Ben Bolstad
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_20 |
| git_last_commit: 32b6f6a |
| git_last_commit_date: 2024-10-29 09:27:20 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:05 -0500 (Thu, 09 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 251/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.70.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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: 1.70.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BufferedMatrix_1.70.0.tar.gz |
| StartedAt: 2025-01-02 23:38:53 -0500 (Thu, 02 Jan 2025) |
| EndedAt: 2025-01-02 23:44:56 -0500 (Thu, 02 Jan 2025) |
| EllapsedTime: 362.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BufferedMatrix_1.70.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BufferedMatrix/DESCRIPTION' ... OK
* this is package 'BufferedMatrix' version '1.70.0'
* 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) 13.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... 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-3.20-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
'F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/00check.log'
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'BufferedMatrix' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc -I"F:/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"F:/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"F:/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"F:/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 -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
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
0.40 0.07 2.81
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
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-3.20-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 468478 25.1 1021802 54.6 633411 33.9
Vcells 853910 6.6 8388608 64.0 2003128 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 Jan 2 23:39:39 2025"
> 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 Jan 2 23:39:45 2025"
>
>
> 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: 0x000001a6950fa890>
>
>
>
> 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 Jan 2 23:41:03 2025"
> 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 Jan 2 23:41:25 2025"
>
> ColMode(tmp2)
<pointer: 0x000001a6950fa890>
>
>
>
> ### 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,] 100.63697640 0.4060968 -0.01958948 -0.8801770
[2,] 0.39761621 -1.0217144 -0.13043905 1.3854965
[3,] -0.03795614 1.0698066 0.29266603 -0.5361793
[4,] -0.96614291 -0.6675656 -0.47742083 -1.3950338
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-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,] 100.63697640 0.4060968 0.01958948 0.8801770
[2,] 0.39761621 1.0217144 0.13043905 1.3854965
[3,] 0.03795614 1.0698066 0.29266603 0.5361793
[4,] 0.96614291 0.6675656 0.47742083 1.3950338
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-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,] 10.0317983 0.6372572 0.1399624 0.9381775
[2,] 0.6305682 1.0107989 0.3611635 1.1770711
[3,] 0.1948234 1.0343145 0.5409862 0.7322426
[4,] 0.9829257 0.8170469 0.6909565 1.1811155
>
> 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-3.20-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,] 225.95496 31.77867 26.41921 35.26195
[2,] 31.70330 36.12970 28.74207 38.15621
[3,] 26.98619 36.41295 30.70253 32.85861
[4,] 35.79540 33.83803 32.38699 38.20619
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x000001a6950fa530>
> exp(tmp5)
<pointer: 0x000001a6950fa530>
> log(tmp5,2)
<pointer: 0x000001a6950fa530>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 470.2956
> Min(tmp5)
[1] 53.73005
> mean(tmp5)
[1] 72.94842
> Sum(tmp5)
[1] 14589.68
> Var(tmp5)
[1] 872.0504
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.38613 70.27019 67.43689 73.51831 70.15526 68.52469 73.29912 70.59562
[9] 71.92441 72.37362
> rowSums(tmp5)
[1] 1827.723 1405.404 1348.738 1470.366 1403.105 1370.494 1465.982 1411.912
[9] 1438.488 1447.472
> rowVars(tmp5)
[1] 8049.74409 75.48520 97.96135 94.50228 62.73880 83.59153
[7] 81.24333 64.69312 42.65462 47.03766
> rowSd(tmp5)
[1] 89.720366 8.688222 9.897543 9.721228 7.920783 9.142840 9.013508
[8] 8.043203 6.531050 6.858401
> rowMax(tmp5)
[1] 470.29564 84.08675 95.26696 89.71407 92.35135 83.73548 89.48767
[8] 82.16089 85.70353 84.50565
> rowMin(tmp5)
[1] 54.98813 58.01213 55.10556 54.86796 59.41856 53.73005 57.85517 55.49511
[9] 58.29583 61.76797
>
> colMeans(tmp5)
[1] 108.32110 72.40172 66.37090 71.17687 72.81160 69.92916 70.67461
[8] 72.32872 73.03977 70.60832 73.27365 69.37099 71.62681 72.41978
[15] 66.51349 70.67374 76.92302 69.26387 71.40145 69.83893
> colSums(tmp5)
[1] 1083.2110 724.0172 663.7090 711.7687 728.1160 699.2916 706.7461
[8] 723.2872 730.3977 706.0832 732.7365 693.7099 716.2681 724.1978
[15] 665.1349 706.7374 769.2302 692.6387 714.0145 698.3893
> colVars(tmp5)
[1] 16245.50091 53.48162 37.00670 77.63434 153.00701 51.23584
[7] 88.25907 43.26509 96.81066 73.87117 123.23200 67.78652
[13] 51.26246 154.49403 48.81285 56.67169 43.69404 79.51285
[19] 57.16180 100.36064
> colSd(tmp5)
[1] 127.457840 7.313113 6.083313 8.811035 12.369600 7.157921
[7] 9.394630 6.577620 9.839241 8.594834 11.100991 8.233257
[13] 7.159781 12.429563 6.986619 7.528060 6.610147 8.916998
[19] 7.560542 10.018016
> colMax(tmp5)
[1] 470.29564 85.70353 74.55373 82.17525 89.71407 78.42334 88.92153
[8] 82.16089 89.48767 84.55635 92.35135 81.17884 79.79558 95.26696
[15] 79.00112 84.02184 84.24209 88.73897 85.67131 86.78365
> colMin(tmp5)
[1] 56.16822 64.01676 54.98813 56.99792 53.73005 54.86796 55.10556 62.43926
[9] 59.38679 57.85517 60.90935 57.13114 58.01213 58.29583 55.49511 60.26923
[17] 66.02789 58.40903 59.58223 56.82168
>
>
> ### 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] 91.38613 70.27019 67.43689 NA 70.15526 68.52469 73.29912 70.59562
[9] 71.92441 72.37362
> rowSums(tmp5)
[1] 1827.723 1405.404 1348.738 NA 1403.105 1370.494 1465.982 1411.912
[9] 1438.488 1447.472
> rowVars(tmp5)
[1] 8049.74409 75.48520 97.96135 96.92773 62.73880 83.59153
[7] 81.24333 64.69312 42.65462 47.03766
> rowSd(tmp5)
[1] 89.720366 8.688222 9.897543 9.845188 7.920783 9.142840 9.013508
[8] 8.043203 6.531050 6.858401
> rowMax(tmp5)
[1] 470.29564 84.08675 95.26696 NA 92.35135 83.73548 89.48767
[8] 82.16089 85.70353 84.50565
> rowMin(tmp5)
[1] 54.98813 58.01213 55.10556 NA 59.41856 53.73005 57.85517 55.49511
[9] 58.29583 61.76797
>
> colMeans(tmp5)
[1] 108.32110 72.40172 66.37090 71.17687 72.81160 69.92916 70.67461
[8] 72.32872 73.03977 70.60832 73.27365 69.37099 71.62681 72.41978
[15] 66.51349 70.67374 76.92302 69.26387 NA 69.83893
> colSums(tmp5)
[1] 1083.2110 724.0172 663.7090 711.7687 728.1160 699.2916 706.7461
[8] 723.2872 730.3977 706.0832 732.7365 693.7099 716.2681 724.1978
[15] 665.1349 706.7374 769.2302 692.6387 NA 698.3893
> colVars(tmp5)
[1] 16245.50091 53.48162 37.00670 77.63434 153.00701 51.23584
[7] 88.25907 43.26509 96.81066 73.87117 123.23200 67.78652
[13] 51.26246 154.49403 48.81285 56.67169 43.69404 79.51285
[19] NA 100.36064
> colSd(tmp5)
[1] 127.457840 7.313113 6.083313 8.811035 12.369600 7.157921
[7] 9.394630 6.577620 9.839241 8.594834 11.100991 8.233257
[13] 7.159781 12.429563 6.986619 7.528060 6.610147 8.916998
[19] NA 10.018016
> colMax(tmp5)
[1] 470.29564 85.70353 74.55373 82.17525 89.71407 78.42334 88.92153
[8] 82.16089 89.48767 84.55635 92.35135 81.17884 79.79558 95.26696
[15] 79.00112 84.02184 84.24209 88.73897 NA 86.78365
> colMin(tmp5)
[1] 56.16822 64.01676 54.98813 56.99792 53.73005 54.86796 55.10556 62.43926
[9] 59.38679 57.85517 60.90935 57.13114 58.01213 58.29583 55.49511 60.26923
[17] 66.02789 58.40903 NA 56.82168
>
> Max(tmp5,na.rm=TRUE)
[1] 470.2956
> Min(tmp5,na.rm=TRUE)
[1] 53.73005
> mean(tmp5,na.rm=TRUE)
[1] 72.98048
> Sum(tmp5,na.rm=TRUE)
[1] 14523.12
> Var(tmp5,na.rm=TRUE)
[1] 876.2481
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.38613 70.27019 67.43689 73.88410 70.15526 68.52469 73.29912 70.59562
[9] 71.92441 72.37362
> rowSums(tmp5,na.rm=TRUE)
[1] 1827.723 1405.404 1348.738 1403.798 1403.105 1370.494 1465.982 1411.912
[9] 1438.488 1447.472
> rowVars(tmp5,na.rm=TRUE)
[1] 8049.74409 75.48520 97.96135 96.92773 62.73880 83.59153
[7] 81.24333 64.69312 42.65462 47.03766
> rowSd(tmp5,na.rm=TRUE)
[1] 89.720366 8.688222 9.897543 9.845188 7.920783 9.142840 9.013508
[8] 8.043203 6.531050 6.858401
> rowMax(tmp5,na.rm=TRUE)
[1] 470.29564 84.08675 95.26696 89.71407 92.35135 83.73548 89.48767
[8] 82.16089 85.70353 84.50565
> rowMin(tmp5,na.rm=TRUE)
[1] 54.98813 58.01213 55.10556 54.86796 59.41856 53.73005 57.85517 55.49511
[9] 58.29583 61.76797
>
> colMeans(tmp5,na.rm=TRUE)
[1] 108.32110 72.40172 66.37090 71.17687 72.81160 69.92916 70.67461
[8] 72.32872 73.03977 70.60832 73.27365 69.37099 71.62681 72.41978
[15] 66.51349 70.67374 76.92302 69.26387 71.93846 69.83893
> colSums(tmp5,na.rm=TRUE)
[1] 1083.2110 724.0172 663.7090 711.7687 728.1160 699.2916 706.7461
[8] 723.2872 730.3977 706.0832 732.7365 693.7099 716.2681 724.1978
[15] 665.1349 706.7374 769.2302 692.6387 647.4462 698.3893
> colVars(tmp5,na.rm=TRUE)
[1] 16245.50091 53.48162 37.00670 77.63434 153.00701 51.23584
[7] 88.25907 43.26509 96.81066 73.87117 123.23200 67.78652
[13] 51.26246 154.49403 48.81285 56.67169 43.69404 79.51285
[19] 61.06273 100.36064
> colSd(tmp5,na.rm=TRUE)
[1] 127.457840 7.313113 6.083313 8.811035 12.369600 7.157921
[7] 9.394630 6.577620 9.839241 8.594834 11.100991 8.233257
[13] 7.159781 12.429563 6.986619 7.528060 6.610147 8.916998
[19] 7.814265 10.018016
> colMax(tmp5,na.rm=TRUE)
[1] 470.29564 85.70353 74.55373 82.17525 89.71407 78.42334 88.92153
[8] 82.16089 89.48767 84.55635 92.35135 81.17884 79.79558 95.26696
[15] 79.00112 84.02184 84.24209 88.73897 85.67131 86.78365
> colMin(tmp5,na.rm=TRUE)
[1] 56.16822 64.01676 54.98813 56.99792 53.73005 54.86796 55.10556 62.43926
[9] 59.38679 57.85517 60.90935 57.13114 58.01213 58.29583 55.49511 60.26923
[17] 66.02789 58.40903 59.58223 56.82168
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.38613 70.27019 67.43689 NaN 70.15526 68.52469 73.29912 70.59562
[9] 71.92441 72.37362
> rowSums(tmp5,na.rm=TRUE)
[1] 1827.723 1405.404 1348.738 0.000 1403.105 1370.494 1465.982 1411.912
[9] 1438.488 1447.472
> rowVars(tmp5,na.rm=TRUE)
[1] 8049.74409 75.48520 97.96135 NA 62.73880 83.59153
[7] 81.24333 64.69312 42.65462 47.03766
> rowSd(tmp5,na.rm=TRUE)
[1] 89.720366 8.688222 9.897543 NA 7.920783 9.142840 9.013508
[8] 8.043203 6.531050 6.858401
> rowMax(tmp5,na.rm=TRUE)
[1] 470.29564 84.08675 95.26696 NA 92.35135 83.73548 89.48767
[8] 82.16089 85.70353 84.50565
> rowMin(tmp5,na.rm=TRUE)
[1] 54.98813 58.01213 55.10556 NA 59.41856 53.73005 57.85517 55.49511
[9] 58.29583 61.76797
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 112.07861 72.62086 66.25552 70.24972 70.93355 71.60262 68.64718
[8] 73.42755 73.84391 71.65012 72.84712 68.85277 71.54298 71.76780
[15] 65.12597 69.19062 78.13359 67.09997 NaN 69.89315
> colSums(tmp5,na.rm=TRUE)
[1] 1008.7075 653.5878 596.2997 632.2475 638.4019 644.4236 617.8246
[8] 660.8480 664.5952 644.8511 655.6241 619.6749 643.8868 645.9102
[15] 586.1337 622.7156 703.2023 603.8997 0.0000 629.0383
> colVars(tmp5,na.rm=TRUE)
[1] 18117.35045 59.62656 41.48279 77.66816 132.45325 26.13483
[7] 53.04839 35.08967 101.63729 70.89496 136.58935 73.23862
[13] 57.59119 169.02374 33.25598 39.00959 32.66915 36.77425
[19] NA 112.87266
> colSd(tmp5,na.rm=TRUE)
[1] 134.600707 7.721824 6.440713 8.812954 11.508833 5.112223
[7] 7.283433 5.923654 10.081532 8.419915 11.687145 8.557956
[13] 7.588886 13.000913 5.766800 6.245766 5.715694 6.064177
[19] NA 10.624154
> colMax(tmp5,na.rm=TRUE)
[1] 470.29564 85.70353 74.55373 82.17525 86.63355 78.42334 76.73124
[8] 82.16089 89.48767 84.55635 92.35135 81.17884 79.79558 95.26696
[15] 75.97718 79.00804 84.24209 78.79872 -Inf 86.78365
> colMin(tmp5,na.rm=TRUE)
[1] 56.16822 64.01676 54.98813 56.99792 53.73005 61.61163 55.10556 65.68347
[9] 59.38679 57.85517 60.90935 57.13114 58.01213 58.29583 55.49511 60.26923
[17] 69.10452 58.40903 Inf 56.82168
>
>
>
>
> 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] 132.8914 193.3169 396.0614 243.9357 256.5203 194.5097 193.4299 219.9724
[9] 146.8604 134.6546
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 132.8914 193.3169 396.0614 243.9357 256.5203 194.5097 193.4299 219.9724
[9] 146.8604 134.6546
>
>
>
> 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] 0.000000e+00 -2.842171e-14 -2.842171e-14 5.684342e-14 -5.684342e-14
[6] -2.842171e-14 -5.684342e-14 5.684342e-14 1.136868e-13 1.136868e-13
[11] -5.684342e-14 0.000000e+00 5.684342e-14 -8.526513e-14 -8.526513e-14
[16] -8.526513e-14 -2.842171e-14 1.705303e-13 -2.842171e-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)
+ }
10 12
4 19
6 17
4 1
9 16
9 2
10 17
7 5
7 20
8 10
2 19
8 15
9 9
1 14
10 16
4 9
2 20
2 3
8 11
1 15
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] 2.74193
> Min(tmp)
[1] -1.638504
> mean(tmp)
[1] 0.09807583
> Sum(tmp)
[1] 9.807583
> Var(tmp)
[1] 0.7959642
>
> rowMeans(tmp)
[1] 0.09807583
> rowSums(tmp)
[1] 9.807583
> rowVars(tmp)
[1] 0.7959642
> rowSd(tmp)
[1] 0.8921683
> rowMax(tmp)
[1] 2.74193
> rowMin(tmp)
[1] -1.638504
>
> colMeans(tmp)
[1] 0.266780302 -1.385240463 -0.328497198 -0.358193454 -1.638503896
[6] -0.518308188 -0.533664923 -0.661992596 -0.744826698 0.275301641
[11] -0.984526552 -0.782650887 0.189105856 -0.488662590 -0.679058543
[16] 0.197296758 0.315984738 0.604549352 0.053514007 0.988255124
[21] 0.235879034 -0.046589037 -1.349360638 0.041229598 1.445216264
[26] -0.384355484 1.799066595 0.607552629 0.810098102 0.120225542
[31] -0.038144064 -0.107184960 -1.488030194 -0.063037205 0.207380455
[36] -0.987542061 -0.288692341 -1.049847244 1.333258241 0.821974433
[41] 0.147120025 0.552374329 -1.150882491 0.934643795 1.939455171
[46] -0.633795649 0.538702291 -0.180331578 -0.842417822 -0.212718680
[51] -0.751908613 -0.022704523 0.403193388 0.105986713 0.929471576
[56] 0.297806837 1.610493642 0.828213230 2.741930083 -0.879962545
[61] -0.376166034 1.448374115 1.006186368 -0.734869445 -0.348115586
[66] -0.238395668 -1.308816137 2.640982766 0.626998468 0.700022763
[71] -0.211936579 -0.438391489 -0.062517795 1.150487984 -0.781679195
[76] 0.947090456 0.454414276 0.787889987 -0.033541555 0.092435260
[81] -0.003415863 1.995851979 0.049249360 0.616403766 0.676339123
[86] -0.614150834 -0.762148889 0.612176965 1.216256137 0.285323566
[91] -0.225802983 -0.358259204 0.580246727 1.294273327 -1.306836960
[96] 0.959048186 -0.904710149 0.336662905 -0.259902095 -1.459903494
> colSums(tmp)
[1] 0.266780302 -1.385240463 -0.328497198 -0.358193454 -1.638503896
[6] -0.518308188 -0.533664923 -0.661992596 -0.744826698 0.275301641
[11] -0.984526552 -0.782650887 0.189105856 -0.488662590 -0.679058543
[16] 0.197296758 0.315984738 0.604549352 0.053514007 0.988255124
[21] 0.235879034 -0.046589037 -1.349360638 0.041229598 1.445216264
[26] -0.384355484 1.799066595 0.607552629 0.810098102 0.120225542
[31] -0.038144064 -0.107184960 -1.488030194 -0.063037205 0.207380455
[36] -0.987542061 -0.288692341 -1.049847244 1.333258241 0.821974433
[41] 0.147120025 0.552374329 -1.150882491 0.934643795 1.939455171
[46] -0.633795649 0.538702291 -0.180331578 -0.842417822 -0.212718680
[51] -0.751908613 -0.022704523 0.403193388 0.105986713 0.929471576
[56] 0.297806837 1.610493642 0.828213230 2.741930083 -0.879962545
[61] -0.376166034 1.448374115 1.006186368 -0.734869445 -0.348115586
[66] -0.238395668 -1.308816137 2.640982766 0.626998468 0.700022763
[71] -0.211936579 -0.438391489 -0.062517795 1.150487984 -0.781679195
[76] 0.947090456 0.454414276 0.787889987 -0.033541555 0.092435260
[81] -0.003415863 1.995851979 0.049249360 0.616403766 0.676339123
[86] -0.614150834 -0.762148889 0.612176965 1.216256137 0.285323566
[91] -0.225802983 -0.358259204 0.580246727 1.294273327 -1.306836960
[96] 0.959048186 -0.904710149 0.336662905 -0.259902095 -1.459903494
> 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] 0.266780302 -1.385240463 -0.328497198 -0.358193454 -1.638503896
[6] -0.518308188 -0.533664923 -0.661992596 -0.744826698 0.275301641
[11] -0.984526552 -0.782650887 0.189105856 -0.488662590 -0.679058543
[16] 0.197296758 0.315984738 0.604549352 0.053514007 0.988255124
[21] 0.235879034 -0.046589037 -1.349360638 0.041229598 1.445216264
[26] -0.384355484 1.799066595 0.607552629 0.810098102 0.120225542
[31] -0.038144064 -0.107184960 -1.488030194 -0.063037205 0.207380455
[36] -0.987542061 -0.288692341 -1.049847244 1.333258241 0.821974433
[41] 0.147120025 0.552374329 -1.150882491 0.934643795 1.939455171
[46] -0.633795649 0.538702291 -0.180331578 -0.842417822 -0.212718680
[51] -0.751908613 -0.022704523 0.403193388 0.105986713 0.929471576
[56] 0.297806837 1.610493642 0.828213230 2.741930083 -0.879962545
[61] -0.376166034 1.448374115 1.006186368 -0.734869445 -0.348115586
[66] -0.238395668 -1.308816137 2.640982766 0.626998468 0.700022763
[71] -0.211936579 -0.438391489 -0.062517795 1.150487984 -0.781679195
[76] 0.947090456 0.454414276 0.787889987 -0.033541555 0.092435260
[81] -0.003415863 1.995851979 0.049249360 0.616403766 0.676339123
[86] -0.614150834 -0.762148889 0.612176965 1.216256137 0.285323566
[91] -0.225802983 -0.358259204 0.580246727 1.294273327 -1.306836960
[96] 0.959048186 -0.904710149 0.336662905 -0.259902095 -1.459903494
> colMin(tmp)
[1] 0.266780302 -1.385240463 -0.328497198 -0.358193454 -1.638503896
[6] -0.518308188 -0.533664923 -0.661992596 -0.744826698 0.275301641
[11] -0.984526552 -0.782650887 0.189105856 -0.488662590 -0.679058543
[16] 0.197296758 0.315984738 0.604549352 0.053514007 0.988255124
[21] 0.235879034 -0.046589037 -1.349360638 0.041229598 1.445216264
[26] -0.384355484 1.799066595 0.607552629 0.810098102 0.120225542
[31] -0.038144064 -0.107184960 -1.488030194 -0.063037205 0.207380455
[36] -0.987542061 -0.288692341 -1.049847244 1.333258241 0.821974433
[41] 0.147120025 0.552374329 -1.150882491 0.934643795 1.939455171
[46] -0.633795649 0.538702291 -0.180331578 -0.842417822 -0.212718680
[51] -0.751908613 -0.022704523 0.403193388 0.105986713 0.929471576
[56] 0.297806837 1.610493642 0.828213230 2.741930083 -0.879962545
[61] -0.376166034 1.448374115 1.006186368 -0.734869445 -0.348115586
[66] -0.238395668 -1.308816137 2.640982766 0.626998468 0.700022763
[71] -0.211936579 -0.438391489 -0.062517795 1.150487984 -0.781679195
[76] 0.947090456 0.454414276 0.787889987 -0.033541555 0.092435260
[81] -0.003415863 1.995851979 0.049249360 0.616403766 0.676339123
[86] -0.614150834 -0.762148889 0.612176965 1.216256137 0.285323566
[91] -0.225802983 -0.358259204 0.580246727 1.294273327 -1.306836960
[96] 0.959048186 -0.904710149 0.336662905 -0.259902095 -1.459903494
> colMedians(tmp)
[1] 0.266780302 -1.385240463 -0.328497198 -0.358193454 -1.638503896
[6] -0.518308188 -0.533664923 -0.661992596 -0.744826698 0.275301641
[11] -0.984526552 -0.782650887 0.189105856 -0.488662590 -0.679058543
[16] 0.197296758 0.315984738 0.604549352 0.053514007 0.988255124
[21] 0.235879034 -0.046589037 -1.349360638 0.041229598 1.445216264
[26] -0.384355484 1.799066595 0.607552629 0.810098102 0.120225542
[31] -0.038144064 -0.107184960 -1.488030194 -0.063037205 0.207380455
[36] -0.987542061 -0.288692341 -1.049847244 1.333258241 0.821974433
[41] 0.147120025 0.552374329 -1.150882491 0.934643795 1.939455171
[46] -0.633795649 0.538702291 -0.180331578 -0.842417822 -0.212718680
[51] -0.751908613 -0.022704523 0.403193388 0.105986713 0.929471576
[56] 0.297806837 1.610493642 0.828213230 2.741930083 -0.879962545
[61] -0.376166034 1.448374115 1.006186368 -0.734869445 -0.348115586
[66] -0.238395668 -1.308816137 2.640982766 0.626998468 0.700022763
[71] -0.211936579 -0.438391489 -0.062517795 1.150487984 -0.781679195
[76] 0.947090456 0.454414276 0.787889987 -0.033541555 0.092435260
[81] -0.003415863 1.995851979 0.049249360 0.616403766 0.676339123
[86] -0.614150834 -0.762148889 0.612176965 1.216256137 0.285323566
[91] -0.225802983 -0.358259204 0.580246727 1.294273327 -1.306836960
[96] 0.959048186 -0.904710149 0.336662905 -0.259902095 -1.459903494
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.2667803 -1.38524 -0.3284972 -0.3581935 -1.638504 -0.5183082 -0.5336649
[2,] 0.2667803 -1.38524 -0.3284972 -0.3581935 -1.638504 -0.5183082 -0.5336649
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.6619926 -0.7448267 0.2753016 -0.9845266 -0.7826509 0.1891059 -0.4886626
[2,] -0.6619926 -0.7448267 0.2753016 -0.9845266 -0.7826509 0.1891059 -0.4886626
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.6790585 0.1972968 0.3159847 0.6045494 0.05351401 0.9882551 0.235879
[2,] -0.6790585 0.1972968 0.3159847 0.6045494 0.05351401 0.9882551 0.235879
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.04658904 -1.349361 0.0412296 1.445216 -0.3843555 1.799067 0.6075526
[2,] -0.04658904 -1.349361 0.0412296 1.445216 -0.3843555 1.799067 0.6075526
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.8100981 0.1202255 -0.03814406 -0.107185 -1.48803 -0.06303721 0.2073805
[2,] 0.8100981 0.1202255 -0.03814406 -0.107185 -1.48803 -0.06303721 0.2073805
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.9875421 -0.2886923 -1.049847 1.333258 0.8219744 0.14712 0.5523743
[2,] -0.9875421 -0.2886923 -1.049847 1.333258 0.8219744 0.14712 0.5523743
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -1.150882 0.9346438 1.939455 -0.6337956 0.5387023 -0.1803316 -0.8424178
[2,] -1.150882 0.9346438 1.939455 -0.6337956 0.5387023 -0.1803316 -0.8424178
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.2127187 -0.7519086 -0.02270452 0.4031934 0.1059867 0.9294716 0.2978068
[2,] -0.2127187 -0.7519086 -0.02270452 0.4031934 0.1059867 0.9294716 0.2978068
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 1.610494 0.8282132 2.74193 -0.8799625 -0.376166 1.448374 1.006186
[2,] 1.610494 0.8282132 2.74193 -0.8799625 -0.376166 1.448374 1.006186
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -0.7348694 -0.3481156 -0.2383957 -1.308816 2.640983 0.6269985 0.7000228
[2,] -0.7348694 -0.3481156 -0.2383957 -1.308816 2.640983 0.6269985 0.7000228
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.2119366 -0.4383915 -0.06251779 1.150488 -0.7816792 0.9470905 0.4544143
[2,] -0.2119366 -0.4383915 -0.06251779 1.150488 -0.7816792 0.9470905 0.4544143
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.78789 -0.03354156 0.09243526 -0.003415863 1.995852 0.04924936 0.6164038
[2,] 0.78789 -0.03354156 0.09243526 -0.003415863 1.995852 0.04924936 0.6164038
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.6763391 -0.6141508 -0.7621489 0.612177 1.216256 0.2853236 -0.225803
[2,] 0.6763391 -0.6141508 -0.7621489 0.612177 1.216256 0.2853236 -0.225803
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.3582592 0.5802467 1.294273 -1.306837 0.9590482 -0.9047101 0.3366629
[2,] -0.3582592 0.5802467 1.294273 -1.306837 0.9590482 -0.9047101 0.3366629
[,99] [,100]
[1,] -0.2599021 -1.459903
[2,] -0.2599021 -1.459903
>
>
> Max(tmp2)
[1] 3.206771
> Min(tmp2)
[1] -2.197405
> mean(tmp2)
[1] 0.05137597
> Sum(tmp2)
[1] 5.137597
> Var(tmp2)
[1] 0.9855723
>
> rowMeans(tmp2)
[1] 1.406426826 -0.850961900 -0.586613727 0.086254937 -0.677302708
[6] 0.685097472 1.090338287 1.056878301 -0.741386695 0.081520040
[11] 0.493040379 0.970831567 0.849078735 0.247663617 -1.265358621
[16] 1.034864782 -0.252829742 2.043326648 0.893301310 -2.088914230
[21] -0.004144960 0.958303701 -0.998983347 -0.465704913 0.260639460
[26] 0.259596326 -0.339760793 0.468536621 0.462320287 1.651801204
[31] 0.897634236 -0.113517088 1.342734956 0.215842106 1.119299049
[36] 0.448783094 0.194847501 -0.948415759 -0.657287803 1.345242005
[41] 0.615913336 0.688847446 -0.585293890 1.850660735 -0.788976253
[46] -0.372305730 0.539020624 1.118849001 1.342716016 -1.900238534
[51] -0.467719512 -0.740219631 0.038155132 0.163397996 -0.304649684
[56] -0.272123610 0.728254270 0.964292545 3.206771356 0.142553955
[61] -2.197405262 -0.628738225 -0.292284958 -1.100714001 1.362983627
[66] -1.475554553 -0.191188635 0.363618312 -0.032331331 -0.268905010
[71] 1.462903850 -0.506136351 -0.991540338 1.137968358 -0.810869567
[76] 1.179669729 -0.250759482 -1.759323605 0.791662639 -1.053414883
[81] -0.635919208 1.563180684 -0.972202689 0.005233318 0.148085582
[86] -0.231607297 -0.737978077 0.672730409 -0.579687944 -1.222834935
[91] 0.925207504 -1.490820562 0.004511866 -2.085334894 0.362921827
[96] 0.278834279 -0.228801639 -1.392242572 0.020113204 -0.546358586
> rowSums(tmp2)
[1] 1.406426826 -0.850961900 -0.586613727 0.086254937 -0.677302708
[6] 0.685097472 1.090338287 1.056878301 -0.741386695 0.081520040
[11] 0.493040379 0.970831567 0.849078735 0.247663617 -1.265358621
[16] 1.034864782 -0.252829742 2.043326648 0.893301310 -2.088914230
[21] -0.004144960 0.958303701 -0.998983347 -0.465704913 0.260639460
[26] 0.259596326 -0.339760793 0.468536621 0.462320287 1.651801204
[31] 0.897634236 -0.113517088 1.342734956 0.215842106 1.119299049
[36] 0.448783094 0.194847501 -0.948415759 -0.657287803 1.345242005
[41] 0.615913336 0.688847446 -0.585293890 1.850660735 -0.788976253
[46] -0.372305730 0.539020624 1.118849001 1.342716016 -1.900238534
[51] -0.467719512 -0.740219631 0.038155132 0.163397996 -0.304649684
[56] -0.272123610 0.728254270 0.964292545 3.206771356 0.142553955
[61] -2.197405262 -0.628738225 -0.292284958 -1.100714001 1.362983627
[66] -1.475554553 -0.191188635 0.363618312 -0.032331331 -0.268905010
[71] 1.462903850 -0.506136351 -0.991540338 1.137968358 -0.810869567
[76] 1.179669729 -0.250759482 -1.759323605 0.791662639 -1.053414883
[81] -0.635919208 1.563180684 -0.972202689 0.005233318 0.148085582
[86] -0.231607297 -0.737978077 0.672730409 -0.579687944 -1.222834935
[91] 0.925207504 -1.490820562 0.004511866 -2.085334894 0.362921827
[96] 0.278834279 -0.228801639 -1.392242572 0.020113204 -0.546358586
> 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] 1.406426826 -0.850961900 -0.586613727 0.086254937 -0.677302708
[6] 0.685097472 1.090338287 1.056878301 -0.741386695 0.081520040
[11] 0.493040379 0.970831567 0.849078735 0.247663617 -1.265358621
[16] 1.034864782 -0.252829742 2.043326648 0.893301310 -2.088914230
[21] -0.004144960 0.958303701 -0.998983347 -0.465704913 0.260639460
[26] 0.259596326 -0.339760793 0.468536621 0.462320287 1.651801204
[31] 0.897634236 -0.113517088 1.342734956 0.215842106 1.119299049
[36] 0.448783094 0.194847501 -0.948415759 -0.657287803 1.345242005
[41] 0.615913336 0.688847446 -0.585293890 1.850660735 -0.788976253
[46] -0.372305730 0.539020624 1.118849001 1.342716016 -1.900238534
[51] -0.467719512 -0.740219631 0.038155132 0.163397996 -0.304649684
[56] -0.272123610 0.728254270 0.964292545 3.206771356 0.142553955
[61] -2.197405262 -0.628738225 -0.292284958 -1.100714001 1.362983627
[66] -1.475554553 -0.191188635 0.363618312 -0.032331331 -0.268905010
[71] 1.462903850 -0.506136351 -0.991540338 1.137968358 -0.810869567
[76] 1.179669729 -0.250759482 -1.759323605 0.791662639 -1.053414883
[81] -0.635919208 1.563180684 -0.972202689 0.005233318 0.148085582
[86] -0.231607297 -0.737978077 0.672730409 -0.579687944 -1.222834935
[91] 0.925207504 -1.490820562 0.004511866 -2.085334894 0.362921827
[96] 0.278834279 -0.228801639 -1.392242572 0.020113204 -0.546358586
> rowMin(tmp2)
[1] 1.406426826 -0.850961900 -0.586613727 0.086254937 -0.677302708
[6] 0.685097472 1.090338287 1.056878301 -0.741386695 0.081520040
[11] 0.493040379 0.970831567 0.849078735 0.247663617 -1.265358621
[16] 1.034864782 -0.252829742 2.043326648 0.893301310 -2.088914230
[21] -0.004144960 0.958303701 -0.998983347 -0.465704913 0.260639460
[26] 0.259596326 -0.339760793 0.468536621 0.462320287 1.651801204
[31] 0.897634236 -0.113517088 1.342734956 0.215842106 1.119299049
[36] 0.448783094 0.194847501 -0.948415759 -0.657287803 1.345242005
[41] 0.615913336 0.688847446 -0.585293890 1.850660735 -0.788976253
[46] -0.372305730 0.539020624 1.118849001 1.342716016 -1.900238534
[51] -0.467719512 -0.740219631 0.038155132 0.163397996 -0.304649684
[56] -0.272123610 0.728254270 0.964292545 3.206771356 0.142553955
[61] -2.197405262 -0.628738225 -0.292284958 -1.100714001 1.362983627
[66] -1.475554553 -0.191188635 0.363618312 -0.032331331 -0.268905010
[71] 1.462903850 -0.506136351 -0.991540338 1.137968358 -0.810869567
[76] 1.179669729 -0.250759482 -1.759323605 0.791662639 -1.053414883
[81] -0.635919208 1.563180684 -0.972202689 0.005233318 0.148085582
[86] -0.231607297 -0.737978077 0.672730409 -0.579687944 -1.222834935
[91] 0.925207504 -1.490820562 0.004511866 -2.085334894 0.362921827
[96] 0.278834279 -0.228801639 -1.392242572 0.020113204 -0.546358586
>
> colMeans(tmp2)
[1] 0.05137597
> colSums(tmp2)
[1] 5.137597
> colVars(tmp2)
[1] 0.9855723
> colSd(tmp2)
[1] 0.9927599
> colMax(tmp2)
[1] 3.206771
> colMin(tmp2)
[1] -2.197405
> colMedians(tmp2)
[1] 0.02913417
> colRanges(tmp2)
[,1]
[1,] -2.197405
[2,] 3.206771
>
> 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] -1.5805664 3.5074737 -4.2854151 0.4854994 -2.2645679 -4.3410172
[7] 2.3109357 -4.7294175 2.4389254 1.0229721
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.15216325
[2,] -1.09941258
[3,] -0.02154166
[4,] 0.85812811
[5,] 1.19481142
>
> rowApply(tmp,sum)
[1] 3.4786723 -5.5593797 -0.4129443 0.1050779 -1.1929085 -2.9188355
[7] -7.1824294 2.1254743 0.6310154 3.4910797
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 7 10 6 6 3 2 1 1 10 8
[2,] 10 1 8 9 7 10 9 4 1 10
[3,] 4 8 3 4 1 4 2 8 9 4
[4,] 3 2 7 2 9 5 5 10 7 9
[5,] 2 5 5 3 2 8 7 2 8 5
[6,] 9 4 1 5 5 1 3 9 6 6
[7,] 5 3 10 8 8 3 8 7 2 7
[8,] 1 6 4 7 4 7 4 3 4 2
[9,] 6 7 9 1 10 6 10 6 5 3
[10,] 8 9 2 10 6 9 6 5 3 1
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.3885386 0.1295419 -4.6164606 0.3527160 0.5961563 4.0561276
[7] -1.0164585 0.1192089 -1.1982698 -1.0178006 0.5434294 0.7681440
[13] -0.0514960 0.7270001 -1.8664816 -0.1988539 -0.9213921 -2.6583147
[19] -1.4159822 -0.3082956
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.8335305
[2,] -0.1214399
[3,] 0.4080492
[4,] 1.0666176
[5,] 1.8688422
>
> rowApply(tmp,sum)
[1] -11.9066053 -1.8506472 0.2266809 2.3164689 4.6251600
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 15 17 2 7 18
[2,] 10 11 15 15 6
[3,] 16 1 1 2 7
[4,] 20 8 11 14 4
[5,] 2 5 9 19 20
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.4080492 -0.6205482 0.5206016 0.8389824 -1.99605540 -0.2969231
[2,] 1.0666176 -0.2985723 -1.4679415 -0.7665283 -1.03254034 2.2302790
[3,] -1.8335305 0.9367693 -2.1866442 0.2102362 0.01421431 1.4474488
[4,] -0.1214399 0.5258879 -1.2603151 0.5081956 1.38156605 0.2517336
[5,] 1.8688422 -0.4139948 -0.2221614 -0.4381699 2.22897171 0.4235892
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.59996192 0.53663032 -2.2167889 -1.7754786 0.5436115 -1.4680734
[2,] 0.49278860 -0.90907585 -0.6656346 1.8288764 1.4202671 0.4720004
[3,] -1.37487011 1.02562573 2.1750668 -0.1599586 -1.4937250 1.4282432
[4,] 0.41349712 -0.03578058 1.0144118 -1.1488055 -0.7431187 0.5341762
[5,] 0.05208782 -0.49819071 -1.5053249 0.2375656 0.8163945 -0.1982025
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -1.5855866 0.2441402 -1.3316081 0.56169601 -1.7569475 -0.6387445
[2,] 0.1367437 -0.8772638 -1.0468097 0.38776583 0.1661983 -1.1200484
[3,] 0.2240678 1.0103007 0.4399175 0.07175944 0.7875386 -1.4657124
[4,] 1.6048689 -1.5426058 0.2935774 -0.32776666 -0.6462213 0.1888827
[5,] -0.4315897 1.8924288 -0.2215587 -0.89230855 0.5280397 0.3773079
[,19] [,20]
[1,] -0.5789882 -0.6946122
[2,] -1.3451616 -0.5226079
[3,] -0.3345565 -0.6955102
[4,] 1.0397311 0.3859940
[5,] -0.1970070 1.2184406
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-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-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 626 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 542 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-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 -0.9881639 0.8424552 -0.1178344 0.9643328 -1.771864 0.144223 -1.29201
col8 col9 col10 col11 col12 col13 col14
row1 -0.08171623 -1.980258 -1.2515 -0.04211254 -0.8626649 -1.119964 -0.0547491
col15 col16 col17 col18 col19 col20
row1 -0.2813378 -0.02463443 1.828854 -0.1705101 -1.62418 1.051869
> tmp[,"col10"]
col10
row1 -1.2514997
row2 -0.8428914
row3 -0.4231374
row4 -0.5335053
row5 0.9521972
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.98816387 0.8424552 -0.1178344 0.9643328 -1.771864 0.144223 -1.292010
row5 0.08117055 -1.1058975 -0.4157133 -1.1161215 2.084823 1.459562 1.074825
col8 col9 col10 col11 col12 col13
row1 -0.08171623 -1.9802579 -1.2514997 -0.04211254 -0.8626649 -1.1199637
row5 -0.56149871 0.4008333 0.9521972 -0.22241848 -0.4527431 0.1439763
col14 col15 col16 col17 col18 col19
row1 -0.0547491 -0.2813378 -0.02463443 1.8288543 -0.1705101 -1.6241800
row5 -0.2025294 -0.6613795 0.51415000 0.6787669 -1.7051640 0.7398434
col20
row1 1.0518689
row5 -0.5362003
> tmp[,c("col6","col20")]
col6 col20
row1 0.1442230 1.0518689
row2 0.3650734 2.0806343
row3 0.2174769 0.0537134
row4 0.5450906 -1.1772673
row5 1.4595624 -0.5362003
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.144223 1.0518689
row5 1.459562 -0.5362003
>
>
>
>
> 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 50.10555 50.3525 50.35679 52.31398 50.7484 106.3382 51.29728 48.99614
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.70079 49.66958 50.36642 50.84534 50.97169 48.30889 49.23294 51.42526
col17 col18 col19 col20
row1 49.78574 50.29296 49.41897 106.7124
> tmp[,"col10"]
col10
row1 49.66958
row2 28.94890
row3 30.23837
row4 29.47306
row5 49.76081
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.10555 50.35250 50.35679 52.31398 50.74840 106.3382 51.29728 48.99614
row5 48.82847 49.59583 48.85717 50.68683 50.82995 104.9610 48.98760 49.95259
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.70079 49.66958 50.36642 50.84534 50.97169 48.30889 49.23294 51.42526
row5 52.26498 49.76081 50.43270 49.46552 50.23849 49.65788 50.86011 49.61520
col17 col18 col19 col20
row1 49.78574 50.29296 49.41897 106.7124
row5 49.27693 49.92176 50.85886 104.4829
> tmp[,c("col6","col20")]
col6 col20
row1 106.33819 106.71243
row2 74.68868 73.91533
row3 74.41775 75.92145
row4 75.03944 75.15001
row5 104.96103 104.48290
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 106.3382 106.7124
row5 104.9610 104.4829
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 106.3382 106.7124
row5 104.9610 104.4829
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.9784832
[2,] 1.3222833
[3,] 1.5124945
[4,] 0.5874738
[5,] 0.5738473
> tmp[,c("col17","col7")]
col17 col7
[1,] 1.8816184 -0.17432412
[2,] 1.6490977 -0.28646128
[3,] -0.8820788 0.65134412
[4,] 0.4136512 -1.15420186
[5,] 1.2908582 0.06040057
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.1049863 -0.56123885
[2,] 0.8250996 -0.09113784
[3,] -0.9886018 0.44837234
[4,] 0.3739049 -0.02950677
[5,] 0.7378343 0.05699919
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.1049863
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.1049863
[2,] 0.8250996
>
>
>
> 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] [,7]
row3 1.7165075 -0.00461643 2.2622601 1.573052 -2.020426 1.8778493 -1.0989882
row1 -0.2022056 0.60378937 -0.6078823 1.189109 -1.300571 -0.8572035 -0.5591544
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 0.4816076 1.163053 -1.134446 -0.1287146 -0.2961603 -0.1154169 -0.2123179
row1 -0.5202340 0.418902 1.225409 -0.1997696 -0.8942885 -0.3703318 0.5535099
[,15] [,16] [,17] [,18] [,19] [,20]
row3 1.247151 1.0794711 0.1187745 -0.8096871 1.4520695 0.9500562
row1 -1.793658 -0.2153047 0.9752787 0.5427731 -0.1215224 -1.1717263
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.3721931 1.089646 -2.741292 0.4257214 -1.496089 1.111174 0.06736277
[,8] [,9] [,10]
row2 -0.06023348 0.5012281 0.1985409
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -1.849886 -0.5958129 0.6153139 -1.003025 -0.5182446 -0.1182636 1.446647
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.9224283 1.963225 -0.429307 1.436108 0.6134317 -2.475905 0.08927247
[,15] [,16] [,17] [,18] [,19] [,20]
row5 0.8411194 0.03887787 -0.4260124 -0.08717947 0.9668309 0.2030105
>
>
> 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: 0x000001a6950fa230>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c33a56f8b"
[2] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c38067804"
[3] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c1ea408"
[4] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c65f37050"
[5] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c460b16d7"
[6] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c5d2f13e3"
[7] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c76c5c94"
[8] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c55744ad9"
[9] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c6dcf61e8"
[10] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c7b5c67b6"
[11] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c6ab47308"
[12] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c29d44b06"
[13] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c37df5c7e"
[14] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c57ce6a40"
[15] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM523c25f4592c"
>
>
> ### 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: 0x000001a6966ff950>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x000001a6966ff950>
Warning message:
In dir.create(new.directory) :
'F:\biocbuild\bbs-3.20-bioc\meat\BufferedMatrix.Rcheck\tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x000001a6966ff950>
> rowMedians(tmp)
[1] -0.643593071 0.341088503 0.653866375 -0.174845407 0.260409928
[6] -0.022616385 0.290177388 -0.458465081 -0.385638494 -0.194584034
[11] -0.046913136 -0.112697005 -0.050418034 -1.148804268 0.182493539
[16] 0.046352163 0.087882927 0.380558669 -0.263683188 -0.515418359
[21] -0.003627213 -0.112559663 -0.038387652 -0.078031627 0.275537627
[26] 0.364467526 -0.359424583 0.152765522 -0.114123197 -0.596348040
[31] -0.379182931 -0.240737280 0.349419697 -0.038410603 -0.547795237
[36] 0.023163348 -0.205011399 0.279106621 0.126999439 -0.202485508
[41] -0.506170124 0.161095327 -0.200512951 0.303959019 0.311761412
[46] -0.627035192 -0.044021214 -0.009268048 0.274946956 -0.561033589
[51] 0.312250707 -0.220868430 -0.057142441 0.542978165 -0.029132533
[56] 0.178411925 0.251639861 0.068747064 -0.382728805 0.084197480
[61] -0.148042468 -0.530715375 0.438284537 -0.150274577 -0.559028092
[66] 0.173512452 0.734659040 0.077068695 0.394578609 0.083013403
[71] -0.102463093 0.297115274 -0.214149098 0.313043815 -0.258250360
[76] 0.052676213 0.365935250 -0.115298143 0.099953533 -0.596869385
[81] 0.513596304 0.172602660 -0.491539331 0.117483651 -0.216756805
[86] 0.316362404 -0.147028097 0.364624148 -0.405280698 0.067715201
[91] 0.554434959 -0.289756204 0.316181809 -0.246411141 0.058389357
[96] 0.116052767 -0.210938481 -0.192290063 0.192864280 -0.788277465
[101] -0.387883791 0.027922140 0.130755422 -0.009310259 0.125730699
[106] 0.107473668 0.273986775 -0.374433965 -0.006543030 -0.248981158
[111] 0.056895529 -0.184249654 0.325927349 0.359189769 0.150290824
[116] -0.309707573 0.755471647 0.521887799 -0.151708207 -0.299930791
[121] -0.560121002 -0.174086984 0.324649056 0.182074560 0.736286637
[126] -0.158500459 0.067997785 -0.185219210 0.197694258 -0.448480685
[131] 0.211167954 0.180574187 -0.165274488 -0.161338495 -0.399329554
[136] -0.183025920 -0.111816109 -0.197368854 -0.102986491 -0.195193805
[141] 0.079306170 -0.040875543 -0.059757062 0.169420558 -0.122418211
[146] -0.261686668 0.266303991 -0.386565838 0.020971088 -0.237581841
[151] -0.110147540 -0.801154829 -0.114477800 -0.141730651 -0.020881799
[156] 0.204794031 0.131076293 0.081030597 -0.145070935 -0.193048875
[161] 0.142925625 -0.445069424 0.310324325 0.208097494 -0.065014119
[166] -0.387286516 -0.223787354 -0.156193652 0.243987846 0.301576537
[171] 0.294955559 -0.076303790 -0.222177806 0.440020683 -0.178678372
[176] -0.384738698 -0.161029354 0.477002862 0.118761298 -0.250560121
[181] 0.051779206 -0.155388530 -0.312205775 0.548561419 -0.203287378
[186] -0.232328178 -0.269636214 -0.106100162 -0.860956977 0.417486535
[191] 0.153783815 0.209940697 0.380232906 -0.251999367 0.286299202
[196] 0.116143511 0.375329068 -0.123513438 -0.348794405 0.026026995
[201] 0.052619278 0.101772881 0.034324518 -0.467878227 0.665855345
[206] 0.401367190 0.005764472 0.553294061 -0.390039568 -0.065222512
[211] 0.152185913 -0.002805568 -0.047314486 0.046529962 0.233719505
[216] -0.144738759 0.070437049 0.003102116 0.028637380 -0.631852989
[221] -0.152776196 0.445388071 0.597653945 0.103002489 -0.227584937
[226] 0.206356691 -0.071412228 0.088042716 -0.436758667 0.396181659
>
> proc.time()
user system elapsed
3.92 16.12 322.48
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
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: 0x0000020cfeafe410>
> .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: 0x0000020cfeafe410>
> .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: 0x0000020cfeafe410>
> .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: 0x0000020cfeafe410>
> 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: 0x0000020cfeafe950>
> .Call("R_bm_AddColumn",P)
<pointer: 0x0000020cfeafe950>
> .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: 0x0000020cfeafe950>
> .Call("R_bm_AddColumn",P)
<pointer: 0x0000020cfeafe950>
> .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: 0x0000020cfeafe950>
> 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: 0x0000020cfeafe110>
> .Call("R_bm_AddColumn",P)
<pointer: 0x0000020cfeafe110>
> .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: 0x0000020cfeafe110>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x0000020cfeafe110>
> .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: 0x0000020cfeafe110>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x0000020cfeafe110>
> .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: 0x0000020cfeafe110>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x0000020cfeafe110>
> .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: 0x0000020cfeafe110>
> 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: 0x0000020cfeafed70>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x0000020cfeafed70>
> .Call("R_bm_AddColumn",P)
<pointer: 0x0000020cfeafed70>
> .Call("R_bm_AddColumn",P)
<pointer: 0x0000020cfeafed70>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1ed28294ede" "BufferedMatrixFile1ed284ba74821"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1ed28294ede" "BufferedMatrixFile1ed284ba74821"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x0000020cfeafecb0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x0000020cfeafecb0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x0000020cfeafecb0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x0000020cfeafecb0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x0000020cfeafecb0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x0000020cfeafecb0>
> .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: 0x0000020d00efd170>
> .Call("R_bm_AddColumn",P)
<pointer: 0x0000020d00efd170>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x0000020d00efd170>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x0000020d00efd170>
> 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: 0x0000020d00efd470>
> .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: 0x0000020d00efd470>
> rm(P)
>
> proc.time()
user system elapsed
0.28 0.21 1.06
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
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.
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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
0.25 0.10 0.34