Ben Bolstad
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: 9250806 |
| git_last_commit_date: 2023-10-24 09:37:50 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:37:25 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 247/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.67.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.67.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BufferedMatrix_1.67.0.tar.gz |
| StartedAt: 2024-03-28 00:00:35 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 00:02:05 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 89.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BufferedMatrix_1.67.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BufferedMatrix/DESCRIPTION' ... OK
* this is package 'BufferedMatrix' version '1.67.0'
* 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 'BufferedMatrix' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/BufferedMatrix/libs/x64/BufferedMatrix.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'Rcodetesting.R'
Running 'c_code_level_tests.R'
Running 'objectTesting.R'
Running 'rawCalltesting.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/00check.log'
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'BufferedMatrix' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function 'dbm_ReadOnlyMode':
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: 'sort_double' defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o
gcc -shared -s -static-libgcc -o BufferedMatrix.dll tmp.def RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'rowMeans' in package 'BufferedMatrix'
Creating a new generic function for 'rowSums' in package 'BufferedMatrix'
Creating a new generic function for 'colMeans' in package 'BufferedMatrix'
Creating a new generic function for 'colSums' in package 'BufferedMatrix'
Creating a generic function for 'ncol' from package 'base' in package 'BufferedMatrix'
Creating a generic function for 'nrow' from package 'base' in package 'BufferedMatrix'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.23 0.14 0.65
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 468418 25.1 1021374 54.6 633925 33.9
Vcells 853869 6.6 8388608 64.0 2003432 15.3
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Thu Mar 28 00:01:04 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Thu Mar 28 00:01:04 2024"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x0000022822ef80b0>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Thu Mar 28 00:01:14 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Thu Mar 28 00:01:17 2024"
>
> ColMode(tmp2)
<pointer: 0x0000022822ef80b0>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.7032010 1.220652 -0.6276773 -0.80465187
[2,] -0.6126047 -1.119727 1.6513898 0.02660305
[3,] -0.2851168 1.454152 1.6910365 -1.77957072
[4,] -2.3244405 1.117742 -0.1364979 -1.09402850
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.7032010 1.220652 0.6276773 0.80465187
[2,] 0.6126047 1.119727 1.6513898 0.02660305
[3,] 0.2851168 1.454152 1.6910365 1.77957072
[4,] 2.3244405 1.117742 0.1364979 1.09402850
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0350985 1.104831 0.7922609 0.8970239
[2,] 0.7826907 1.058172 1.2850641 0.1631044
[3,] 0.5339633 1.205882 1.3003986 1.3340055
[4,] 1.5246116 1.057233 0.3694563 1.0459582
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 226.05419 37.26896 33.55029 34.77489
[2,] 33.43951 36.70144 39.50203 26.65765
[3,] 30.62475 38.51297 39.69502 40.11963
[4,] 42.57056 36.69007 28.83106 36.55361
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x0000022822ef8110>
> exp(tmp5)
<pointer: 0x0000022822ef8110>
> log(tmp5,2)
<pointer: 0x0000022822ef8110>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 470.5022
> Min(tmp5)
[1] 54.86545
> mean(tmp5)
[1] 73.43891
> Sum(tmp5)
[1] 14687.78
> Var(tmp5)
[1] 866.7951
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.44325 72.66625 72.54142 71.16159 71.06717 74.71600 72.34908 71.02211
[9] 68.51189 68.91029
> rowSums(tmp5)
[1] 1828.865 1453.325 1450.828 1423.232 1421.343 1494.320 1446.982 1420.442
[9] 1370.238 1378.206
> rowVars(tmp5)
[1] 7997.38812 73.84345 72.78311 94.26833 83.45308 68.20285
[7] 91.24885 90.26256 73.20300 23.55474
> rowSd(tmp5)
[1] 89.428117 8.593221 8.531302 9.709188 9.135266 8.258502 9.552427
[8] 9.500661 8.555875 4.853322
> rowMax(tmp5)
[1] 470.50217 82.55426 83.70073 88.60504 93.11012 88.42828 92.77736
[8] 89.18774 83.21420 81.25330
> rowMin(tmp5)
[1] 60.43477 55.48440 56.58647 54.86545 57.88145 60.52801 59.61821 58.15518
[9] 55.30139 59.76318
>
> colMeans(tmp5)
[1] 110.16531 72.27495 72.83774 69.56506 68.32728 72.06493 73.64313
[8] 68.84914 65.37591 70.54154 76.56276 74.75323 73.43611 72.88913
[15] 70.30330 73.94183 74.56702 68.60288 68.22443 71.85243
> colSums(tmp5)
[1] 1101.6531 722.7495 728.3774 695.6506 683.2728 720.6493 736.4313
[8] 688.4914 653.7591 705.4154 765.6276 747.5323 734.3611 728.8913
[15] 703.0330 739.4183 745.6702 686.0288 682.2443 718.5243
> colVars(tmp5)
[1] 16091.79417 49.90311 88.18548 89.98350 140.47191 69.37359
[7] 38.96906 100.01862 42.69470 52.93593 100.84103 43.15231
[13] 90.95469 86.02125 44.74671 61.33685 71.66033 62.03631
[19] 26.41302 76.17330
> colSd(tmp5)
[1] 126.853436 7.064213 9.390712 9.485963 11.852085 8.329081
[7] 6.242520 10.000931 6.534118 7.275708 10.041964 6.569042
[13] 9.537017 9.274764 6.689298 7.831785 8.465243 7.876313
[19] 5.139360 8.727732
> colMax(tmp5)
[1] 470.50217 80.15971 88.25066 83.50374 88.42828 82.64343 83.70073
[8] 82.10622 76.06844 80.31596 93.11012 83.33892 92.77736 81.77824
[15] 82.40952 83.30045 87.41186 85.15675 74.83420 84.23792
> colMin(tmp5)
[1] 60.52801 59.61821 60.00808 55.48440 55.62372 57.02161 61.93727 54.86545
[9] 55.30139 61.20901 60.59848 65.17283 60.30657 56.78800 60.77805 62.40678
[17] 58.79861 58.49412 60.43146 56.58864
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 91.44325 72.66625 72.54142 71.16159 71.06717 74.71600 72.34908 NA
[9] 68.51189 68.91029
> rowSums(tmp5)
[1] 1828.865 1453.325 1450.828 1423.232 1421.343 1494.320 1446.982 NA
[9] 1370.238 1378.206
> rowVars(tmp5)
[1] 7997.38812 73.84345 72.78311 94.26833 83.45308 68.20285
[7] 91.24885 89.67017 73.20300 23.55474
> rowSd(tmp5)
[1] 89.428117 8.593221 8.531302 9.709188 9.135266 8.258502 9.552427
[8] 9.469434 8.555875 4.853322
> rowMax(tmp5)
[1] 470.50217 82.55426 83.70073 88.60504 93.11012 88.42828 92.77736
[8] NA 83.21420 81.25330
> rowMin(tmp5)
[1] 60.43477 55.48440 56.58647 54.86545 57.88145 60.52801 59.61821 NA
[9] 55.30139 59.76318
>
> colMeans(tmp5)
[1] 110.16531 NA 72.83774 69.56506 68.32728 72.06493 73.64313
[8] 68.84914 65.37591 70.54154 76.56276 74.75323 73.43611 72.88913
[15] 70.30330 73.94183 74.56702 68.60288 68.22443 71.85243
> colSums(tmp5)
[1] 1101.6531 NA 728.3774 695.6506 683.2728 720.6493 736.4313
[8] 688.4914 653.7591 705.4154 765.6276 747.5323 734.3611 728.8913
[15] 703.0330 739.4183 745.6702 686.0288 682.2443 718.5243
> colVars(tmp5)
[1] 16091.79417 NA 88.18548 89.98350 140.47191 69.37359
[7] 38.96906 100.01862 42.69470 52.93593 100.84103 43.15231
[13] 90.95469 86.02125 44.74671 61.33685 71.66033 62.03631
[19] 26.41302 76.17330
> colSd(tmp5)
[1] 126.853436 NA 9.390712 9.485963 11.852085 8.329081
[7] 6.242520 10.000931 6.534118 7.275708 10.041964 6.569042
[13] 9.537017 9.274764 6.689298 7.831785 8.465243 7.876313
[19] 5.139360 8.727732
> colMax(tmp5)
[1] 470.50217 NA 88.25066 83.50374 88.42828 82.64343 83.70073
[8] 82.10622 76.06844 80.31596 93.11012 83.33892 92.77736 81.77824
[15] 82.40952 83.30045 87.41186 85.15675 74.83420 84.23792
> colMin(tmp5)
[1] 60.52801 NA 60.00808 55.48440 55.62372 57.02161 61.93727 54.86545
[9] 55.30139 61.20901 60.59848 65.17283 60.30657 56.78800 60.77805 62.40678
[17] 58.79861 58.49412 60.43146 56.58864
>
> Max(tmp5,na.rm=TRUE)
[1] 470.5022
> Min(tmp5,na.rm=TRUE)
[1] 54.86545
> mean(tmp5,na.rm=TRUE)
[1] 73.50026
> Sum(tmp5,na.rm=TRUE)
[1] 14626.55
> Var(tmp5,na.rm=TRUE)
[1] 870.4163
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.44325 72.66625 72.54142 71.16159 71.06717 74.71600 72.34908 71.53747
[9] 68.51189 68.91029
> rowSums(tmp5,na.rm=TRUE)
[1] 1828.865 1453.325 1450.828 1423.232 1421.343 1494.320 1446.982 1359.212
[9] 1370.238 1378.206
> rowVars(tmp5,na.rm=TRUE)
[1] 7997.38812 73.84345 72.78311 94.26833 83.45308 68.20285
[7] 91.24885 89.67017 73.20300 23.55474
> rowSd(tmp5,na.rm=TRUE)
[1] 89.428117 8.593221 8.531302 9.709188 9.135266 8.258502 9.552427
[8] 9.469434 8.555875 4.853322
> rowMax(tmp5,na.rm=TRUE)
[1] 470.50217 82.55426 83.70073 88.60504 93.11012 88.42828 92.77736
[8] 89.18774 83.21420 81.25330
> rowMin(tmp5,na.rm=TRUE)
[1] 60.43477 55.48440 56.58647 54.86545 57.88145 60.52801 59.61821 58.15518
[9] 55.30139 59.76318
>
> colMeans(tmp5,na.rm=TRUE)
[1] 110.16531 73.50213 72.83774 69.56506 68.32728 72.06493 73.64313
[8] 68.84914 65.37591 70.54154 76.56276 74.75323 73.43611 72.88913
[15] 70.30330 73.94183 74.56702 68.60288 68.22443 71.85243
> colSums(tmp5,na.rm=TRUE)
[1] 1101.6531 661.5191 728.3774 695.6506 683.2728 720.6493 736.4313
[8] 688.4914 653.7591 705.4154 765.6276 747.5323 734.3611 728.8913
[15] 703.0330 739.4183 745.6702 686.0288 682.2443 718.5243
> colVars(tmp5,na.rm=TRUE)
[1] 16091.79417 39.19881 88.18548 89.98350 140.47191 69.37359
[7] 38.96906 100.01862 42.69470 52.93593 100.84103 43.15231
[13] 90.95469 86.02125 44.74671 61.33685 71.66033 62.03631
[19] 26.41302 76.17330
> colSd(tmp5,na.rm=TRUE)
[1] 126.853436 6.260895 9.390712 9.485963 11.852085 8.329081
[7] 6.242520 10.000931 6.534118 7.275708 10.041964 6.569042
[13] 9.537017 9.274764 6.689298 7.831785 8.465243 7.876313
[19] 5.139360 8.727732
> colMax(tmp5,na.rm=TRUE)
[1] 470.50217 80.15971 88.25066 83.50374 88.42828 82.64343 83.70073
[8] 82.10622 76.06844 80.31596 93.11012 83.33892 92.77736 81.77824
[15] 82.40952 83.30045 87.41186 85.15675 74.83420 84.23792
> colMin(tmp5,na.rm=TRUE)
[1] 60.52801 59.61821 60.00808 55.48440 55.62372 57.02161 61.93727 54.86545
[9] 55.30139 61.20901 60.59848 65.17283 60.30657 56.78800 60.77805 62.40678
[17] 58.79861 58.49412 60.43146 56.58864
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.44325 72.66625 72.54142 71.16159 71.06717 74.71600 72.34908 NaN
[9] 68.51189 68.91029
> rowSums(tmp5,na.rm=TRUE)
[1] 1828.865 1453.325 1450.828 1423.232 1421.343 1494.320 1446.982 0.000
[9] 1370.238 1378.206
> rowVars(tmp5,na.rm=TRUE)
[1] 7997.38812 73.84345 72.78311 94.26833 83.45308 68.20285
[7] 91.24885 NA 73.20300 23.55474
> rowSd(tmp5,na.rm=TRUE)
[1] 89.428117 8.593221 8.531302 9.709188 9.135266 8.258502 9.552427
[8] NA 8.555875 4.853322
> rowMax(tmp5,na.rm=TRUE)
[1] 470.50217 82.55426 83.70073 88.60504 93.11012 88.42828 92.77736
[8] NA 83.21420 81.25330
> rowMin(tmp5,na.rm=TRUE)
[1] 60.43477 55.48440 56.58647 54.86545 57.88145 60.52801 59.61821 NA
[9] 55.30139 59.76318
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 114.91432 NaN 73.10611 70.83283 69.29897 70.88954 73.18052
[8] 67.37613 65.08670 69.92440 75.15999 74.38770 74.24624 72.74013
[15] 71.26494 73.75509 75.19037 69.72608 69.09031 70.47627
> colSums(tmp5,na.rm=TRUE)
[1] 1034.2289 0.0000 657.9550 637.4955 623.6908 638.0059 658.6247
[8] 606.3852 585.7803 629.3196 676.4399 669.4893 668.2162 654.6612
[15] 641.3845 663.7958 676.7133 627.5347 621.8128 634.2864
> colVars(tmp5,na.rm=TRUE)
[1] 17849.54600 NA 98.39840 83.15013 147.40874 62.50297
[7] 41.43263 88.11120 47.09051 55.26824 91.30865 47.04316
[13] 94.94042 96.52415 39.93654 68.61163 76.24654 55.59820
[19] 21.27988 64.38937
> colSd(tmp5,na.rm=TRUE)
[1] 133.602193 NA 9.919597 9.118669 12.141200 7.905882
[7] 6.436818 9.386756 6.862252 7.434261 9.555556 6.858802
[13] 9.743738 9.824671 6.319536 8.283214 8.731926 7.456420
[19] 4.613012 8.024298
> colMax(tmp5,na.rm=TRUE)
[1] 470.50217 -Inf 88.25066 83.50374 88.42828 80.90801 83.70073
[8] 80.16374 76.06844 80.31596 93.11012 83.33892 92.77736 81.77824
[15] 82.40952 83.30045 87.41186 85.15675 74.83420 83.18440
> colMin(tmp5,na.rm=TRUE)
[1] 60.52801 Inf 60.00808 55.48440 55.62372 57.02161 61.93727 54.86545
[9] 55.30139 61.20901 60.59848 65.17283 60.30657 56.78800 60.77805 62.40678
[17] 58.79861 62.50381 60.43477 56.58864
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 302.24480 239.55027 221.05677 203.00529 186.18800 196.38153 201.94858
[8] 251.66317 81.63633 210.95526
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 302.24480 239.55027 221.05677 203.00529 186.18800 196.38153 201.94858
[8] 251.66317 81.63633 210.95526
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] -5.684342e-14 0.000000e+00 3.410605e-13 0.000000e+00 0.000000e+00
[6] 5.684342e-14 -1.136868e-13 -2.842171e-14 -1.136868e-13 1.989520e-13
[11] 1.421085e-13 -1.136868e-13 -2.415845e-13 -2.131628e-14 0.000000e+00
[16] 5.684342e-14 -5.684342e-14 -2.842171e-14 -1.136868e-13 0.000000e+00
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
8 14
9 16
1 19
7 9
3 13
8 14
4 9
1 4
4 9
5 20
2 18
7 7
5 15
5 5
6 11
8 10
7 5
7 9
4 3
6 2
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.158215
> Min(tmp)
[1] -2.600686
> mean(tmp)
[1] -0.05141157
> Sum(tmp)
[1] -5.141157
> Var(tmp)
[1] 0.8732697
>
> rowMeans(tmp)
[1] -0.05141157
> rowSums(tmp)
[1] -5.141157
> rowVars(tmp)
[1] 0.8732697
> rowSd(tmp)
[1] 0.934489
> rowMax(tmp)
[1] 2.158215
> rowMin(tmp)
[1] -2.600686
>
> colMeans(tmp)
[1] 1.373508915 1.044214261 0.304345923 -1.317127810 -0.906157058
[6] -0.083691030 0.103749052 0.044593362 1.119570192 0.505499977
[11] -2.228859600 -0.290261306 0.173368538 -1.826411272 0.292053035
[16] 1.486930605 -0.023932543 -0.006917284 -0.323500655 0.690271364
[21] -0.375981770 0.334804749 0.275542511 0.297458700 0.064507158
[26] -0.050535541 0.782862255 0.426445187 1.304523279 -0.078132151
[31] -0.596625539 0.479672592 -0.438411305 -0.804578584 -0.433951159
[36] -0.539829072 -0.623102492 -1.907155927 1.257694538 -1.586426768
[41] 0.723340061 -0.121922697 -0.744318258 -0.832088741 0.807645329
[46] -0.183527462 -1.445561057 -0.652622626 -0.010871994 0.534007817
[51] 0.120927941 -0.036104636 -2.461059943 2.158215124 1.890564168
[56] 0.104750281 -0.624355344 -0.379165693 1.303686621 0.532057914
[61] 0.605155344 0.599362749 -0.057839533 -0.649501620 -1.236056494
[66] -0.452957814 -1.560504305 -0.730002958 0.596697433 0.877930288
[71] 0.066786931 0.058872199 -0.034102922 -1.455093739 -1.095168755
[76] 1.343766173 1.371448634 0.956068012 0.056909500 -0.056352550
[81] -0.202570836 -0.352181133 -0.635280805 0.519157174 1.901046838
[86] 0.246428763 0.585577394 0.065422543 0.531727663 -0.444262373
[91] 0.366410126 -2.600685587 0.373967251 0.573250167 -0.530631778
[96] -2.001851007 0.083380380 -0.109126439 -0.206610959 -1.113365292
> colSums(tmp)
[1] 1.373508915 1.044214261 0.304345923 -1.317127810 -0.906157058
[6] -0.083691030 0.103749052 0.044593362 1.119570192 0.505499977
[11] -2.228859600 -0.290261306 0.173368538 -1.826411272 0.292053035
[16] 1.486930605 -0.023932543 -0.006917284 -0.323500655 0.690271364
[21] -0.375981770 0.334804749 0.275542511 0.297458700 0.064507158
[26] -0.050535541 0.782862255 0.426445187 1.304523279 -0.078132151
[31] -0.596625539 0.479672592 -0.438411305 -0.804578584 -0.433951159
[36] -0.539829072 -0.623102492 -1.907155927 1.257694538 -1.586426768
[41] 0.723340061 -0.121922697 -0.744318258 -0.832088741 0.807645329
[46] -0.183527462 -1.445561057 -0.652622626 -0.010871994 0.534007817
[51] 0.120927941 -0.036104636 -2.461059943 2.158215124 1.890564168
[56] 0.104750281 -0.624355344 -0.379165693 1.303686621 0.532057914
[61] 0.605155344 0.599362749 -0.057839533 -0.649501620 -1.236056494
[66] -0.452957814 -1.560504305 -0.730002958 0.596697433 0.877930288
[71] 0.066786931 0.058872199 -0.034102922 -1.455093739 -1.095168755
[76] 1.343766173 1.371448634 0.956068012 0.056909500 -0.056352550
[81] -0.202570836 -0.352181133 -0.635280805 0.519157174 1.901046838
[86] 0.246428763 0.585577394 0.065422543 0.531727663 -0.444262373
[91] 0.366410126 -2.600685587 0.373967251 0.573250167 -0.530631778
[96] -2.001851007 0.083380380 -0.109126439 -0.206610959 -1.113365292
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] 1.373508915 1.044214261 0.304345923 -1.317127810 -0.906157058
[6] -0.083691030 0.103749052 0.044593362 1.119570192 0.505499977
[11] -2.228859600 -0.290261306 0.173368538 -1.826411272 0.292053035
[16] 1.486930605 -0.023932543 -0.006917284 -0.323500655 0.690271364
[21] -0.375981770 0.334804749 0.275542511 0.297458700 0.064507158
[26] -0.050535541 0.782862255 0.426445187 1.304523279 -0.078132151
[31] -0.596625539 0.479672592 -0.438411305 -0.804578584 -0.433951159
[36] -0.539829072 -0.623102492 -1.907155927 1.257694538 -1.586426768
[41] 0.723340061 -0.121922697 -0.744318258 -0.832088741 0.807645329
[46] -0.183527462 -1.445561057 -0.652622626 -0.010871994 0.534007817
[51] 0.120927941 -0.036104636 -2.461059943 2.158215124 1.890564168
[56] 0.104750281 -0.624355344 -0.379165693 1.303686621 0.532057914
[61] 0.605155344 0.599362749 -0.057839533 -0.649501620 -1.236056494
[66] -0.452957814 -1.560504305 -0.730002958 0.596697433 0.877930288
[71] 0.066786931 0.058872199 -0.034102922 -1.455093739 -1.095168755
[76] 1.343766173 1.371448634 0.956068012 0.056909500 -0.056352550
[81] -0.202570836 -0.352181133 -0.635280805 0.519157174 1.901046838
[86] 0.246428763 0.585577394 0.065422543 0.531727663 -0.444262373
[91] 0.366410126 -2.600685587 0.373967251 0.573250167 -0.530631778
[96] -2.001851007 0.083380380 -0.109126439 -0.206610959 -1.113365292
> colMin(tmp)
[1] 1.373508915 1.044214261 0.304345923 -1.317127810 -0.906157058
[6] -0.083691030 0.103749052 0.044593362 1.119570192 0.505499977
[11] -2.228859600 -0.290261306 0.173368538 -1.826411272 0.292053035
[16] 1.486930605 -0.023932543 -0.006917284 -0.323500655 0.690271364
[21] -0.375981770 0.334804749 0.275542511 0.297458700 0.064507158
[26] -0.050535541 0.782862255 0.426445187 1.304523279 -0.078132151
[31] -0.596625539 0.479672592 -0.438411305 -0.804578584 -0.433951159
[36] -0.539829072 -0.623102492 -1.907155927 1.257694538 -1.586426768
[41] 0.723340061 -0.121922697 -0.744318258 -0.832088741 0.807645329
[46] -0.183527462 -1.445561057 -0.652622626 -0.010871994 0.534007817
[51] 0.120927941 -0.036104636 -2.461059943 2.158215124 1.890564168
[56] 0.104750281 -0.624355344 -0.379165693 1.303686621 0.532057914
[61] 0.605155344 0.599362749 -0.057839533 -0.649501620 -1.236056494
[66] -0.452957814 -1.560504305 -0.730002958 0.596697433 0.877930288
[71] 0.066786931 0.058872199 -0.034102922 -1.455093739 -1.095168755
[76] 1.343766173 1.371448634 0.956068012 0.056909500 -0.056352550
[81] -0.202570836 -0.352181133 -0.635280805 0.519157174 1.901046838
[86] 0.246428763 0.585577394 0.065422543 0.531727663 -0.444262373
[91] 0.366410126 -2.600685587 0.373967251 0.573250167 -0.530631778
[96] -2.001851007 0.083380380 -0.109126439 -0.206610959 -1.113365292
> colMedians(tmp)
[1] 1.373508915 1.044214261 0.304345923 -1.317127810 -0.906157058
[6] -0.083691030 0.103749052 0.044593362 1.119570192 0.505499977
[11] -2.228859600 -0.290261306 0.173368538 -1.826411272 0.292053035
[16] 1.486930605 -0.023932543 -0.006917284 -0.323500655 0.690271364
[21] -0.375981770 0.334804749 0.275542511 0.297458700 0.064507158
[26] -0.050535541 0.782862255 0.426445187 1.304523279 -0.078132151
[31] -0.596625539 0.479672592 -0.438411305 -0.804578584 -0.433951159
[36] -0.539829072 -0.623102492 -1.907155927 1.257694538 -1.586426768
[41] 0.723340061 -0.121922697 -0.744318258 -0.832088741 0.807645329
[46] -0.183527462 -1.445561057 -0.652622626 -0.010871994 0.534007817
[51] 0.120927941 -0.036104636 -2.461059943 2.158215124 1.890564168
[56] 0.104750281 -0.624355344 -0.379165693 1.303686621 0.532057914
[61] 0.605155344 0.599362749 -0.057839533 -0.649501620 -1.236056494
[66] -0.452957814 -1.560504305 -0.730002958 0.596697433 0.877930288
[71] 0.066786931 0.058872199 -0.034102922 -1.455093739 -1.095168755
[76] 1.343766173 1.371448634 0.956068012 0.056909500 -0.056352550
[81] -0.202570836 -0.352181133 -0.635280805 0.519157174 1.901046838
[86] 0.246428763 0.585577394 0.065422543 0.531727663 -0.444262373
[91] 0.366410126 -2.600685587 0.373967251 0.573250167 -0.530631778
[96] -2.001851007 0.083380380 -0.109126439 -0.206610959 -1.113365292
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 1.373509 1.044214 0.3043459 -1.317128 -0.9061571 -0.08369103 0.1037491
[2,] 1.373509 1.044214 0.3043459 -1.317128 -0.9061571 -0.08369103 0.1037491
[,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15]
[1,] 0.04459336 1.11957 0.5055 -2.22886 -0.2902613 0.1733685 -1.826411 0.292053
[2,] 0.04459336 1.11957 0.5055 -2.22886 -0.2902613 0.1733685 -1.826411 0.292053
[,16] [,17] [,18] [,19] [,20] [,21]
[1,] 1.486931 -0.02393254 -0.006917284 -0.3235007 0.6902714 -0.3759818
[2,] 1.486931 -0.02393254 -0.006917284 -0.3235007 0.6902714 -0.3759818
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.3348047 0.2755425 0.2974587 0.06450716 -0.05053554 0.7828623 0.4264452
[2,] 0.3348047 0.2755425 0.2974587 0.06450716 -0.05053554 0.7828623 0.4264452
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 1.304523 -0.07813215 -0.5966255 0.4796726 -0.4384113 -0.8045786 -0.4339512
[2,] 1.304523 -0.07813215 -0.5966255 0.4796726 -0.4384113 -0.8045786 -0.4339512
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.5398291 -0.6231025 -1.907156 1.257695 -1.586427 0.7233401 -0.1219227
[2,] -0.5398291 -0.6231025 -1.907156 1.257695 -1.586427 0.7233401 -0.1219227
[,43] [,44] [,45] [,46] [,47] [,48]
[1,] -0.7443183 -0.8320887 0.8076453 -0.1835275 -1.445561 -0.6526226
[2,] -0.7443183 -0.8320887 0.8076453 -0.1835275 -1.445561 -0.6526226
[,49] [,50] [,51] [,52] [,53] [,54] [,55]
[1,] -0.01087199 0.5340078 0.1209279 -0.03610464 -2.46106 2.158215 1.890564
[2,] -0.01087199 0.5340078 0.1209279 -0.03610464 -2.46106 2.158215 1.890564
[,56] [,57] [,58] [,59] [,60] [,61] [,62]
[1,] 0.1047503 -0.6243553 -0.3791657 1.303687 0.5320579 0.6051553 0.5993627
[2,] 0.1047503 -0.6243553 -0.3791657 1.303687 0.5320579 0.6051553 0.5993627
[,63] [,64] [,65] [,66] [,67] [,68] [,69]
[1,] -0.05783953 -0.6495016 -1.236056 -0.4529578 -1.560504 -0.730003 0.5966974
[2,] -0.05783953 -0.6495016 -1.236056 -0.4529578 -1.560504 -0.730003 0.5966974
[,70] [,71] [,72] [,73] [,74] [,75] [,76]
[1,] 0.8779303 0.06678693 0.0588722 -0.03410292 -1.455094 -1.095169 1.343766
[2,] 0.8779303 0.06678693 0.0588722 -0.03410292 -1.455094 -1.095169 1.343766
[,77] [,78] [,79] [,80] [,81] [,82] [,83]
[1,] 1.371449 0.956068 0.0569095 -0.05635255 -0.2025708 -0.3521811 -0.6352808
[2,] 1.371449 0.956068 0.0569095 -0.05635255 -0.2025708 -0.3521811 -0.6352808
[,84] [,85] [,86] [,87] [,88] [,89] [,90]
[1,] 0.5191572 1.901047 0.2464288 0.5855774 0.06542254 0.5317277 -0.4442624
[2,] 0.5191572 1.901047 0.2464288 0.5855774 0.06542254 0.5317277 -0.4442624
[,91] [,92] [,93] [,94] [,95] [,96] [,97]
[1,] 0.3664101 -2.600686 0.3739673 0.5732502 -0.5306318 -2.001851 0.08338038
[2,] 0.3664101 -2.600686 0.3739673 0.5732502 -0.5306318 -2.001851 0.08338038
[,98] [,99] [,100]
[1,] -0.1091264 -0.206611 -1.113365
[2,] -0.1091264 -0.206611 -1.113365
>
>
> Max(tmp2)
[1] 1.855399
> Min(tmp2)
[1] -2.90884
> mean(tmp2)
[1] -0.09629088
> Sum(tmp2)
[1] -9.629088
> Var(tmp2)
[1] 1.035887
>
> rowMeans(tmp2)
[1] 1.029161264 0.560846184 1.786606456 0.068163651 -1.759447933
[6] -1.110233427 -0.925119817 -0.344386454 -1.251562513 -0.089619038
[11] 0.337760298 -2.452569626 0.296427907 0.683466842 0.242383228
[16] 0.032145664 -0.008620507 -0.904866398 0.559884403 0.882187601
[21] 1.305130729 -2.046944885 -0.760174615 -0.459880022 -2.180527935
[26] 0.358147890 1.054662571 -0.315919616 1.619998734 0.682056232
[31] -0.172887957 0.104839753 -1.465848253 -1.104328125 0.131863531
[36] -0.940923483 -1.655296091 -0.452247331 0.022613173 -0.401278188
[41] 1.496589357 1.131852258 1.050664618 -0.101121830 0.244632765
[46] 1.385386486 -1.039008534 0.484673293 0.335316364 0.319514039
[51] 0.987185586 -1.191561057 -0.520326249 -1.879423330 1.227891168
[56] -1.100549737 -0.250935531 0.030834477 -0.324381196 -1.301340617
[61] 0.191726056 1.584837304 1.096085860 0.268566713 0.027065105
[66] -0.898486520 0.078232594 -0.617558004 -1.252398941 -0.187986997
[71] 0.443769937 0.589249690 0.332428526 -2.782381937 0.199454208
[76] 1.855398699 -0.031802221 0.165118934 0.867653100 0.404497502
[81] 0.206247475 0.660985322 -0.350492747 -2.104699776 0.482375661
[86] -1.314143916 0.211021288 0.170501516 -1.284436217 0.416848712
[91] -0.675942955 0.284933460 -0.142527695 -0.683736880 1.260844391
[96] 1.230693935 0.124591292 0.478509128 0.033153616 -2.908839883
> rowSums(tmp2)
[1] 1.029161264 0.560846184 1.786606456 0.068163651 -1.759447933
[6] -1.110233427 -0.925119817 -0.344386454 -1.251562513 -0.089619038
[11] 0.337760298 -2.452569626 0.296427907 0.683466842 0.242383228
[16] 0.032145664 -0.008620507 -0.904866398 0.559884403 0.882187601
[21] 1.305130729 -2.046944885 -0.760174615 -0.459880022 -2.180527935
[26] 0.358147890 1.054662571 -0.315919616 1.619998734 0.682056232
[31] -0.172887957 0.104839753 -1.465848253 -1.104328125 0.131863531
[36] -0.940923483 -1.655296091 -0.452247331 0.022613173 -0.401278188
[41] 1.496589357 1.131852258 1.050664618 -0.101121830 0.244632765
[46] 1.385386486 -1.039008534 0.484673293 0.335316364 0.319514039
[51] 0.987185586 -1.191561057 -0.520326249 -1.879423330 1.227891168
[56] -1.100549737 -0.250935531 0.030834477 -0.324381196 -1.301340617
[61] 0.191726056 1.584837304 1.096085860 0.268566713 0.027065105
[66] -0.898486520 0.078232594 -0.617558004 -1.252398941 -0.187986997
[71] 0.443769937 0.589249690 0.332428526 -2.782381937 0.199454208
[76] 1.855398699 -0.031802221 0.165118934 0.867653100 0.404497502
[81] 0.206247475 0.660985322 -0.350492747 -2.104699776 0.482375661
[86] -1.314143916 0.211021288 0.170501516 -1.284436217 0.416848712
[91] -0.675942955 0.284933460 -0.142527695 -0.683736880 1.260844391
[96] 1.230693935 0.124591292 0.478509128 0.033153616 -2.908839883
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] 1.029161264 0.560846184 1.786606456 0.068163651 -1.759447933
[6] -1.110233427 -0.925119817 -0.344386454 -1.251562513 -0.089619038
[11] 0.337760298 -2.452569626 0.296427907 0.683466842 0.242383228
[16] 0.032145664 -0.008620507 -0.904866398 0.559884403 0.882187601
[21] 1.305130729 -2.046944885 -0.760174615 -0.459880022 -2.180527935
[26] 0.358147890 1.054662571 -0.315919616 1.619998734 0.682056232
[31] -0.172887957 0.104839753 -1.465848253 -1.104328125 0.131863531
[36] -0.940923483 -1.655296091 -0.452247331 0.022613173 -0.401278188
[41] 1.496589357 1.131852258 1.050664618 -0.101121830 0.244632765
[46] 1.385386486 -1.039008534 0.484673293 0.335316364 0.319514039
[51] 0.987185586 -1.191561057 -0.520326249 -1.879423330 1.227891168
[56] -1.100549737 -0.250935531 0.030834477 -0.324381196 -1.301340617
[61] 0.191726056 1.584837304 1.096085860 0.268566713 0.027065105
[66] -0.898486520 0.078232594 -0.617558004 -1.252398941 -0.187986997
[71] 0.443769937 0.589249690 0.332428526 -2.782381937 0.199454208
[76] 1.855398699 -0.031802221 0.165118934 0.867653100 0.404497502
[81] 0.206247475 0.660985322 -0.350492747 -2.104699776 0.482375661
[86] -1.314143916 0.211021288 0.170501516 -1.284436217 0.416848712
[91] -0.675942955 0.284933460 -0.142527695 -0.683736880 1.260844391
[96] 1.230693935 0.124591292 0.478509128 0.033153616 -2.908839883
> rowMin(tmp2)
[1] 1.029161264 0.560846184 1.786606456 0.068163651 -1.759447933
[6] -1.110233427 -0.925119817 -0.344386454 -1.251562513 -0.089619038
[11] 0.337760298 -2.452569626 0.296427907 0.683466842 0.242383228
[16] 0.032145664 -0.008620507 -0.904866398 0.559884403 0.882187601
[21] 1.305130729 -2.046944885 -0.760174615 -0.459880022 -2.180527935
[26] 0.358147890 1.054662571 -0.315919616 1.619998734 0.682056232
[31] -0.172887957 0.104839753 -1.465848253 -1.104328125 0.131863531
[36] -0.940923483 -1.655296091 -0.452247331 0.022613173 -0.401278188
[41] 1.496589357 1.131852258 1.050664618 -0.101121830 0.244632765
[46] 1.385386486 -1.039008534 0.484673293 0.335316364 0.319514039
[51] 0.987185586 -1.191561057 -0.520326249 -1.879423330 1.227891168
[56] -1.100549737 -0.250935531 0.030834477 -0.324381196 -1.301340617
[61] 0.191726056 1.584837304 1.096085860 0.268566713 0.027065105
[66] -0.898486520 0.078232594 -0.617558004 -1.252398941 -0.187986997
[71] 0.443769937 0.589249690 0.332428526 -2.782381937 0.199454208
[76] 1.855398699 -0.031802221 0.165118934 0.867653100 0.404497502
[81] 0.206247475 0.660985322 -0.350492747 -2.104699776 0.482375661
[86] -1.314143916 0.211021288 0.170501516 -1.284436217 0.416848712
[91] -0.675942955 0.284933460 -0.142527695 -0.683736880 1.260844391
[96] 1.230693935 0.124591292 0.478509128 0.033153616 -2.908839883
>
> colMeans(tmp2)
[1] -0.09629088
> colSums(tmp2)
[1] -9.629088
> colVars(tmp2)
[1] 1.035887
> colSd(tmp2)
[1] 1.017785
> colMax(tmp2)
[1] 1.855399
> colMin(tmp2)
[1] -2.90884
> colMedians(tmp2)
[1] 0.07319812
> colRanges(tmp2)
[,1]
[1,] -2.908840
[2,] 1.855399
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 5.1521240 -4.2310378 1.7707802 -4.6517011 -2.7184082 -3.5226303
[7] -3.7268742 -0.9930765 4.0256601 -0.2272596
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.9402027
[2,] -0.1104395
[3,] 0.6829574
[4,] 1.1424792
[5,] 1.9466559
>
> rowApply(tmp,sum)
[1] -1.275558 2.326483 2.650803 -1.087369 -1.600911 -5.695690 2.370588
[8] -1.346107 -6.713196 1.248535
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 9 10 8 3 10 3 6 9 6 6
[2,] 1 2 1 6 1 4 9 10 1 2
[3,] 7 4 9 7 8 8 5 6 3 10
[4,] 4 9 4 1 4 10 7 1 8 3
[5,] 2 1 5 5 2 2 8 8 5 9
[6,] 5 7 2 4 5 6 1 5 9 4
[7,] 8 8 3 10 3 1 4 2 4 5
[8,] 6 6 6 2 7 7 10 3 7 8
[9,] 3 5 10 9 9 9 3 4 10 7
[10,] 10 3 7 8 6 5 2 7 2 1
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -4.45696756 -0.92555403 0.79858099 -1.64456182 -4.14152931 0.80571953
[7] -0.84508928 -1.26090994 3.97139760 0.06842002 -0.49046870 0.11937671
[13] 3.10282897 0.55594082 -3.42352675 -2.05132149 0.59887973 -0.91370523
[19] -2.91926950 2.46903199
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.8242675
[2,] -1.1567572
[3,] -0.8866929
[4,] -0.7322393
[5,] 0.1429894
>
> rowApply(tmp,sum)
[1] -2.9808513 -2.8185840 0.5955207 -2.8038874 -2.5749253
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 1 6 3 13 6
[2,] 11 4 8 8 15
[3,] 17 20 10 17 2
[4,] 2 2 9 19 17
[5,] 3 8 12 14 1
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -1.8242675 0.0008471041 0.91715648 -1.4340748 -1.1604777 0.2999107
[2,] -0.8866929 -0.9134545693 1.34637147 -1.7715163 -0.7839136 -0.7085926
[3,] -0.7322393 -0.1408846913 -0.09090903 -0.1089741 0.1038793 0.1703337
[4,] 0.1429894 -0.5195055789 0.66562115 0.7454071 0.1540178 0.1187293
[5,] -1.1567572 0.6474437103 -2.03965907 0.9245963 -2.4550352 0.9253384
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.37224873 -0.8921671 0.1592361 -0.9510734 -0.7017909 0.5724136
[2,] 0.85659515 -1.1554978 0.8781915 0.1638553 -0.7941563 1.1103738
[3,] -1.08963672 0.3593199 -0.2415858 0.3932751 1.2113923 -0.2837764
[4,] -0.90669410 1.6018482 0.7359228 -0.8118302 0.0817233 -0.5197157
[5,] -0.07760235 -1.1744132 2.4396330 1.2741932 -0.2876371 -0.7599185
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 1.3099347 -0.8894708 -0.70045418 1.7892182 1.0481235 -1.0101121
[2,] 1.2709173 0.5102195 -0.90947231 -0.2126112 0.4190570 0.5639647
[3,] -0.1975329 1.5487482 -0.01915803 -0.6869392 -1.5520508 0.1996143
[4,] 0.4771980 -0.8673805 -0.47457100 -1.0807262 0.1339308 -0.8327380
[5,] 0.2423118 0.2538245 -1.31987123 -1.8602631 0.5498193 0.1655660
[,19] [,20]
[1,] -0.1827875 0.2967358
[2,] -2.2988775 0.4966556
[3,] 0.6345291 1.1181158
[4,] -1.9902020 0.3420880
[5,] 0.9180684 0.2154369
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.8 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 625 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 541 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.8 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 -0.8317198 2.593922 -1.596908 0.8187061 0.2538861 -0.8706657 1.23151
col8 col9 col10 col11 col12 col13 col14
row1 0.7333119 1.262685 0.5017014 1.316717 1.272305 0.1953661 0.8827193
col15 col16 col17 col18 col19 col20
row1 -0.7078461 -1.90173 0.2554452 0.5460732 0.1992547 -0.1641956
> tmp[,"col10"]
col10
row1 0.50170138
row2 1.82094172
row3 0.69111753
row4 -0.09078996
row5 -0.60890422
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.8317198 2.5939218 -1.596908 0.8187061 0.2538861 -0.8706657 1.231510
row5 1.7704773 -0.9290716 -2.368566 -1.0388670 0.6196521 -0.1491993 -1.561785
col8 col9 col10 col11 col12 col13 col14
row1 0.7333119 1.2626847 0.5017014 1.316717 1.272305 0.1953661 0.8827193
row5 0.4808510 -0.3542296 -0.6089042 1.366921 1.023688 1.4860545 -0.4017655
col15 col16 col17 col18 col19 col20
row1 -0.7078461 -1.901730 0.2554452 0.5460732 0.1992547 -0.1641956
row5 0.6251058 1.314237 -1.2467277 0.6699424 0.2970301 -1.4628702
> tmp[,c("col6","col20")]
col6 col20
row1 -0.87066568 -0.1641956
row2 0.07249203 0.2606642
row3 0.57607924 0.3849477
row4 0.33291299 0.7814376
row5 -0.14919928 -1.4628702
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.8706657 -0.1641956
row5 -0.1491993 -1.4628702
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.40997 50.48272 49.55524 49.39314 51.35092 104.7945 52.71242 50.09214
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.00509 48.7002 49.06889 49.63962 49.65666 51.01677 49.66231 48.82612
col17 col18 col19 col20
row1 49.42646 51.01161 50.27004 105.3181
> tmp[,"col10"]
col10
row1 48.70020
row2 31.62563
row3 29.38697
row4 31.55014
row5 51.81715
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.40997 50.48272 49.55524 49.39314 51.35092 104.7945 52.71242 50.09214
row5 50.26864 50.47572 49.04887 50.22834 50.75799 104.7264 50.91488 48.86673
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.00509 48.70020 49.06889 49.63962 49.65666 51.01677 49.66231 48.82612
row5 49.29156 51.81715 51.32456 50.28847 48.50274 49.00326 50.13730 49.61188
col17 col18 col19 col20
row1 49.42646 51.01161 50.27004 105.3181
row5 50.46230 48.64685 52.10529 104.2147
> tmp[,c("col6","col20")]
col6 col20
row1 104.79448 105.31809
row2 75.11416 75.77521
row3 75.22997 74.50705
row4 75.50216 73.06525
row5 104.72644 104.21467
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.7945 105.3181
row5 104.7264 104.2147
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.7945 105.3181
row5 104.7264 104.2147
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -1.4711396
[2,] 0.5344182
[3,] -1.6147388
[4,] 0.9087233
[5,] 0.5205487
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.1580911 0.6028749
[2,] -0.1592685 1.4460323
[3,] 0.6696576 -1.2355901
[4,] 1.3395810 1.2570175
[5,] -0.6137350 1.3175549
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.4980472 0.81439382
[2,] 0.6030284 -0.53561616
[3,] 0.3422758 0.06508651
[4,] -0.3778873 0.63466033
[5,] -1.2007933 -0.23692195
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.4980472
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.4980472
[2,] 0.6030284
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 -1.33561089 -1.9684011 -1.199553 0.4577828 -0.1679934 0.8846229
row1 -0.03821074 0.9328183 1.295907 -0.5906093 0.4596438 1.4047705
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 -0.4825506 1.301852 1.3201980 -0.2564290 -1.3630695 0.9080766 -0.7035089
row1 2.5818819 -1.658893 0.2717454 0.6214373 -0.9275498 0.3119036 0.3460133
[,14] [,15] [,16] [,17] [,18] [,19]
row3 -2.221017 0.519859003 -0.2143099 -1.102566 -0.1235067 1.42203927
row1 -2.076393 -0.008354026 0.9110575 0.118386 -0.4590605 0.06280646
[,20]
row3 -1.062043
row1 -1.133672
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.3214377 -1.23609 0.3068568 0.8399969 -0.01984972 0.3742408 -0.05239366
[,8] [,9] [,10]
row2 -1.694059 0.2527219 -0.2698819
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
row5 0.4394199 1.249913 1.138192 0.1845547 -2.257815 1.01807 -1.343259 1.892018
[,9] [,10] [,11] [,12] [,13] [,14] [,15]
row5 -1.394554 -0.4782966 -0.3593664 -1.354199 -0.1721309 0.6429713 0.3049808
[,16] [,17] [,18] [,19] [,20]
row5 0.7820895 -1.635984 -0.9324399 -0.668449 -0.487161
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x000002282227aa10>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238cc6a1578"
[2] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238c572a2f4"
[3] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238c56a9193e"
[4] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238cf924ccb"
[5] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238c653359b4"
[6] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238c793940ff"
[7] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238c5e5b312f"
[8] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238c5d2b3c3d"
[9] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238c44aae65"
[10] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238c4c5a3479"
[11] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238c7bd5358b"
[12] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238c6c392332"
[13] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238c19ed1cba"
[14] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238c718664f7"
[15] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM238c58d66797"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x00000228258ff8f0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x00000228258ff8f0>
Warning message:
In dir.create(new.directory) :
'F:\biocbuild\bbs-3.19-bioc\meat\BufferedMatrix.Rcheck\tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x00000228258ff8f0>
> rowMedians(tmp)
[1] 0.268156903 0.116330177 -0.669262150 -0.255292315 -0.212755961
[6] -0.441966144 0.155412331 0.357259745 0.555470233 -0.412178706
[11] 0.240443674 -0.321903840 0.706599558 0.067800900 -0.556925578
[16] -0.044111825 0.256160641 0.029599145 0.651575221 0.357589994
[21] -0.115305589 -0.035171831 -0.242188215 -0.101261051 0.004371667
[26] 0.394530319 -0.580463222 0.019875877 -0.524459432 -0.183486480
[31] -0.293715961 0.446407976 0.272110457 0.203414063 0.090274609
[36] 0.062811849 -0.483860749 -0.161708489 -0.366950093 -0.274568037
[41] 0.300262727 -0.505144628 0.152323714 0.072516804 0.027736390
[46] -0.001897982 -0.165186768 0.122954019 -0.096906818 0.255862478
[51] 0.199951537 -0.622846563 -0.455696974 -0.215133101 0.150613695
[56] 0.018531795 -0.210819696 0.569112406 0.615045032 -0.179776295
[61] -0.656951827 0.120099505 0.056214708 0.243803990 0.347282975
[66] -0.481332340 0.240111180 0.492348217 -0.066629542 0.093160902
[71] -0.703090328 -0.171213452 -0.117453889 -0.444922733 0.286293054
[76] 0.184622414 -0.492481698 -0.264935021 0.150814797 -0.137994626
[81] 0.316899954 -0.038948501 0.314644901 0.227467028 -0.042583606
[86] 0.559314386 -0.751346182 0.174923840 -0.139534611 0.078211509
[91] 0.196062770 0.710316274 -0.068870045 0.132899526 0.596084088
[96] 0.304027378 -0.273790872 0.007221071 0.011909050 -0.257766869
[101] -0.258550778 -0.254910826 -0.234711860 -0.166950348 -0.186663065
[106] 0.353833230 -0.265592757 0.196442983 -0.441973110 -0.368949431
[111] 0.367518135 -0.299756113 -0.422938575 0.221175336 0.014172755
[116] -0.015830629 -0.534628136 -0.482727855 0.002350681 -0.194655649
[121] -0.186547391 -0.456180641 0.057212748 0.027433833 -0.085980583
[126] 0.020595986 0.204285731 -0.260144879 -0.175791193 0.656471075
[131] -0.009913745 0.714410110 -0.251985553 0.134754003 0.112130046
[136] 0.771084944 0.332332319 0.075595779 -0.047061212 0.189181841
[141] 0.006122013 -0.009305622 0.287613787 0.186606585 0.339187963
[146] 0.959876281 0.218338093 -0.402073756 -0.105825850 0.185923476
[151] 0.079061729 -0.402198614 -0.407792294 -0.166959431 -0.206560728
[156] -0.293161345 -0.284716855 0.623601085 -0.127897817 0.081561358
[161] 0.071909413 0.234696778 0.037053574 -0.307879643 -0.370645178
[166] 0.342551759 -0.563068132 -0.221068807 -0.010075962 -0.218406796
[171] -0.030013016 -0.655638673 0.195176967 0.112631890 0.214640474
[176] -0.032262212 0.264204019 -0.278690856 0.743713500 -0.109680027
[181] 0.062341032 0.233580599 0.243901773 0.216831891 0.291880191
[186] 0.356645649 0.773371744 0.065931547 -0.209992351 -0.378208694
[191] 0.006035532 0.347940485 -0.535410312 0.139543228 0.227761158
[196] -0.117129523 0.155716120 -0.246048140 0.155864787 -0.171448623
[201] -0.204443646 -0.243450769 -0.335797084 -0.107996951 -0.614353826
[206] -0.429527984 -0.616329142 0.095912010 -0.197457951 0.244355399
[211] 0.381767075 -0.135759588 -0.365706439 -0.144192837 0.179306865
[216] 0.134446372 0.240007397 -0.192525717 0.228267008 0.287154334
[221] 0.427737123 -0.200785386 -0.262665794 -0.208432912 0.582994706
[226] 0.154757411 0.007291990 0.226288742 0.316623449 -0.002025916
>
> proc.time()
user system elapsed
3.81 19.42 50.84
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000207486fd530>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000207486fd530>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000207486fd530>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x00000207486fd530>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x00000207486fd710>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000207486fd710>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x00000207486fd710>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000207486fd710>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000207486fd710>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000207486fd9b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000207486fd9b0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000207486fd9b0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x00000207486fd9b0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000207486fd9b0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x00000207486fd9b0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000207486fd9b0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x00000207486fd9b0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000207486fd9b0>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000207486fd6b0>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x00000207486fd6b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000207486fd6b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000207486fd6b0>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile345c15ba78aa" "BufferedMatrixFile345c87123c9"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile345c15ba78aa" "BufferedMatrixFile345c87123c9"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000207486fd0b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000207486fd0b0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x00000207486fd0b0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x00000207486fd0b0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x00000207486fd0b0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x00000207486fd0b0>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000207486fdb90>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000207486fdb90>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x00000207486fdb90>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x00000207486fdb90>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000207486fd470>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000207486fd470>
> rm(P)
>
> proc.time()
user system elapsed
0.34 0.14 1.57
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
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Platform: x86_64-w64-mingw32/x64
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> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.26 0.07 0.34