Ben Bolstad
| Snapshot Date: 2024-07-12 14:00 -0400 (Fri, 12 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: d422a05 |
| git_last_commit_date: 2024-04-30 10:16:21 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-13 11:39 -0400 (Sat, 13 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| 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 246/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.69.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | 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: 1.69.0 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BufferedMatrix_1.69.0.tar.gz |
| StartedAt: 2024-07-12 22:21:39 -0400 (Fri, 12 Jul 2024) |
| EndedAt: 2024-07-12 22:22:35 -0400 (Fri, 12 Jul 2024) |
| EllapsedTime: 55.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BufferedMatrix_1.69.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck'
* using R version 4.4.1 (2024-06-14 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 '1.69.0'
* 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 'C:/Users/biocbuild/bbs-3.20-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
'C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/00check.log'
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'BufferedMatrix' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc -I"C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-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 -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-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 version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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
0.28 0.07 0.54
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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] "C:/Users/biocbuild/bbs-3.20-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 468464 25.1 1021772 54.6 633391 33.9
Vcells 853911 6.6 8388608 64.0 2003323 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] "Fri Jul 12 22:22:00 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] "Fri Jul 12 22:22:00 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: 0x000001c675767a10>
>
>
>
> 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] "Fri Jul 12 22:22:06 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] "Fri Jul 12 22:22:09 2024"
>
> ColMode(tmp2)
<pointer: 0x000001c675767a10>
>
>
>
> ### 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,] 101.7985549 0.43450965 1.0257258 -0.5719922
[2,] 0.6513481 -0.34661411 0.7916667 0.2658728
[3,] -0.7297492 0.08420910 0.1510774 -0.7169550
[4,] -0.0324837 0.03576865 1.9435987 1.2049589
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 101.7985549 0.43450965 1.0257258 0.5719922
[2,] 0.6513481 0.34661411 0.7916667 0.2658728
[3,] 0.7297492 0.08420910 0.1510774 0.7169550
[4,] 0.0324837 0.03576865 1.9435987 1.2049589
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0895270 0.6591735 1.0127812 0.7563016
[2,] 0.8070614 0.5887394 0.8897565 0.5156285
[3,] 0.8542536 0.2901880 0.3886868 0.8467320
[4,] 0.1802324 0.1891260 1.3941301 1.0977062
>
> 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: C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 227.69382 32.02624 36.15354 33.13501
[2,] 33.72196 31.23401 34.68923 30.42216
[3,] 34.27229 27.98609 29.03795 34.18427
[4,] 26.83481 26.92703 40.88490 37.18202
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x000001c6776ff470>
> exp(tmp5)
<pointer: 0x000001c6776ff470>
> log(tmp5,2)
<pointer: 0x000001c6776ff470>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 473.9149
> Min(tmp5)
[1] 54.59404
> mean(tmp5)
[1] 72.08928
> Sum(tmp5)
[1] 14417.86
> Var(tmp5)
[1] 886.8877
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.52613 68.72637 69.79263 70.11068 68.91701 67.52210 69.72265 70.22426
[9] 71.68665 71.66434
> rowSums(tmp5)
[1] 1850.523 1374.527 1395.853 1402.214 1378.340 1350.442 1394.453 1404.485
[9] 1433.733 1433.287
> rowVars(tmp5)
[1] 8136.23338 33.66853 101.58372 97.12410 87.10995 82.87737
[7] 53.49346 39.91153 70.88302 82.40436
> rowSd(tmp5)
[1] 90.201072 5.802459 10.078875 9.855156 9.333271 9.103701 7.313922
[8] 6.317557 8.419205 9.077685
> rowMax(tmp5)
[1] 473.91486 80.01383 86.88258 86.56111 90.03439 90.49119 84.10700
[8] 81.77137 87.18560 91.25713
> rowMin(tmp5)
[1] 57.62170 58.83546 54.59404 55.85314 56.22669 55.70033 56.72480 54.77746
[9] 57.44164 59.21811
>
> colMeans(tmp5)
[1] 109.26063 68.00382 70.73275 71.17998 69.73759 68.29018 71.61885
[8] 76.52292 65.08579 68.81036 76.09493 68.87690 71.33149 70.46394
[15] 69.23210 67.02213 65.18650 71.26549 73.87108 69.19820
> colSums(tmp5)
[1] 1092.6063 680.0382 707.3275 711.7998 697.3759 682.9018 716.1885
[8] 765.2292 650.8579 688.1036 760.9493 688.7690 713.3149 704.6394
[15] 692.3210 670.2213 651.8650 712.6549 738.7108 691.9820
> colVars(tmp5)
[1] 16453.72350 85.74012 54.02461 43.78317 57.25676 101.45858
[7] 84.75985 113.49920 80.99913 69.82286 77.23359 60.31442
[13] 69.11115 36.21614 127.83243 47.76402 67.18031 33.04180
[19] 116.94610 24.93210
> colSd(tmp5)
[1] 128.272068 9.259596 7.350144 6.616885 7.566820 10.072665
[7] 9.206511 10.653600 8.999952 8.356008 8.788264 7.766236
[13] 8.313312 6.017985 11.306300 6.911152 8.196360 5.748200
[19] 10.814162 4.993206
> colMax(tmp5)
[1] 473.91486 82.90798 85.09656 81.63706 83.06227 86.90533 84.10700
[8] 91.25713 82.57288 84.08511 86.56111 83.23785 81.82082 77.94304
[15] 90.49119 79.17205 78.38844 82.08219 90.03439 76.89712
> colMin(tmp5)
[1] 55.85314 56.04508 60.43868 61.67184 59.96396 57.64410 55.70033 58.83546
[9] 56.17440 59.63668 58.26760 56.10171 56.50760 60.21375 54.77746 59.20183
[17] 54.59404 65.05556 56.72480 59.69143
>
>
> ### 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] 92.52613 68.72637 69.79263 70.11068 68.91701 67.52210 NA 70.22426
[9] 71.68665 71.66434
> rowSums(tmp5)
[1] 1850.523 1374.527 1395.853 1402.214 1378.340 1350.442 NA 1404.485
[9] 1433.733 1433.287
> rowVars(tmp5)
[1] 8136.23338 33.66853 101.58372 97.12410 87.10995 82.87737
[7] 56.42246 39.91153 70.88302 82.40436
> rowSd(tmp5)
[1] 90.201072 5.802459 10.078875 9.855156 9.333271 9.103701 7.511489
[8] 6.317557 8.419205 9.077685
> rowMax(tmp5)
[1] 473.91486 80.01383 86.88258 86.56111 90.03439 90.49119 NA
[8] 81.77137 87.18560 91.25713
> rowMin(tmp5)
[1] 57.62170 58.83546 54.59404 55.85314 56.22669 55.70033 NA 54.77746
[9] 57.44164 59.21811
>
> colMeans(tmp5)
[1] 109.26063 NA 70.73275 71.17998 69.73759 68.29018 71.61885
[8] 76.52292 65.08579 68.81036 76.09493 68.87690 71.33149 70.46394
[15] 69.23210 67.02213 65.18650 71.26549 73.87108 69.19820
> colSums(tmp5)
[1] 1092.6063 NA 707.3275 711.7998 697.3759 682.9018 716.1885
[8] 765.2292 650.8579 688.1036 760.9493 688.7690 713.3149 704.6394
[15] 692.3210 670.2213 651.8650 712.6549 738.7108 691.9820
> colVars(tmp5)
[1] 16453.72350 NA 54.02461 43.78317 57.25676 101.45858
[7] 84.75985 113.49920 80.99913 69.82286 77.23359 60.31442
[13] 69.11115 36.21614 127.83243 47.76402 67.18031 33.04180
[19] 116.94610 24.93210
> colSd(tmp5)
[1] 128.272068 NA 7.350144 6.616885 7.566820 10.072665
[7] 9.206511 10.653600 8.999952 8.356008 8.788264 7.766236
[13] 8.313312 6.017985 11.306300 6.911152 8.196360 5.748200
[19] 10.814162 4.993206
> colMax(tmp5)
[1] 473.91486 NA 85.09656 81.63706 83.06227 86.90533 84.10700
[8] 91.25713 82.57288 84.08511 86.56111 83.23785 81.82082 77.94304
[15] 90.49119 79.17205 78.38844 82.08219 90.03439 76.89712
> colMin(tmp5)
[1] 55.85314 NA 60.43868 61.67184 59.96396 57.64410 55.70033 58.83546
[9] 56.17440 59.63668 58.26760 56.10171 56.50760 60.21375 54.77746 59.20183
[17] 54.59404 65.05556 56.72480 59.69143
>
> Max(tmp5,na.rm=TRUE)
[1] 473.9149
> Min(tmp5,na.rm=TRUE)
[1] 54.59404
> mean(tmp5,na.rm=TRUE)
[1] 72.10548
> Sum(tmp5,na.rm=TRUE)
[1] 14348.99
> Var(tmp5,na.rm=TRUE)
[1] 891.3142
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.52613 68.72637 69.79263 70.11068 68.91701 67.52210 69.76771 70.22426
[9] 71.68665 71.66434
> rowSums(tmp5,na.rm=TRUE)
[1] 1850.523 1374.527 1395.853 1402.214 1378.340 1350.442 1325.586 1404.485
[9] 1433.733 1433.287
> rowVars(tmp5,na.rm=TRUE)
[1] 8136.23338 33.66853 101.58372 97.12410 87.10995 82.87737
[7] 56.42246 39.91153 70.88302 82.40436
> rowSd(tmp5,na.rm=TRUE)
[1] 90.201072 5.802459 10.078875 9.855156 9.333271 9.103701 7.511489
[8] 6.317557 8.419205 9.077685
> rowMax(tmp5,na.rm=TRUE)
[1] 473.91486 80.01383 86.88258 86.56111 90.03439 90.49119 84.10700
[8] 81.77137 87.18560 91.25713
> rowMin(tmp5,na.rm=TRUE)
[1] 57.62170 58.83546 54.59404 55.85314 56.22669 55.70033 56.72480 54.77746
[9] 57.44164 59.21811
>
> colMeans(tmp5,na.rm=TRUE)
[1] 109.26063 67.90796 70.73275 71.17998 69.73759 68.29018 71.61885
[8] 76.52292 65.08579 68.81036 76.09493 68.87690 71.33149 70.46394
[15] 69.23210 67.02213 65.18650 71.26549 73.87108 69.19820
> colSums(tmp5,na.rm=TRUE)
[1] 1092.6063 611.1716 707.3275 711.7998 697.3759 682.9018 716.1885
[8] 765.2292 650.8579 688.1036 760.9493 688.7690 713.3149 704.6394
[15] 692.3210 670.2213 651.8650 712.6549 738.7108 691.9820
> colVars(tmp5,na.rm=TRUE)
[1] 16453.72350 96.35425 54.02461 43.78317 57.25676 101.45858
[7] 84.75985 113.49920 80.99913 69.82286 77.23359 60.31442
[13] 69.11115 36.21614 127.83243 47.76402 67.18031 33.04180
[19] 116.94610 24.93210
> colSd(tmp5,na.rm=TRUE)
[1] 128.272068 9.816020 7.350144 6.616885 7.566820 10.072665
[7] 9.206511 10.653600 8.999952 8.356008 8.788264 7.766236
[13] 8.313312 6.017985 11.306300 6.911152 8.196360 5.748200
[19] 10.814162 4.993206
> colMax(tmp5,na.rm=TRUE)
[1] 473.91486 82.90798 85.09656 81.63706 83.06227 86.90533 84.10700
[8] 91.25713 82.57288 84.08511 86.56111 83.23785 81.82082 77.94304
[15] 90.49119 79.17205 78.38844 82.08219 90.03439 76.89712
> colMin(tmp5,na.rm=TRUE)
[1] 55.85314 56.04508 60.43868 61.67184 59.96396 57.64410 55.70033 58.83546
[9] 56.17440 59.63668 58.26760 56.10171 56.50760 60.21375 54.77746 59.20183
[17] 54.59404 65.05556 56.72480 59.69143
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.52613 68.72637 69.79263 70.11068 68.91701 67.52210 NaN 70.22426
[9] 71.68665 71.66434
> rowSums(tmp5,na.rm=TRUE)
[1] 1850.523 1374.527 1395.853 1402.214 1378.340 1350.442 0.000 1404.485
[9] 1433.733 1433.287
> rowVars(tmp5,na.rm=TRUE)
[1] 8136.23338 33.66853 101.58372 97.12410 87.10995 82.87737
[7] NA 39.91153 70.88302 82.40436
> rowSd(tmp5,na.rm=TRUE)
[1] 90.201072 5.802459 10.078875 9.855156 9.333271 9.103701 NA
[8] 6.317557 8.419205 9.077685
> rowMax(tmp5,na.rm=TRUE)
[1] 473.91486 80.01383 86.88258 86.56111 90.03439 90.49119 NA
[8] 81.77137 87.18560 91.25713
> rowMin(tmp5,na.rm=TRUE)
[1] 57.62170 58.83546 54.59404 55.85314 56.22669 55.70033 NA 54.77746
[9] 57.44164 59.21811
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 114.35098 NaN 71.23909 70.46077 70.53558 68.95691 70.23127
[8] 76.80084 64.68763 68.62129 78.07575 67.91290 70.47300 70.23902
[15] 68.88641 66.78159 63.71961 71.73456 75.77623 69.65344
> colSums(tmp5,na.rm=TRUE)
[1] 1029.1589 0.0000 641.1518 634.1470 634.8202 620.6122 632.0815
[8] 691.2075 582.1887 617.5916 702.6817 611.2161 634.2570 632.1512
[15] 619.9777 601.0343 573.4765 645.6110 681.9860 626.8809
> colVars(tmp5,na.rm=TRUE)
[1] 18218.93244 NA 57.89334 43.43686 57.25003 109.13999
[7] 73.69457 126.81768 89.34057 78.14855 42.74698 57.39911
[13] 69.45869 40.17403 142.46706 53.08359 51.37074 34.69677
[19] 90.73173 25.71719
> colSd(tmp5,na.rm=TRUE)
[1] 134.977526 NA 7.608767 6.590665 7.566375 10.447009
[7] 8.584554 11.261336 9.452014 8.840167 6.538118 7.576220
[13] 8.334188 6.338298 11.935957 7.285848 7.167338 5.890396
[19] 9.525321 5.071212
> colMax(tmp5,na.rm=TRUE)
[1] 473.91486 -Inf 85.09656 81.63706 83.06227 86.90533 81.77137
[8] 91.25713 82.57288 84.08511 86.56111 83.23785 81.82082 77.94304
[15] 90.49119 79.17205 75.29803 82.08219 90.03439 76.89712
> colMin(tmp5,na.rm=TRUE)
[1] 55.85314 Inf 60.43868 61.67184 59.96396 57.64410 55.70033 58.83546
[9] 56.17440 59.63668 69.35499 56.10171 56.50760 60.21375 54.77746 59.20183
[17] 54.59404 65.05556 59.76797 59.69143
>
>
>
>
> 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] 247.20247 175.99979 171.80676 257.03312 345.24098 220.54451 92.70107
[8] 195.65944 255.59058 324.11842
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 247.20247 175.99979 171.80676 257.03312 345.24098 220.54451 92.70107
[8] 195.65944 255.59058 324.11842
>
>
>
> 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] -1.136868e-13 5.684342e-14 -1.421085e-13 5.684342e-14 -1.136868e-13
[6] -1.705303e-13 1.705303e-13 5.684342e-14 -5.684342e-14 -1.136868e-13
[11] -2.842171e-14 -2.842171e-14 8.526513e-14 -2.842171e-14 5.684342e-14
[16] 0.000000e+00 -5.684342e-14 -4.263256e-14 5.684342e-14 2.842171e-14
>
>
>
>
>
>
>
>
>
>
> ## 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)
+ }
4 9
8 2
4 4
8 16
8 13
9 16
4 18
8 18
2 6
4 16
4 15
5 16
5 9
2 7
7 9
8 14
7 3
7 16
7 15
1 10
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] 2.063787
> Min(tmp)
[1] -2.332494
> mean(tmp)
[1] 0.04760018
> Sum(tmp)
[1] 4.760018
> Var(tmp)
[1] 1.029881
>
> rowMeans(tmp)
[1] 0.04760018
> rowSums(tmp)
[1] 4.760018
> rowVars(tmp)
[1] 1.029881
> rowSd(tmp)
[1] 1.014831
> rowMax(tmp)
[1] 2.063787
> rowMin(tmp)
[1] -2.332494
>
> colMeans(tmp)
[1] -0.52792172 0.89285571 -1.21688243 -0.11823598 1.24211722 0.54876545
[7] -0.19536731 1.16334189 0.46013984 0.64916192 0.18897069 1.39049843
[13] 0.79585222 1.02382239 -0.34486976 1.33266380 -1.22287896 1.61282977
[19] 0.58258033 0.99415230 1.77772613 0.79665418 -0.57159444 -1.96155867
[25] 0.10543868 0.94013015 0.49894648 -1.16228469 1.42363194 -1.68597404
[31] -0.04012450 0.76086792 -1.32314020 -0.84463043 1.68965755 0.05753542
[37] -0.14563602 -0.78224587 -0.70696572 0.03822117 0.51334795 0.25197524
[43] -0.35543629 0.97350540 0.13438148 1.34333543 0.33316051 0.63427246
[49] 2.06378742 -2.20213496 -1.91727506 -0.14846869 0.29522618 -2.33249412
[55] 0.46068771 0.33258406 0.29993425 -0.85949258 0.88422797 -1.90791432
[61] 0.13426204 -1.05901426 -1.14193717 -0.80813216 1.27475148 -0.60219558
[67] -0.49558885 0.16822889 -0.21323415 -0.61291472 -1.07333286 0.53016924
[73] -0.96488858 -0.91343151 1.06750869 -1.50892739 1.91887664 1.03392917
[79] 1.12046012 0.15788192 -0.23824805 1.41057259 0.19877583 0.79513096
[85] 0.74563153 -1.03856346 0.78427621 -1.67276282 -1.54524238 0.23814338
[91] 1.16059538 0.75187139 -0.94426543 -0.94449719 0.48955092 -0.81368156
[97] -0.67733722 0.65213625 0.75368711 -0.27168752
> colSums(tmp)
[1] -0.52792172 0.89285571 -1.21688243 -0.11823598 1.24211722 0.54876545
[7] -0.19536731 1.16334189 0.46013984 0.64916192 0.18897069 1.39049843
[13] 0.79585222 1.02382239 -0.34486976 1.33266380 -1.22287896 1.61282977
[19] 0.58258033 0.99415230 1.77772613 0.79665418 -0.57159444 -1.96155867
[25] 0.10543868 0.94013015 0.49894648 -1.16228469 1.42363194 -1.68597404
[31] -0.04012450 0.76086792 -1.32314020 -0.84463043 1.68965755 0.05753542
[37] -0.14563602 -0.78224587 -0.70696572 0.03822117 0.51334795 0.25197524
[43] -0.35543629 0.97350540 0.13438148 1.34333543 0.33316051 0.63427246
[49] 2.06378742 -2.20213496 -1.91727506 -0.14846869 0.29522618 -2.33249412
[55] 0.46068771 0.33258406 0.29993425 -0.85949258 0.88422797 -1.90791432
[61] 0.13426204 -1.05901426 -1.14193717 -0.80813216 1.27475148 -0.60219558
[67] -0.49558885 0.16822889 -0.21323415 -0.61291472 -1.07333286 0.53016924
[73] -0.96488858 -0.91343151 1.06750869 -1.50892739 1.91887664 1.03392917
[79] 1.12046012 0.15788192 -0.23824805 1.41057259 0.19877583 0.79513096
[85] 0.74563153 -1.03856346 0.78427621 -1.67276282 -1.54524238 0.23814338
[91] 1.16059538 0.75187139 -0.94426543 -0.94449719 0.48955092 -0.81368156
[97] -0.67733722 0.65213625 0.75368711 -0.27168752
> 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] -0.52792172 0.89285571 -1.21688243 -0.11823598 1.24211722 0.54876545
[7] -0.19536731 1.16334189 0.46013984 0.64916192 0.18897069 1.39049843
[13] 0.79585222 1.02382239 -0.34486976 1.33266380 -1.22287896 1.61282977
[19] 0.58258033 0.99415230 1.77772613 0.79665418 -0.57159444 -1.96155867
[25] 0.10543868 0.94013015 0.49894648 -1.16228469 1.42363194 -1.68597404
[31] -0.04012450 0.76086792 -1.32314020 -0.84463043 1.68965755 0.05753542
[37] -0.14563602 -0.78224587 -0.70696572 0.03822117 0.51334795 0.25197524
[43] -0.35543629 0.97350540 0.13438148 1.34333543 0.33316051 0.63427246
[49] 2.06378742 -2.20213496 -1.91727506 -0.14846869 0.29522618 -2.33249412
[55] 0.46068771 0.33258406 0.29993425 -0.85949258 0.88422797 -1.90791432
[61] 0.13426204 -1.05901426 -1.14193717 -0.80813216 1.27475148 -0.60219558
[67] -0.49558885 0.16822889 -0.21323415 -0.61291472 -1.07333286 0.53016924
[73] -0.96488858 -0.91343151 1.06750869 -1.50892739 1.91887664 1.03392917
[79] 1.12046012 0.15788192 -0.23824805 1.41057259 0.19877583 0.79513096
[85] 0.74563153 -1.03856346 0.78427621 -1.67276282 -1.54524238 0.23814338
[91] 1.16059538 0.75187139 -0.94426543 -0.94449719 0.48955092 -0.81368156
[97] -0.67733722 0.65213625 0.75368711 -0.27168752
> colMin(tmp)
[1] -0.52792172 0.89285571 -1.21688243 -0.11823598 1.24211722 0.54876545
[7] -0.19536731 1.16334189 0.46013984 0.64916192 0.18897069 1.39049843
[13] 0.79585222 1.02382239 -0.34486976 1.33266380 -1.22287896 1.61282977
[19] 0.58258033 0.99415230 1.77772613 0.79665418 -0.57159444 -1.96155867
[25] 0.10543868 0.94013015 0.49894648 -1.16228469 1.42363194 -1.68597404
[31] -0.04012450 0.76086792 -1.32314020 -0.84463043 1.68965755 0.05753542
[37] -0.14563602 -0.78224587 -0.70696572 0.03822117 0.51334795 0.25197524
[43] -0.35543629 0.97350540 0.13438148 1.34333543 0.33316051 0.63427246
[49] 2.06378742 -2.20213496 -1.91727506 -0.14846869 0.29522618 -2.33249412
[55] 0.46068771 0.33258406 0.29993425 -0.85949258 0.88422797 -1.90791432
[61] 0.13426204 -1.05901426 -1.14193717 -0.80813216 1.27475148 -0.60219558
[67] -0.49558885 0.16822889 -0.21323415 -0.61291472 -1.07333286 0.53016924
[73] -0.96488858 -0.91343151 1.06750869 -1.50892739 1.91887664 1.03392917
[79] 1.12046012 0.15788192 -0.23824805 1.41057259 0.19877583 0.79513096
[85] 0.74563153 -1.03856346 0.78427621 -1.67276282 -1.54524238 0.23814338
[91] 1.16059538 0.75187139 -0.94426543 -0.94449719 0.48955092 -0.81368156
[97] -0.67733722 0.65213625 0.75368711 -0.27168752
> colMedians(tmp)
[1] -0.52792172 0.89285571 -1.21688243 -0.11823598 1.24211722 0.54876545
[7] -0.19536731 1.16334189 0.46013984 0.64916192 0.18897069 1.39049843
[13] 0.79585222 1.02382239 -0.34486976 1.33266380 -1.22287896 1.61282977
[19] 0.58258033 0.99415230 1.77772613 0.79665418 -0.57159444 -1.96155867
[25] 0.10543868 0.94013015 0.49894648 -1.16228469 1.42363194 -1.68597404
[31] -0.04012450 0.76086792 -1.32314020 -0.84463043 1.68965755 0.05753542
[37] -0.14563602 -0.78224587 -0.70696572 0.03822117 0.51334795 0.25197524
[43] -0.35543629 0.97350540 0.13438148 1.34333543 0.33316051 0.63427246
[49] 2.06378742 -2.20213496 -1.91727506 -0.14846869 0.29522618 -2.33249412
[55] 0.46068771 0.33258406 0.29993425 -0.85949258 0.88422797 -1.90791432
[61] 0.13426204 -1.05901426 -1.14193717 -0.80813216 1.27475148 -0.60219558
[67] -0.49558885 0.16822889 -0.21323415 -0.61291472 -1.07333286 0.53016924
[73] -0.96488858 -0.91343151 1.06750869 -1.50892739 1.91887664 1.03392917
[79] 1.12046012 0.15788192 -0.23824805 1.41057259 0.19877583 0.79513096
[85] 0.74563153 -1.03856346 0.78427621 -1.67276282 -1.54524238 0.23814338
[91] 1.16059538 0.75187139 -0.94426543 -0.94449719 0.48955092 -0.81368156
[97] -0.67733722 0.65213625 0.75368711 -0.27168752
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.5279217 0.8928557 -1.216882 -0.118236 1.242117 0.5487654 -0.1953673
[2,] -0.5279217 0.8928557 -1.216882 -0.118236 1.242117 0.5487654 -0.1953673
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 1.163342 0.4601398 0.6491619 0.1889707 1.390498 0.7958522 1.023822
[2,] 1.163342 0.4601398 0.6491619 0.1889707 1.390498 0.7958522 1.023822
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.3448698 1.332664 -1.222879 1.61283 0.5825803 0.9941523 1.777726
[2,] -0.3448698 1.332664 -1.222879 1.61283 0.5825803 0.9941523 1.777726
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.7966542 -0.5715944 -1.961559 0.1054387 0.9401301 0.4989465 -1.162285
[2,] 0.7966542 -0.5715944 -1.961559 0.1054387 0.9401301 0.4989465 -1.162285
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 1.423632 -1.685974 -0.0401245 0.7608679 -1.32314 -0.8446304 1.689658
[2,] 1.423632 -1.685974 -0.0401245 0.7608679 -1.32314 -0.8446304 1.689658
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.05753542 -0.145636 -0.7822459 -0.7069657 0.03822117 0.5133479 0.2519752
[2,] 0.05753542 -0.145636 -0.7822459 -0.7069657 0.03822117 0.5133479 0.2519752
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.3554363 0.9735054 0.1343815 1.343335 0.3331605 0.6342725 2.063787
[2,] -0.3554363 0.9735054 0.1343815 1.343335 0.3331605 0.6342725 2.063787
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -2.202135 -1.917275 -0.1484687 0.2952262 -2.332494 0.4606877 0.3325841
[2,] -2.202135 -1.917275 -0.1484687 0.2952262 -2.332494 0.4606877 0.3325841
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.2999342 -0.8594926 0.884228 -1.907914 0.134262 -1.059014 -1.141937
[2,] 0.2999342 -0.8594926 0.884228 -1.907914 0.134262 -1.059014 -1.141937
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -0.8081322 1.274751 -0.6021956 -0.4955888 0.1682289 -0.2132342 -0.6129147
[2,] -0.8081322 1.274751 -0.6021956 -0.4955888 0.1682289 -0.2132342 -0.6129147
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -1.073333 0.5301692 -0.9648886 -0.9134315 1.067509 -1.508927 1.918877
[2,] -1.073333 0.5301692 -0.9648886 -0.9134315 1.067509 -1.508927 1.918877
[,78] [,79] [,80] [,81] [,82] [,83] [,84] [,85]
[1,] 1.033929 1.12046 0.1578819 -0.238248 1.410573 0.1987758 0.795131 0.7456315
[2,] 1.033929 1.12046 0.1578819 -0.238248 1.410573 0.1987758 0.795131 0.7456315
[,86] [,87] [,88] [,89] [,90] [,91] [,92]
[1,] -1.038563 0.7842762 -1.672763 -1.545242 0.2381434 1.160595 0.7518714
[2,] -1.038563 0.7842762 -1.672763 -1.545242 0.2381434 1.160595 0.7518714
[,93] [,94] [,95] [,96] [,97] [,98] [,99]
[1,] -0.9442654 -0.9444972 0.4895509 -0.8136816 -0.6773372 0.6521363 0.7536871
[2,] -0.9442654 -0.9444972 0.4895509 -0.8136816 -0.6773372 0.6521363 0.7536871
[,100]
[1,] -0.2716875
[2,] -0.2716875
>
>
> Max(tmp2)
[1] 2.820606
> Min(tmp2)
[1] -1.852501
> mean(tmp2)
[1] 0.05104207
> Sum(tmp2)
[1] 5.104207
> Var(tmp2)
[1] 0.9788721
>
> rowMeans(tmp2)
[1] 0.54265381 -1.51766254 0.36900537 2.45781360 -0.17933950 -1.05162911
[7] -0.16154999 -0.19889649 -1.21677514 -0.96559281 0.83244124 -1.42895431
[13] -0.89217978 -0.31089525 -0.27741539 0.74477569 -0.18265953 -0.48413410
[19] -0.97236175 0.56109643 -0.13202384 -0.57144221 0.42511419 2.82060609
[25] 0.21019367 1.01409060 -0.57437492 1.05689588 1.25262428 0.54226825
[31] 0.58842672 0.18729935 -0.73183688 0.50731486 -1.85250143 -1.31378861
[37] 1.29659627 -0.57178793 -0.11458927 1.94558908 0.55938665 -0.86010096
[43] 1.59960647 0.19610105 1.51410848 0.36237043 0.14695422 -0.60137519
[49] -0.03606366 -1.04395762 -1.35681567 -0.29035621 -0.08333441 -0.29729049
[55] 0.51317286 -1.84587228 0.50604257 -0.99926295 -0.06693448 1.82204509
[61] 0.60802680 1.12874583 -1.35039818 0.41681890 0.50242143 0.27352962
[67] -0.83126599 -0.21999577 -1.52782414 1.67614172 0.45045998 0.33170424
[73] 1.94438002 0.28259895 -0.74533043 0.08349970 -1.38980353 0.56469962
[79] -0.87033407 0.82062552 -0.87303177 1.36669350 0.30627431 -0.93385325
[85] -0.23282532 0.08806020 1.26132266 0.39689713 1.08465102 1.00901042
[91] -0.05650117 0.32257008 -0.08194441 -1.56539232 2.04478973 -0.50031590
[97] 0.49503504 -0.40719570 -0.54970997 -1.60986622
> rowSums(tmp2)
[1] 0.54265381 -1.51766254 0.36900537 2.45781360 -0.17933950 -1.05162911
[7] -0.16154999 -0.19889649 -1.21677514 -0.96559281 0.83244124 -1.42895431
[13] -0.89217978 -0.31089525 -0.27741539 0.74477569 -0.18265953 -0.48413410
[19] -0.97236175 0.56109643 -0.13202384 -0.57144221 0.42511419 2.82060609
[25] 0.21019367 1.01409060 -0.57437492 1.05689588 1.25262428 0.54226825
[31] 0.58842672 0.18729935 -0.73183688 0.50731486 -1.85250143 -1.31378861
[37] 1.29659627 -0.57178793 -0.11458927 1.94558908 0.55938665 -0.86010096
[43] 1.59960647 0.19610105 1.51410848 0.36237043 0.14695422 -0.60137519
[49] -0.03606366 -1.04395762 -1.35681567 -0.29035621 -0.08333441 -0.29729049
[55] 0.51317286 -1.84587228 0.50604257 -0.99926295 -0.06693448 1.82204509
[61] 0.60802680 1.12874583 -1.35039818 0.41681890 0.50242143 0.27352962
[67] -0.83126599 -0.21999577 -1.52782414 1.67614172 0.45045998 0.33170424
[73] 1.94438002 0.28259895 -0.74533043 0.08349970 -1.38980353 0.56469962
[79] -0.87033407 0.82062552 -0.87303177 1.36669350 0.30627431 -0.93385325
[85] -0.23282532 0.08806020 1.26132266 0.39689713 1.08465102 1.00901042
[91] -0.05650117 0.32257008 -0.08194441 -1.56539232 2.04478973 -0.50031590
[97] 0.49503504 -0.40719570 -0.54970997 -1.60986622
> 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] 0.54265381 -1.51766254 0.36900537 2.45781360 -0.17933950 -1.05162911
[7] -0.16154999 -0.19889649 -1.21677514 -0.96559281 0.83244124 -1.42895431
[13] -0.89217978 -0.31089525 -0.27741539 0.74477569 -0.18265953 -0.48413410
[19] -0.97236175 0.56109643 -0.13202384 -0.57144221 0.42511419 2.82060609
[25] 0.21019367 1.01409060 -0.57437492 1.05689588 1.25262428 0.54226825
[31] 0.58842672 0.18729935 -0.73183688 0.50731486 -1.85250143 -1.31378861
[37] 1.29659627 -0.57178793 -0.11458927 1.94558908 0.55938665 -0.86010096
[43] 1.59960647 0.19610105 1.51410848 0.36237043 0.14695422 -0.60137519
[49] -0.03606366 -1.04395762 -1.35681567 -0.29035621 -0.08333441 -0.29729049
[55] 0.51317286 -1.84587228 0.50604257 -0.99926295 -0.06693448 1.82204509
[61] 0.60802680 1.12874583 -1.35039818 0.41681890 0.50242143 0.27352962
[67] -0.83126599 -0.21999577 -1.52782414 1.67614172 0.45045998 0.33170424
[73] 1.94438002 0.28259895 -0.74533043 0.08349970 -1.38980353 0.56469962
[79] -0.87033407 0.82062552 -0.87303177 1.36669350 0.30627431 -0.93385325
[85] -0.23282532 0.08806020 1.26132266 0.39689713 1.08465102 1.00901042
[91] -0.05650117 0.32257008 -0.08194441 -1.56539232 2.04478973 -0.50031590
[97] 0.49503504 -0.40719570 -0.54970997 -1.60986622
> rowMin(tmp2)
[1] 0.54265381 -1.51766254 0.36900537 2.45781360 -0.17933950 -1.05162911
[7] -0.16154999 -0.19889649 -1.21677514 -0.96559281 0.83244124 -1.42895431
[13] -0.89217978 -0.31089525 -0.27741539 0.74477569 -0.18265953 -0.48413410
[19] -0.97236175 0.56109643 -0.13202384 -0.57144221 0.42511419 2.82060609
[25] 0.21019367 1.01409060 -0.57437492 1.05689588 1.25262428 0.54226825
[31] 0.58842672 0.18729935 -0.73183688 0.50731486 -1.85250143 -1.31378861
[37] 1.29659627 -0.57178793 -0.11458927 1.94558908 0.55938665 -0.86010096
[43] 1.59960647 0.19610105 1.51410848 0.36237043 0.14695422 -0.60137519
[49] -0.03606366 -1.04395762 -1.35681567 -0.29035621 -0.08333441 -0.29729049
[55] 0.51317286 -1.84587228 0.50604257 -0.99926295 -0.06693448 1.82204509
[61] 0.60802680 1.12874583 -1.35039818 0.41681890 0.50242143 0.27352962
[67] -0.83126599 -0.21999577 -1.52782414 1.67614172 0.45045998 0.33170424
[73] 1.94438002 0.28259895 -0.74533043 0.08349970 -1.38980353 0.56469962
[79] -0.87033407 0.82062552 -0.87303177 1.36669350 0.30627431 -0.93385325
[85] -0.23282532 0.08806020 1.26132266 0.39689713 1.08465102 1.00901042
[91] -0.05650117 0.32257008 -0.08194441 -1.56539232 2.04478973 -0.50031590
[97] 0.49503504 -0.40719570 -0.54970997 -1.60986622
>
> colMeans(tmp2)
[1] 0.05104207
> colSums(tmp2)
[1] 5.104207
> colVars(tmp2)
[1] 0.9788721
> colSd(tmp2)
[1] 0.9893796
> colMax(tmp2)
[1] 2.820606
> colMin(tmp2)
[1] -1.852501
> colMedians(tmp2)
[1] 0.02371802
> colRanges(tmp2)
[,1]
[1,] -1.852501
[2,] 2.820606
>
> 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] -0.8322399 -1.2352000 1.6460426 -2.3263693 -3.8229975 -3.7046441
[7] 4.9268573 -2.6488207 -0.7264646 1.8959732
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.8043895
[2,] -1.1062044
[3,] 0.1416326
[4,] 0.9046984
[5,] 1.1743264
>
> rowApply(tmp,sum)
[1] -4.4435950 0.5800416 -2.3426368 3.9648067 0.9239718 -1.4854850
[7] 1.8813400 -4.2697395 -1.7521904 0.1156238
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 2 7 7 8 1 6 9 8 1 8
[2,] 5 3 5 5 8 5 8 4 9 4
[3,] 6 10 9 2 3 10 6 7 4 1
[4,] 3 2 1 10 10 8 2 2 6 5
[5,] 9 6 2 9 2 3 5 5 2 3
[6,] 8 1 6 4 6 1 3 9 5 2
[7,] 10 8 10 3 7 9 4 6 8 7
[8,] 4 4 4 7 9 2 7 1 3 6
[9,] 1 5 8 6 4 4 10 3 10 9
[10,] 7 9 3 1 5 7 1 10 7 10
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 4.73987909 1.48203817 -2.22329840 1.60610375 3.38884657 -2.70254902
[7] 0.01073257 1.13745201 1.08931856 -0.02002270 2.29246924 -0.65301268
[13] -3.74406021 -0.79542753 3.58297337 -0.63523780 -1.47637894 1.20479044
[19] -2.48584895 -0.90106118
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.3981497
[2,] -0.1165806
[3,] 0.7639370
[4,] 1.9237774
[5,] 2.5668950
>
> rowApply(tmp,sum)
[1] 2.4475825 -4.0138175 3.8388035 2.0555242 0.5696136
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 9 20 20 16 7
[2,] 15 12 17 7 13
[3,] 2 16 9 1 10
[4,] 20 6 18 3 9
[5,] 14 15 1 20 17
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.1165806 0.4899350 -1.159263316 2.5510508 0.4674433 -1.72995055
[2,] 1.9237774 0.2230026 0.487087872 -1.0601102 0.4840619 1.08593355
[3,] 2.5668950 1.0593546 0.055471138 1.2259451 -1.7043684 0.08678832
[4,] 0.7639370 -0.4436249 -1.600079238 -0.9161389 2.9880482 -0.02994239
[5,] -0.3981497 0.1533708 -0.006514855 -0.1946431 1.1536616 -2.11537794
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.5779939 0.3271274 0.1688875 1.7311513 1.3308044 0.2936343
[2,] 0.7029874 -1.2793540 -0.6764417 0.3082962 -0.4092240 -0.2493787
[3,] 0.9825049 -1.0934546 1.0583138 -0.7197137 0.5812757 1.2510378
[4,] -1.5538125 0.6793400 0.4812998 -0.4223091 1.3947535 -0.6018316
[5,] 0.4570466 2.5037932 0.0572591 -0.9174474 -0.6051404 -1.3464745
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -1.0051607 -0.7286601 0.840771401 -0.30716803 -0.6843892 -0.1636691
[2,] -1.4179117 -0.7723018 0.728534798 -1.42543233 0.1983614 0.4581777
[3,] -0.9331827 0.9875323 0.694315593 -0.25715461 1.0367548 -0.5102464
[4,] -0.1219759 0.8779799 0.003503397 -0.01184907 -0.7874025 0.4438694
[5,] -0.2658292 -1.1599778 1.315848181 1.36636624 -1.2397034 0.9766588
[,19] [,20]
[1,] -0.0545560 0.7741685
[2,] -1.0790676 -2.2448163
[3,] -0.8504885 -1.6787768
[4,] -0.5856272 1.4973864
[5,] 0.0838904 0.7509769
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 664 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 576 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 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 0.7337941 0.459849 0.8764147 -0.2849767 0.1378042 0.3230238 -0.932052
col8 col9 col10 col11 col12 col13 col14
row1 -2.156593 -1.252266 0.04923202 -0.4656811 1.260407 -0.8657595 0.7653107
col15 col16 col17 col18 col19 col20
row1 -1.053883 0.3399226 -0.6205752 0.1380679 -1.231085 1.405303
> tmp[,"col10"]
col10
row1 0.04923202
row2 1.04759639
row3 0.01723095
row4 0.04273980
row5 -1.95366665
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.73379414 0.4598490 0.8764147 -0.2849767 0.1378042 0.3230238 -0.9320520
row5 -0.05186736 0.3982432 0.8491230 0.7125223 0.2831988 -0.5627262 0.7989547
col8 col9 col10 col11 col12 col13 col14
row1 -2.156593 -1.252266 0.04923202 -0.4656811 1.2604067 -0.8657595 0.7653107
row5 -1.119680 0.616955 -1.95366665 0.5080229 0.4258796 0.7471939 -0.3738301
col15 col16 col17 col18 col19 col20
row1 -1.0538830 0.3399226 -0.6205752 0.1380679 -1.231085 1.4053030
row5 -0.3839169 -0.2158151 -0.1868736 0.4068390 -1.119513 -0.2111668
> tmp[,c("col6","col20")]
col6 col20
row1 0.3230238 1.4053030
row2 -1.1488180 -0.1317626
row3 -0.9057898 0.3238900
row4 -0.8026014 -1.6311428
row5 -0.5627262 -0.2111668
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.3230238 1.4053030
row5 -0.5627262 -0.2111668
>
>
>
>
> 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 49.28125 50.89183 52.66398 50.41845 48.01306 105.1985 48.8049 50.23662
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.11331 50.7625 50.06847 51.60152 50.06402 48.85839 52.33254 49.53669
col17 col18 col19 col20
row1 48.1256 49.72467 48.99675 104.7161
> tmp[,"col10"]
col10
row1 50.76250
row2 30.54058
row3 30.13142
row4 30.58757
row5 49.14469
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.28125 50.89183 52.66398 50.41845 48.01306 105.1985 48.8049 50.23662
row5 47.69482 50.19668 50.00996 48.95156 50.37310 105.8028 49.5469 50.03399
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.11331 50.76250 50.06847 51.60152 50.06402 48.85839 52.33254 49.53669
row5 50.09482 49.14469 49.94233 50.08648 50.84894 51.37346 48.80833 49.41732
col17 col18 col19 col20
row1 48.12560 49.72467 48.99675 104.7161
row5 51.52241 51.17945 51.01954 105.1343
> tmp[,c("col6","col20")]
col6 col20
row1 105.19853 104.71615
row2 75.82064 73.72092
row3 76.39507 74.04394
row4 73.29990 75.37217
row5 105.80284 105.13431
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.1985 104.7161
row5 105.8028 105.1343
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.1985 104.7161
row5 105.8028 105.1343
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.70371170
[2,] -0.53873487
[3,] -0.51037171
[4,] -0.08063295
[5,] -0.54888876
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.7427752 0.3726106
[2,] -0.1847203 0.3013220
[3,] -2.3919852 0.5630425
[4,] 0.7674540 -0.6795661
[5,] -0.7511505 0.4705123
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.17680291 -0.12678420
[2,] -0.94552782 -0.64780465
[3,] 0.25629945 -0.05337168
[4,] -0.04380159 -0.11856033
[5,] 0.05646960 0.83873639
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.1768029
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.1768029
[2,] -0.9455278
>
>
>
> 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 -0.1879512 -1.8924896 0.4024357 -0.1878145 -0.7890707 0.7953074
row1 -0.5411493 0.1426077 -0.9817745 -0.8433198 -0.8582333 -1.2653740
[,7] [,8] [,9] [,10] [,11] [,12]
row3 -0.09326211 1.0039743 0.05667032 0.1405681 -0.9365526 -1.1193774
row1 1.10065708 0.9198301 -0.68540770 2.5135215 -2.6774157 -0.4493679
[,13] [,14] [,15] [,16] [,17] [,18]
row3 -1.603790 0.2562128 -0.5820470 -0.7736032 -0.0379590 -1.1207926
row1 1.275949 -0.2954460 -0.9030697 1.1668785 -0.8736793 0.8885243
[,19] [,20]
row3 0.6464133 0.3429548
row1 -0.2691671 1.6324269
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.5065406 0.001618431 1.267467 2.272545 -0.09858287 -0.5856316 0.4681629
[,8] [,9] [,10]
row2 0.4136521 0.8104926 -0.7268877
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 1.68319 -0.6185981 0.6017955 -1.666613 0.1686404 -0.8009634 0.6300037
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.1087917 -2.230025 -2.155513 1.652356 -0.07772057 0.1388898 0.5222463
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -1.542782 0.4038064 -1.494723 -0.8368518 -1.378741 -0.8358376
>
>
> 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: 0x000001c6792cebb0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM30770bd33754"
[2] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3077025714028"
[3] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM307705c0e32b1"
[4] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM307702476500a"
[5] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3077064db512d"
[6] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3077077923f43"
[7] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM30770bf5710"
[8] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM30770168018fb"
[9] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3077077547258"
[10] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3077028d111ca"
[11] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3077068e14801"
[12] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM307706e261f1e"
[13] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM30770182e6683"
[14] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3077076a21ddd"
[15] "C:/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM30770697419d"
>
>
> ### 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: 0x000001c678dd4010>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x000001c678dd4010>
Warning message:
In dir.create(new.directory) :
'C:\Users\biocbuild\bbs-3.20-bioc\meat\BufferedMatrix.Rcheck\tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x000001c678dd4010>
> rowMedians(tmp)
[1] 0.8124981436 0.5184978084 -0.3611455791 0.1887832739 -0.0793257640
[6] -0.4107452787 0.8534246710 0.0705177221 -0.4465521202 0.4008887072
[11] -0.2290553013 -0.2469908873 -0.1673472616 -0.0491534133 -0.1856819776
[16] -0.4209441248 -0.2201206671 0.2881380678 -0.0455382253 0.0010776612
[21] -0.0306015269 -0.1837953741 0.4496835798 -0.0478194778 0.0048134716
[26] 0.0627707878 -0.0856608364 0.0944607899 0.0809150039 -0.1579292795
[31] 0.2855625922 0.0333274091 -0.2802514310 -0.2422188765 -0.3587173504
[36] -0.2192056173 0.1674863734 -0.0296076329 -0.4010633802 -0.3040314873
[41] 0.0825501308 0.3680556775 -0.0887051815 0.5783225311 0.3324230040
[46] 0.0262970701 -0.0004712707 0.1506036837 -0.1443472473 -0.2479062445
[51] -0.4909974847 0.2854150916 -0.4047784466 0.5143596679 -0.0847165883
[56] -0.5150956080 0.5865779730 0.0897430328 0.0929679141 -0.5442150562
[61] -0.0109005121 -0.4243266846 0.0272803474 -0.3151267608 -0.1176927241
[66] 0.4825882684 0.0427748293 0.1934252723 -0.1976327269 0.4301409505
[71] -0.0500970508 0.2648090024 0.1725507674 -0.3513327128 -0.4551871250
[76] -0.6316262755 0.2989853597 -0.4144587754 0.3148130059 0.1314379775
[81] -0.1465926469 -0.4509354616 0.1903474466 0.0495208734 -0.1710030666
[86] -0.0967303001 -0.0981391432 -0.2194175011 0.0022316648 -0.4263840990
[91] 0.5885188110 -0.4472767907 0.5256190646 0.2613430062 0.0406260937
[96] -0.1227488299 -0.3015984672 -0.2698684213 -0.9142991216 -0.1719764202
[101] 0.5291512286 -0.5989816362 0.3010445533 0.1444679035 -0.0017575551
[106] -0.5496031772 0.3915229707 -0.0006373665 0.1995004008 0.4348695638
[111] -0.0662901996 -0.2225386047 0.3367292814 0.7700394157 -0.4166529156
[116] -0.1511476307 -0.2884341371 0.1724746019 -0.1446629082 -0.0620516651
[121] 0.3536132498 -0.3299026656 0.0487072551 0.0820066503 -0.0685958340
[126] -0.1067741216 0.8630036216 -0.1613815291 0.1514437234 0.1319444365
[131] 0.0241855480 -0.5166862487 -0.0206726452 -0.4678664250 -0.0526463962
[136] -0.1567801711 0.4365296602 0.4513934065 0.3987951077 0.0163702687
[141] 0.2220017646 -0.4612282238 -0.0554927088 0.2208541302 -0.0746384431
[146] 0.1549956283 0.7760813912 -0.0978778611 0.1045444979 0.1858748461
[151] 0.0261746919 -0.2794567589 -0.5594067599 -0.2901645204 0.0173241806
[156] -0.2994507927 -0.1070833126 0.2489342382 -0.1035560904 -0.2319760931
[161] 0.0030867991 0.0444010946 -0.2730017812 -0.3667620272 0.1164767242
[166] -0.2798272787 0.3379127204 -0.8133750171 -0.2182712695 -0.1135115917
[171] -0.2155529027 -0.0696402476 -0.0452475292 -0.1963190422 -0.1904478254
[176] -0.1300009825 0.1678079739 -0.2845471860 0.1393598771 -0.0089817641
[181] 0.0502994616 -0.1444643432 0.0572998007 -0.2703512499 -0.3858473675
[186] 0.1082759879 0.4624905109 0.2641707627 0.2367233885 -0.1977461748
[191] 0.0555657205 -0.7303958625 0.3320525272 -0.0350119199 0.1413376203
[196] 0.2995533894 0.4727051568 0.1507514708 0.0989708088 0.0991941184
[201] 0.0403087788 -0.4191392030 -0.0928702935 0.0220608257 -0.8031912381
[206] 0.0983474013 -0.6241363638 0.2559060695 0.7731521436 0.1313473563
[211] -0.2173434442 0.1195140034 -0.7189651151 -0.0281518218 -0.0311362908
[216] 0.0998503801 0.3828991942 -0.1668602121 0.1258671590 -0.4894345112
[221] -0.4407696727 0.3089867110 0.7175627737 -0.2258114348 -0.1502383391
[226] -0.0642914852 -0.0559211215 -0.3272769799 0.2365640858 0.4259091391
>
> proc.time()
user system elapsed
2.31 14.32 29.53
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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: 0x00000241cb7fe4d0>
> .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: 0x00000241cb7fe4d0>
> .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: 0x00000241cb7fe4d0>
> .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: 0x00000241cb7fe4d0>
> 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: 0x00000241cb7fe8f0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000241cb7fe8f0>
> .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: 0x00000241cb7fe8f0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000241cb7fe8f0>
> .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: 0x00000241cb7fe8f0>
> 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: 0x00000241cb7fead0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000241cb7fead0>
> .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: 0x00000241cb7fead0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x00000241cb7fead0>
> .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: 0x00000241cb7fead0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x00000241cb7fead0>
> .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: 0x00000241cb7fead0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x00000241cb7fead0>
> .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: 0x00000241cb7fead0>
> 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: 0x00000241cb7fee90>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x00000241cb7fee90>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000241cb7fee90>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000241cb7fee90>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile30c1c4be8111a" "BufferedMatrixFile30c1c7eb462ca"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile30c1c4be8111a" "BufferedMatrixFile30c1c7eb462ca"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000241cb7feef0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000241cb7feef0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x00000241cb7feef0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x00000241cb7feef0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x00000241cb7feef0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x00000241cb7feef0>
> .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: 0x00000241cd1ffad0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000241cd1ffad0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x00000241cd1ffad0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x00000241cd1ffad0>
> 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: 0x00000241cd1ff9b0>
> .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: 0x00000241cd1ff9b0>
> rm(P)
>
> proc.time()
user system elapsed
0.26 0.07 0.43
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.18 0.07 0.25