigpca.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-release-linux-x86_64
Version: 1.1
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bigpca.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-release-osx-x86_64