Ben Bolstad
| Snapshot Date: 2025-12-03 13:40 -0500 (Wed, 03 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: ecdbf23 |
| git_last_commit_date: 2025-10-29 09:58:55 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-04 11:35 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 253/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.75.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | 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: 1.75.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.75.0.tar.gz |
| StartedAt: 2025-12-03 19:30:10 -0500 (Wed, 03 Dec 2025) |
| EndedAt: 2025-12-03 19:33:17 -0500 (Wed, 03 Dec 2025) |
| EllapsedTime: 187.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.75.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.75.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... WARNING
Found the following significant warnings:
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 ... INFO
Note: information on .o files is not available
* 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: 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.75.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
if (!(Matrix->readonly) & setting){
^ ~
doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function]
static int sort_double(const double *a1,const double *a2){
^
2 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o
clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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
0.117 0.041 0.156
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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] "/Users/biocbuild/bbs-3.23-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) limit (Mb) max used (Mb)
Ncells 481248 25.8 1058085 56.6 NA 633817 33.9
Vcells 891449 6.9 8388608 64.0 196608 2110969 16.2
>
>
>
>
> ##
> ## 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] "Wed Dec 3 19:33:10 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] "Wed Dec 3 19:33:10 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: 0x6000019c0000>
>
>
>
> 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] "Wed Dec 3 19:33:11 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] "Wed Dec 3 19:33:11 2025"
>
> ColMode(tmp2)
<pointer: 0x6000019c0000>
>
>
>
> ### 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,] 100.7348204 0.7652953 0.3415733 0.82925942
[2,] 0.1335970 0.1391485 0.3834399 0.04012894
[3,] -0.4718894 -0.1535894 0.7460603 -1.53847586
[4,] 0.7663975 -0.2375301 -0.8430759 -0.09842782
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-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,] 100.7348204 0.7652953 0.3415733 0.82925942
[2,] 0.1335970 0.1391485 0.3834399 0.04012894
[3,] 0.4718894 0.1535894 0.7460603 1.53847586
[4,] 0.7663975 0.2375301 0.8430759 0.09842782
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-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,] 10.0366738 0.8748116 0.5844427 0.9106368
[2,] 0.3655093 0.3730262 0.6192253 0.2003221
[3,] 0.6869421 0.3919048 0.8637478 1.2403531
[4,] 0.8754413 0.4873706 0.9181917 0.3137321
>
> 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: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 226.10156 34.51341 31.18600 34.93563
[2,] 28.78869 28.86941 31.57569 27.04335
[3,] 32.34131 29.07264 34.38354 38.94201
[4,] 34.52081 30.11124 35.02499 28.23575
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x6000019c82a0>
> exp(tmp5)
<pointer: 0x6000019c82a0>
> log(tmp5,2)
<pointer: 0x6000019c82a0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 470.6008
> Min(tmp5)
[1] 53.81703
> mean(tmp5)
[1] 71.94083
> Sum(tmp5)
[1] 14388.17
> Var(tmp5)
[1] 876.6947
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.35263 65.04024 68.09311 70.83767 70.85910 71.38848 72.74515 67.45050
[9] 68.55595 72.08553
> rowSums(tmp5)
[1] 1847.053 1300.805 1361.862 1416.753 1417.182 1427.770 1454.903 1349.010
[9] 1371.119 1441.711
> rowVars(tmp5)
[1] 7991.47917 47.62197 90.26823 59.74017 62.78998 47.89604
[7] 109.43221 72.31533 76.56746 83.01289
> rowSd(tmp5)
[1] 89.395074 6.900867 9.500960 7.729176 7.924013 6.920697 10.460985
[8] 8.503842 8.750283 9.111141
> rowMax(tmp5)
[1] 470.60077 83.85958 82.86577 85.04771 85.93729 80.82849 92.60886
[8] 81.34984 91.25084 89.44300
> rowMin(tmp5)
[1] 59.99648 56.28719 53.81703 58.76901 54.55715 54.56378 54.81880 53.95149
[9] 54.74035 55.24027
>
> colMeans(tmp5)
[1] 110.85828 68.56840 69.94250 69.17533 64.48765 67.44368 70.94161
[8] 69.65876 68.22606 71.05308 70.29677 69.69690 73.87253 70.27220
[15] 71.17242 70.89024 69.89525 73.42235 67.78431 71.15839
> colSums(tmp5)
[1] 1108.5828 685.6840 699.4250 691.7533 644.8765 674.4368 709.4161
[8] 696.5876 682.2606 710.5308 702.9677 696.9690 738.7253 702.7220
[15] 711.7242 708.9024 698.9525 734.2235 677.8431 711.5839
> colVars(tmp5)
[1] 16025.28262 105.98695 74.22483 95.65936 53.14231 119.92150
[7] 32.44785 105.82568 38.16931 59.22952 72.45813 70.59588
[13] 70.88126 44.19851 59.64217 103.69575 138.52229 100.69772
[19] 93.10381 60.60135
> colSd(tmp5)
[1] 126.591005 10.294996 8.615383 9.780560 7.289877 10.950868
[7] 5.696301 10.287161 6.178132 7.696072 8.512234 8.402135
[13] 8.419101 6.648196 7.722834 10.183111 11.769549 10.034825
[19] 9.649031 7.784687
> colMax(tmp5)
[1] 470.60077 83.18413 85.93729 81.05269 79.04128 90.00474 80.97431
[8] 85.04771 79.86776 82.39877 83.85958 85.42174 89.63914 80.57125
[15] 79.61990 89.44300 92.60886 91.25084 82.86577 82.50208
> colMin(tmp5)
[1] 59.91989 54.56378 56.56356 54.55715 56.50907 53.81703 61.98049 53.89483
[9] 59.89629 57.98412 59.99648 57.57474 63.92236 63.33706 54.74035 54.81880
[17] 58.30791 56.33831 53.95149 62.24643
>
>
> ### 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] 92.35263 65.04024 68.09311 70.83767 70.85910 71.38848 NA 67.45050
[9] 68.55595 72.08553
> rowSums(tmp5)
[1] 1847.053 1300.805 1361.862 1416.753 1417.182 1427.770 NA 1349.010
[9] 1371.119 1441.711
> rowVars(tmp5)
[1] 7991.47917 47.62197 90.26823 59.74017 62.78998 47.89604
[7] 114.68477 72.31533 76.56746 83.01289
> rowSd(tmp5)
[1] 89.395074 6.900867 9.500960 7.729176 7.924013 6.920697 10.709098
[8] 8.503842 8.750283 9.111141
> rowMax(tmp5)
[1] 470.60077 83.85958 82.86577 85.04771 85.93729 80.82849 NA
[8] 81.34984 91.25084 89.44300
> rowMin(tmp5)
[1] 59.99648 56.28719 53.81703 58.76901 54.55715 54.56378 NA 53.95149
[9] 54.74035 55.24027
>
> colMeans(tmp5)
[1] 110.85828 68.56840 69.94250 NA 64.48765 67.44368 70.94161
[8] 69.65876 68.22606 71.05308 70.29677 69.69690 73.87253 70.27220
[15] 71.17242 70.89024 69.89525 73.42235 67.78431 71.15839
> colSums(tmp5)
[1] 1108.5828 685.6840 699.4250 NA 644.8765 674.4368 709.4161
[8] 696.5876 682.2606 710.5308 702.9677 696.9690 738.7253 702.7220
[15] 711.7242 708.9024 698.9525 734.2235 677.8431 711.5839
> colVars(tmp5)
[1] 16025.28262 105.98695 74.22483 NA 53.14231 119.92150
[7] 32.44785 105.82568 38.16931 59.22952 72.45813 70.59588
[13] 70.88126 44.19851 59.64217 103.69575 138.52229 100.69772
[19] 93.10381 60.60135
> colSd(tmp5)
[1] 126.591005 10.294996 8.615383 NA 7.289877 10.950868
[7] 5.696301 10.287161 6.178132 7.696072 8.512234 8.402135
[13] 8.419101 6.648196 7.722834 10.183111 11.769549 10.034825
[19] 9.649031 7.784687
> colMax(tmp5)
[1] 470.60077 83.18413 85.93729 NA 79.04128 90.00474 80.97431
[8] 85.04771 79.86776 82.39877 83.85958 85.42174 89.63914 80.57125
[15] 79.61990 89.44300 92.60886 91.25084 82.86577 82.50208
> colMin(tmp5)
[1] 59.91989 54.56378 56.56356 NA 56.50907 53.81703 61.98049 53.89483
[9] 59.89629 57.98412 59.99648 57.57474 63.92236 63.33706 54.74035 54.81880
[17] 58.30791 56.33831 53.95149 62.24643
>
> Max(tmp5,na.rm=TRUE)
[1] 470.6008
> Min(tmp5,na.rm=TRUE)
[1] 53.81703
> mean(tmp5,na.rm=TRUE)
[1] 71.9179
> Sum(tmp5,na.rm=TRUE)
[1] 14311.66
> Var(tmp5,na.rm=TRUE)
[1] 881.0167
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.35263 65.04024 68.09311 70.83767 70.85910 71.38848 72.54722 67.45050
[9] 68.55595 72.08553
> rowSums(tmp5,na.rm=TRUE)
[1] 1847.053 1300.805 1361.862 1416.753 1417.182 1427.770 1378.397 1349.010
[9] 1371.119 1441.711
> rowVars(tmp5,na.rm=TRUE)
[1] 7991.47917 47.62197 90.26823 59.74017 62.78998 47.89604
[7] 114.68477 72.31533 76.56746 83.01289
> rowSd(tmp5,na.rm=TRUE)
[1] 89.395074 6.900867 9.500960 7.729176 7.924013 6.920697 10.709098
[8] 8.503842 8.750283 9.111141
> rowMax(tmp5,na.rm=TRUE)
[1] 470.60077 83.85958 82.86577 85.04771 85.93729 80.82849 92.60886
[8] 81.34984 91.25084 89.44300
> rowMin(tmp5,na.rm=TRUE)
[1] 59.99648 56.28719 53.81703 58.76901 54.55715 54.56378 54.81880 53.95149
[9] 54.74035 55.24027
>
> colMeans(tmp5,na.rm=TRUE)
[1] 110.85828 68.56840 69.94250 68.36084 64.48765 67.44368 70.94161
[8] 69.65876 68.22606 71.05308 70.29677 69.69690 73.87253 70.27220
[15] 71.17242 70.89024 69.89525 73.42235 67.78431 71.15839
> colSums(tmp5,na.rm=TRUE)
[1] 1108.5828 685.6840 699.4250 615.2476 644.8765 674.4368 709.4161
[8] 696.5876 682.2606 710.5308 702.9677 696.9690 738.7253 702.7220
[15] 711.7242 708.9024 698.9525 734.2235 677.8431 711.5839
> colVars(tmp5,na.rm=TRUE)
[1] 16025.28262 105.98695 74.22483 100.15367 53.14231 119.92150
[7] 32.44785 105.82568 38.16931 59.22952 72.45813 70.59588
[13] 70.88126 44.19851 59.64217 103.69575 138.52229 100.69772
[19] 93.10381 60.60135
> colSd(tmp5,na.rm=TRUE)
[1] 126.591005 10.294996 8.615383 10.007681 7.289877 10.950868
[7] 5.696301 10.287161 6.178132 7.696072 8.512234 8.402135
[13] 8.419101 6.648196 7.722834 10.183111 11.769549 10.034825
[19] 9.649031 7.784687
> colMax(tmp5,na.rm=TRUE)
[1] 470.60077 83.18413 85.93729 81.05269 79.04128 90.00474 80.97431
[8] 85.04771 79.86776 82.39877 83.85958 85.42174 89.63914 80.57125
[15] 79.61990 89.44300 92.60886 91.25084 82.86577 82.50208
> colMin(tmp5,na.rm=TRUE)
[1] 59.91989 54.56378 56.56356 54.55715 56.50907 53.81703 61.98049 53.89483
[9] 59.89629 57.98412 59.99648 57.57474 63.92236 63.33706 54.74035 54.81880
[17] 58.30791 56.33831 53.95149 62.24643
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.35263 65.04024 68.09311 70.83767 70.85910 71.38848 NaN 67.45050
[9] 68.55595 72.08553
> rowSums(tmp5,na.rm=TRUE)
[1] 1847.053 1300.805 1361.862 1416.753 1417.182 1427.770 0.000 1349.010
[9] 1371.119 1441.711
> rowVars(tmp5,na.rm=TRUE)
[1] 7991.47917 47.62197 90.26823 59.74017 62.78998 47.89604
[7] NA 72.31533 76.56746 83.01289
> rowSd(tmp5,na.rm=TRUE)
[1] 89.395074 6.900867 9.500960 7.729176 7.924013 6.920697 NA
[8] 8.503842 8.750283 9.111141
> rowMax(tmp5,na.rm=TRUE)
[1] 470.60077 83.85958 82.86577 85.04771 85.93729 80.82849 NA
[8] 81.34984 91.25084 89.44300
> rowMin(tmp5,na.rm=TRUE)
[1] 59.99648 56.28719 53.81703 58.76901 54.55715 54.56378 NA 53.95149
[9] 54.74035 55.24027
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 113.41076 68.99940 70.03232 NaN 65.17350 66.86260 70.62827
[8] 68.23097 68.61331 69.79244 71.13648 69.76227 72.12069 69.61725
[15] 72.24059 72.67596 67.37152 73.53331 66.85063 71.61622
> colSums(tmp5,na.rm=TRUE)
[1] 1020.6969 620.9946 630.2909 0.0000 586.5615 601.7634 635.6544
[8] 614.0787 617.5198 628.1320 640.2283 627.8604 649.0862 626.5552
[15] 650.1653 654.0836 606.3436 661.7998 601.6557 644.5460
> colVars(tmp5,na.rm=TRUE)
[1] 17955.14702 117.14549 83.41218 NA 54.49322 131.11305
[7] 35.39930 96.11994 41.25334 48.75477 73.58293 79.37229
[13] 45.21562 44.89746 54.26116 80.78394 84.18370 113.14642
[19] 94.93454 65.81845
> colSd(tmp5,na.rm=TRUE)
[1] 133.996817 10.823377 9.133027 NA 7.381952 11.450461
[7] 5.949731 9.804078 6.422876 6.982462 8.578049 8.909113
[13] 6.724256 6.700557 7.366217 8.987989 9.175168 10.637031
[19] 9.743436 8.112857
> colMax(tmp5,na.rm=TRUE)
[1] 470.60077 83.18413 85.93729 -Inf 79.04128 90.00474 80.97431
[8] 85.04771 79.86776 77.79841 83.85958 85.42174 82.60691 80.57125
[15] 79.61990 89.44300 80.82849 91.25084 82.86577 82.50208
> colMin(tmp5,na.rm=TRUE)
[1] 59.91989 54.56378 56.56356 Inf 56.50907 53.81703 61.98049 53.89483
[9] 59.89629 57.98412 59.99648 57.57474 63.92236 63.33706 54.74035 57.83601
[17] 58.30791 56.33831 53.95149 62.24643
>
>
>
>
> 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] 350.7201 285.0750 290.1079 283.2387 149.4424 259.7874 118.6619 236.2452
[9] 214.1657 161.4897
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 350.7201 285.0750 290.1079 283.2387 149.4424 259.7874 118.6619 236.2452
[9] 214.1657 161.4897
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] -5.684342e-14 0.000000e+00 -5.684342e-14 1.136868e-13 -1.421085e-13
[6] -2.273737e-13 2.842171e-13 1.421085e-13 1.136868e-13 5.684342e-14
[11] 5.684342e-14 1.421085e-14 -1.421085e-14 2.273737e-13 -8.526513e-14
[16] 1.705303e-13 2.842171e-14 1.136868e-13 0.000000e+00 -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)
+ }
8 4
8 16
2 8
6 14
8 11
5 15
8 18
10 12
3 10
1 19
3 20
2 17
10 9
7 4
6 12
7 11
9 14
5 20
10 5
2 13
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] 3.045808
> Min(tmp)
[1] -2.752912
> mean(tmp)
[1] 0.0318047
> Sum(tmp)
[1] 3.18047
> Var(tmp)
[1] 1.156106
>
> rowMeans(tmp)
[1] 0.0318047
> rowSums(tmp)
[1] 3.18047
> rowVars(tmp)
[1] 1.156106
> rowSd(tmp)
[1] 1.075224
> rowMax(tmp)
[1] 3.045808
> rowMin(tmp)
[1] -2.752912
>
> colMeans(tmp)
[1] 0.07886301 -1.14178809 -1.76606995 -0.60841598 0.98431080 1.46556369
[7] -2.75291219 -0.19546029 -0.31183286 0.39645461 -0.10427822 0.21198623
[13] 0.01237807 -0.19446972 1.02509640 0.02140839 -0.38639454 0.26141488
[19] -0.92212015 0.99377696 1.53466768 -0.99394613 0.63338727 -0.17634002
[25] -1.14152483 0.22314211 -1.16495214 -0.53655149 -1.26692645 -0.55640532
[31] -0.17162970 0.53014637 0.01992630 1.63940413 -0.45867040 0.01772521
[37] -1.43913902 -0.47749261 -1.21049618 -0.13596134 -0.74053734 1.66976526
[43] 1.85328445 0.79040221 -0.13845711 1.95733465 0.40236687 -2.29204837
[49] -0.12326990 0.76309147 0.12912124 1.01842606 -2.28724639 0.69084937
[55] 0.49636678 -0.56018955 1.26355604 -0.33054064 1.36662640 -2.69317074
[61] -1.21143608 -1.13396342 -0.72700191 1.57788077 -0.61569672 1.02331209
[67] 0.51175252 0.77803027 1.59610466 0.02266781 -0.26568790 3.04580784
[73] -1.17487266 -0.91644655 0.81706300 0.58093232 0.63193050 -0.57814660
[79] -0.59524402 0.25203498 2.06893386 0.86621918 0.01983528 -0.48388960
[85] 0.27982833 0.32240912 1.75676227 0.81076117 0.42611912 -0.41735058
[91] 1.07349795 -0.55389655 -0.52887558 -2.34572021 0.71471815 -0.88815360
[97] 0.96195481 0.88383453 0.01220027 -0.58934400
> colSums(tmp)
[1] 0.07886301 -1.14178809 -1.76606995 -0.60841598 0.98431080 1.46556369
[7] -2.75291219 -0.19546029 -0.31183286 0.39645461 -0.10427822 0.21198623
[13] 0.01237807 -0.19446972 1.02509640 0.02140839 -0.38639454 0.26141488
[19] -0.92212015 0.99377696 1.53466768 -0.99394613 0.63338727 -0.17634002
[25] -1.14152483 0.22314211 -1.16495214 -0.53655149 -1.26692645 -0.55640532
[31] -0.17162970 0.53014637 0.01992630 1.63940413 -0.45867040 0.01772521
[37] -1.43913902 -0.47749261 -1.21049618 -0.13596134 -0.74053734 1.66976526
[43] 1.85328445 0.79040221 -0.13845711 1.95733465 0.40236687 -2.29204837
[49] -0.12326990 0.76309147 0.12912124 1.01842606 -2.28724639 0.69084937
[55] 0.49636678 -0.56018955 1.26355604 -0.33054064 1.36662640 -2.69317074
[61] -1.21143608 -1.13396342 -0.72700191 1.57788077 -0.61569672 1.02331209
[67] 0.51175252 0.77803027 1.59610466 0.02266781 -0.26568790 3.04580784
[73] -1.17487266 -0.91644655 0.81706300 0.58093232 0.63193050 -0.57814660
[79] -0.59524402 0.25203498 2.06893386 0.86621918 0.01983528 -0.48388960
[85] 0.27982833 0.32240912 1.75676227 0.81076117 0.42611912 -0.41735058
[91] 1.07349795 -0.55389655 -0.52887558 -2.34572021 0.71471815 -0.88815360
[97] 0.96195481 0.88383453 0.01220027 -0.58934400
> 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] 0.07886301 -1.14178809 -1.76606995 -0.60841598 0.98431080 1.46556369
[7] -2.75291219 -0.19546029 -0.31183286 0.39645461 -0.10427822 0.21198623
[13] 0.01237807 -0.19446972 1.02509640 0.02140839 -0.38639454 0.26141488
[19] -0.92212015 0.99377696 1.53466768 -0.99394613 0.63338727 -0.17634002
[25] -1.14152483 0.22314211 -1.16495214 -0.53655149 -1.26692645 -0.55640532
[31] -0.17162970 0.53014637 0.01992630 1.63940413 -0.45867040 0.01772521
[37] -1.43913902 -0.47749261 -1.21049618 -0.13596134 -0.74053734 1.66976526
[43] 1.85328445 0.79040221 -0.13845711 1.95733465 0.40236687 -2.29204837
[49] -0.12326990 0.76309147 0.12912124 1.01842606 -2.28724639 0.69084937
[55] 0.49636678 -0.56018955 1.26355604 -0.33054064 1.36662640 -2.69317074
[61] -1.21143608 -1.13396342 -0.72700191 1.57788077 -0.61569672 1.02331209
[67] 0.51175252 0.77803027 1.59610466 0.02266781 -0.26568790 3.04580784
[73] -1.17487266 -0.91644655 0.81706300 0.58093232 0.63193050 -0.57814660
[79] -0.59524402 0.25203498 2.06893386 0.86621918 0.01983528 -0.48388960
[85] 0.27982833 0.32240912 1.75676227 0.81076117 0.42611912 -0.41735058
[91] 1.07349795 -0.55389655 -0.52887558 -2.34572021 0.71471815 -0.88815360
[97] 0.96195481 0.88383453 0.01220027 -0.58934400
> colMin(tmp)
[1] 0.07886301 -1.14178809 -1.76606995 -0.60841598 0.98431080 1.46556369
[7] -2.75291219 -0.19546029 -0.31183286 0.39645461 -0.10427822 0.21198623
[13] 0.01237807 -0.19446972 1.02509640 0.02140839 -0.38639454 0.26141488
[19] -0.92212015 0.99377696 1.53466768 -0.99394613 0.63338727 -0.17634002
[25] -1.14152483 0.22314211 -1.16495214 -0.53655149 -1.26692645 -0.55640532
[31] -0.17162970 0.53014637 0.01992630 1.63940413 -0.45867040 0.01772521
[37] -1.43913902 -0.47749261 -1.21049618 -0.13596134 -0.74053734 1.66976526
[43] 1.85328445 0.79040221 -0.13845711 1.95733465 0.40236687 -2.29204837
[49] -0.12326990 0.76309147 0.12912124 1.01842606 -2.28724639 0.69084937
[55] 0.49636678 -0.56018955 1.26355604 -0.33054064 1.36662640 -2.69317074
[61] -1.21143608 -1.13396342 -0.72700191 1.57788077 -0.61569672 1.02331209
[67] 0.51175252 0.77803027 1.59610466 0.02266781 -0.26568790 3.04580784
[73] -1.17487266 -0.91644655 0.81706300 0.58093232 0.63193050 -0.57814660
[79] -0.59524402 0.25203498 2.06893386 0.86621918 0.01983528 -0.48388960
[85] 0.27982833 0.32240912 1.75676227 0.81076117 0.42611912 -0.41735058
[91] 1.07349795 -0.55389655 -0.52887558 -2.34572021 0.71471815 -0.88815360
[97] 0.96195481 0.88383453 0.01220027 -0.58934400
> colMedians(tmp)
[1] 0.07886301 -1.14178809 -1.76606995 -0.60841598 0.98431080 1.46556369
[7] -2.75291219 -0.19546029 -0.31183286 0.39645461 -0.10427822 0.21198623
[13] 0.01237807 -0.19446972 1.02509640 0.02140839 -0.38639454 0.26141488
[19] -0.92212015 0.99377696 1.53466768 -0.99394613 0.63338727 -0.17634002
[25] -1.14152483 0.22314211 -1.16495214 -0.53655149 -1.26692645 -0.55640532
[31] -0.17162970 0.53014637 0.01992630 1.63940413 -0.45867040 0.01772521
[37] -1.43913902 -0.47749261 -1.21049618 -0.13596134 -0.74053734 1.66976526
[43] 1.85328445 0.79040221 -0.13845711 1.95733465 0.40236687 -2.29204837
[49] -0.12326990 0.76309147 0.12912124 1.01842606 -2.28724639 0.69084937
[55] 0.49636678 -0.56018955 1.26355604 -0.33054064 1.36662640 -2.69317074
[61] -1.21143608 -1.13396342 -0.72700191 1.57788077 -0.61569672 1.02331209
[67] 0.51175252 0.77803027 1.59610466 0.02266781 -0.26568790 3.04580784
[73] -1.17487266 -0.91644655 0.81706300 0.58093232 0.63193050 -0.57814660
[79] -0.59524402 0.25203498 2.06893386 0.86621918 0.01983528 -0.48388960
[85] 0.27982833 0.32240912 1.75676227 0.81076117 0.42611912 -0.41735058
[91] 1.07349795 -0.55389655 -0.52887558 -2.34572021 0.71471815 -0.88815360
[97] 0.96195481 0.88383453 0.01220027 -0.58934400
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.07886301 -1.141788 -1.76607 -0.608416 0.9843108 1.465564 -2.752912
[2,] 0.07886301 -1.141788 -1.76607 -0.608416 0.9843108 1.465564 -2.752912
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.1954603 -0.3118329 0.3964546 -0.1042782 0.2119862 0.01237807 -0.1944697
[2,] -0.1954603 -0.3118329 0.3964546 -0.1042782 0.2119862 0.01237807 -0.1944697
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 1.025096 0.02140839 -0.3863945 0.2614149 -0.9221201 0.993777 1.534668
[2,] 1.025096 0.02140839 -0.3863945 0.2614149 -0.9221201 0.993777 1.534668
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.9939461 0.6333873 -0.17634 -1.141525 0.2231421 -1.164952 -0.5365515
[2,] -0.9939461 0.6333873 -0.17634 -1.141525 0.2231421 -1.164952 -0.5365515
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -1.266926 -0.5564053 -0.1716297 0.5301464 0.0199263 1.639404 -0.4586704
[2,] -1.266926 -0.5564053 -0.1716297 0.5301464 0.0199263 1.639404 -0.4586704
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.01772521 -1.439139 -0.4774926 -1.210496 -0.1359613 -0.7405373 1.669765
[2,] 0.01772521 -1.439139 -0.4774926 -1.210496 -0.1359613 -0.7405373 1.669765
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 1.853284 0.7904022 -0.1384571 1.957335 0.4023669 -2.292048 -0.1232699
[2,] 1.853284 0.7904022 -0.1384571 1.957335 0.4023669 -2.292048 -0.1232699
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.7630915 0.1291212 1.018426 -2.287246 0.6908494 0.4963668 -0.5601895
[2,] 0.7630915 0.1291212 1.018426 -2.287246 0.6908494 0.4963668 -0.5601895
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 1.263556 -0.3305406 1.366626 -2.693171 -1.211436 -1.133963 -0.7270019
[2,] 1.263556 -0.3305406 1.366626 -2.693171 -1.211436 -1.133963 -0.7270019
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 1.577881 -0.6156967 1.023312 0.5117525 0.7780303 1.596105 0.02266781
[2,] 1.577881 -0.6156967 1.023312 0.5117525 0.7780303 1.596105 0.02266781
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.2656879 3.045808 -1.174873 -0.9164466 0.817063 0.5809323 0.6319305
[2,] -0.2656879 3.045808 -1.174873 -0.9164466 0.817063 0.5809323 0.6319305
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -0.5781466 -0.595244 0.252035 2.068934 0.8662192 0.01983528 -0.4838896
[2,] -0.5781466 -0.595244 0.252035 2.068934 0.8662192 0.01983528 -0.4838896
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.2798283 0.3224091 1.756762 0.8107612 0.4261191 -0.4173506 1.073498
[2,] 0.2798283 0.3224091 1.756762 0.8107612 0.4261191 -0.4173506 1.073498
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.5538966 -0.5288756 -2.34572 0.7147182 -0.8881536 0.9619548 0.8838345
[2,] -0.5538966 -0.5288756 -2.34572 0.7147182 -0.8881536 0.9619548 0.8838345
[,99] [,100]
[1,] 0.01220027 -0.589344
[2,] 0.01220027 -0.589344
>
>
> Max(tmp2)
[1] 2.436379
> Min(tmp2)
[1] -2.663276
> mean(tmp2)
[1] -0.1536935
> Sum(tmp2)
[1] -15.36935
> Var(tmp2)
[1] 1.094881
>
> rowMeans(tmp2)
[1] -0.98148186 -1.68848760 -1.44054528 0.31707553 -0.68632394 -0.31656643
[7] -0.12847172 0.56765921 2.43637921 0.48981216 0.16880330 -1.61874127
[13] -0.27288747 1.06621505 0.27858806 -0.75978344 0.91828003 -0.78812831
[19] 0.84334538 0.95678804 0.05271181 -1.22961172 1.56971768 -1.16378365
[25] 0.35488857 -0.41208103 -2.01919296 1.20323689 -2.36472181 -1.15705565
[31] 0.62540697 -1.22380398 1.30597122 1.86931405 1.21866674 -0.87704986
[37] 0.30141641 -0.09449328 0.47388278 -0.77591936 -1.28124590 0.43160356
[43] -0.96537091 -0.26832931 0.65396181 -0.11085036 -2.27183074 -0.44126254
[49] 0.61331631 -0.74408254 1.24965511 0.85332516 -0.34537904 -0.32021520
[55] -1.79765986 -0.98014010 1.76421161 -0.03677897 1.40033923 -0.65290139
[61] 1.83501983 0.82707156 -1.06513842 0.43810607 -0.07234336 -0.57262673
[67] -1.43629769 0.60181443 -1.00925631 -1.60000682 -1.58955765 0.47188725
[73] -0.63748582 -0.37732456 -0.07559043 -0.65088855 -0.39595692 0.27460359
[79] -0.92240127 -0.42416261 1.72799453 -1.25914386 0.14861213 -0.56687056
[85] 0.14976214 1.10531729 -0.66646018 -1.89635312 0.76735790 1.67113642
[91] -0.62791464 0.35240529 -0.31702926 -0.34725144 -0.10620832 0.15823388
[97] -0.93384864 -2.66327560 -0.35240061 0.89772857
> rowSums(tmp2)
[1] -0.98148186 -1.68848760 -1.44054528 0.31707553 -0.68632394 -0.31656643
[7] -0.12847172 0.56765921 2.43637921 0.48981216 0.16880330 -1.61874127
[13] -0.27288747 1.06621505 0.27858806 -0.75978344 0.91828003 -0.78812831
[19] 0.84334538 0.95678804 0.05271181 -1.22961172 1.56971768 -1.16378365
[25] 0.35488857 -0.41208103 -2.01919296 1.20323689 -2.36472181 -1.15705565
[31] 0.62540697 -1.22380398 1.30597122 1.86931405 1.21866674 -0.87704986
[37] 0.30141641 -0.09449328 0.47388278 -0.77591936 -1.28124590 0.43160356
[43] -0.96537091 -0.26832931 0.65396181 -0.11085036 -2.27183074 -0.44126254
[49] 0.61331631 -0.74408254 1.24965511 0.85332516 -0.34537904 -0.32021520
[55] -1.79765986 -0.98014010 1.76421161 -0.03677897 1.40033923 -0.65290139
[61] 1.83501983 0.82707156 -1.06513842 0.43810607 -0.07234336 -0.57262673
[67] -1.43629769 0.60181443 -1.00925631 -1.60000682 -1.58955765 0.47188725
[73] -0.63748582 -0.37732456 -0.07559043 -0.65088855 -0.39595692 0.27460359
[79] -0.92240127 -0.42416261 1.72799453 -1.25914386 0.14861213 -0.56687056
[85] 0.14976214 1.10531729 -0.66646018 -1.89635312 0.76735790 1.67113642
[91] -0.62791464 0.35240529 -0.31702926 -0.34725144 -0.10620832 0.15823388
[97] -0.93384864 -2.66327560 -0.35240061 0.89772857
> 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] -0.98148186 -1.68848760 -1.44054528 0.31707553 -0.68632394 -0.31656643
[7] -0.12847172 0.56765921 2.43637921 0.48981216 0.16880330 -1.61874127
[13] -0.27288747 1.06621505 0.27858806 -0.75978344 0.91828003 -0.78812831
[19] 0.84334538 0.95678804 0.05271181 -1.22961172 1.56971768 -1.16378365
[25] 0.35488857 -0.41208103 -2.01919296 1.20323689 -2.36472181 -1.15705565
[31] 0.62540697 -1.22380398 1.30597122 1.86931405 1.21866674 -0.87704986
[37] 0.30141641 -0.09449328 0.47388278 -0.77591936 -1.28124590 0.43160356
[43] -0.96537091 -0.26832931 0.65396181 -0.11085036 -2.27183074 -0.44126254
[49] 0.61331631 -0.74408254 1.24965511 0.85332516 -0.34537904 -0.32021520
[55] -1.79765986 -0.98014010 1.76421161 -0.03677897 1.40033923 -0.65290139
[61] 1.83501983 0.82707156 -1.06513842 0.43810607 -0.07234336 -0.57262673
[67] -1.43629769 0.60181443 -1.00925631 -1.60000682 -1.58955765 0.47188725
[73] -0.63748582 -0.37732456 -0.07559043 -0.65088855 -0.39595692 0.27460359
[79] -0.92240127 -0.42416261 1.72799453 -1.25914386 0.14861213 -0.56687056
[85] 0.14976214 1.10531729 -0.66646018 -1.89635312 0.76735790 1.67113642
[91] -0.62791464 0.35240529 -0.31702926 -0.34725144 -0.10620832 0.15823388
[97] -0.93384864 -2.66327560 -0.35240061 0.89772857
> rowMin(tmp2)
[1] -0.98148186 -1.68848760 -1.44054528 0.31707553 -0.68632394 -0.31656643
[7] -0.12847172 0.56765921 2.43637921 0.48981216 0.16880330 -1.61874127
[13] -0.27288747 1.06621505 0.27858806 -0.75978344 0.91828003 -0.78812831
[19] 0.84334538 0.95678804 0.05271181 -1.22961172 1.56971768 -1.16378365
[25] 0.35488857 -0.41208103 -2.01919296 1.20323689 -2.36472181 -1.15705565
[31] 0.62540697 -1.22380398 1.30597122 1.86931405 1.21866674 -0.87704986
[37] 0.30141641 -0.09449328 0.47388278 -0.77591936 -1.28124590 0.43160356
[43] -0.96537091 -0.26832931 0.65396181 -0.11085036 -2.27183074 -0.44126254
[49] 0.61331631 -0.74408254 1.24965511 0.85332516 -0.34537904 -0.32021520
[55] -1.79765986 -0.98014010 1.76421161 -0.03677897 1.40033923 -0.65290139
[61] 1.83501983 0.82707156 -1.06513842 0.43810607 -0.07234336 -0.57262673
[67] -1.43629769 0.60181443 -1.00925631 -1.60000682 -1.58955765 0.47188725
[73] -0.63748582 -0.37732456 -0.07559043 -0.65088855 -0.39595692 0.27460359
[79] -0.92240127 -0.42416261 1.72799453 -1.25914386 0.14861213 -0.56687056
[85] 0.14976214 1.10531729 -0.66646018 -1.89635312 0.76735790 1.67113642
[91] -0.62791464 0.35240529 -0.31702926 -0.34725144 -0.10620832 0.15823388
[97] -0.93384864 -2.66327560 -0.35240061 0.89772857
>
> colMeans(tmp2)
[1] -0.1536935
> colSums(tmp2)
[1] -15.36935
> colVars(tmp2)
[1] 1.094881
> colSd(tmp2)
[1] 1.046365
> colMax(tmp2)
[1] 2.436379
> colMin(tmp2)
[1] -2.663276
> colMedians(tmp2)
[1] -0.2706084
> colRanges(tmp2)
[,1]
[1,] -2.663276
[2,] 2.436379
>
> 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] -2.2011815 -0.3888474 -0.2736166 -7.4813669 0.0169153 2.0607229
[7] 2.1112714 0.5618923 6.2862404 2.1608467
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.8237097
[2,] -0.7472519
[3,] -0.2457289
[4,] 0.4977771
[5,] 1.0127271
>
> rowApply(tmp,sum)
[1] 2.1428461 1.4208183 4.2243423 0.2774840 -3.0318501 -3.0781704
[7] -1.6118404 -0.8698551 1.7948561 1.5842458
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 3 3 1 8 5 3 2 10 8 6
[2,] 9 8 8 1 4 8 4 2 7 2
[3,] 5 9 5 3 8 4 6 3 6 5
[4,] 4 2 2 2 2 6 3 8 3 1
[5,] 6 4 9 4 3 1 9 5 2 7
[6,] 2 6 6 10 10 2 7 4 1 9
[7,] 8 1 3 9 7 9 8 7 4 4
[8,] 7 7 7 5 1 5 5 9 5 8
[9,] 10 5 4 7 9 10 10 1 9 10
[10,] 1 10 10 6 6 7 1 6 10 3
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -0.9743112 -0.1992454 -2.8537879 0.7115612 -1.9340613 -1.1256673
[7] -5.3356895 -2.8259391 0.2078500 2.3475987 4.3169381 1.6561161
[13] -0.2237367 3.0402477 2.0422934 1.3411810 0.1546701 0.9853383
[19] -4.4109076 -2.5927672
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.0187822
[2,] -0.6701202
[3,] 0.3842769
[4,] 0.5269080
[5,] 0.8034062
>
> rowApply(tmp,sum)
[1] 0.59440854 0.09924148 -5.00630433 -2.30303166 0.94336737
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 1 13 18 7 12
[2,] 12 9 13 6 9
[3,] 3 1 5 12 15
[4,] 10 12 15 1 20
[5,] 11 16 4 2 18
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -2.0187822 0.27171608 -0.9492235 0.1082467 0.1705579 -0.2553162
[2,] 0.5269080 -0.04308572 -1.1920049 0.2984089 0.7974381 -1.1023240
[3,] 0.8034062 0.29233217 -1.1905354 0.4887097 -1.7669594 1.3529961
[4,] -0.6701202 -0.74319686 -0.1118439 -2.1348337 -1.9906796 -0.5537596
[5,] 0.3842769 0.02298896 0.5898197 1.9510296 0.8555818 -0.5672635
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.2460697 0.6565019 1.6645335 -0.4710243 1.04023464 0.83357236
[2,] -1.0799538 0.2302701 -0.3429142 -0.5769405 1.20232307 0.56195094
[3,] -2.5612775 -0.3349314 -0.1386191 1.3531600 0.01061737 0.58212492
[4,] -1.1532621 -1.2371439 0.7180321 1.2059732 1.20863866 -0.33254459
[5,] -0.2951264 -2.1406357 -1.6931824 0.8364303 0.85512437 0.01101242
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.5692615 0.8330782 0.7764187 0.7508445 -0.9331089 0.47519857
[2,] -1.0868637 0.8145346 0.9084352 0.6731544 0.9082119 -1.08416006
[3,] 0.6679572 0.4518626 -0.4613687 0.2879061 0.1595844 0.06378972
[4,] 0.4375049 1.9654333 -0.5205480 1.4741027 -0.3909578 0.97655639
[5,] 0.3269264 -1.0246611 1.3393561 -1.8448266 0.4109405 0.55395370
[,19] [,20]
[1,] -1.1111425 -0.43256580
[2,] -0.3767428 0.06259592
[3,] -2.1566430 -2.91041631
[4,] -0.7722655 0.32188294
[5,] 0.0058862 0.36573601
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 649 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 563 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-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 0.05369435 0.3511795 0.5602645 0.8756766 1.040334 -0.8479456 0.3208948
col8 col9 col10 col11 col12 col13 col14
row1 0.6218033 1.661843 0.2078401 -0.4332953 0.1917064 -0.1832776 -0.7496876
col15 col16 col17 col18 col19 col20
row1 -0.5848135 -1.334582 0.5831589 -1.404827 1.102281 -1.251573
> tmp[,"col10"]
col10
row1 0.2078401
row2 1.0144114
row3 0.6595440
row4 -1.2629733
row5 -0.3831563
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.05369435 0.3511795 0.5602645 0.8756766 1.040334 -0.84794563 0.3208948
row5 0.55789640 1.0032970 1.1802815 0.1436462 -1.071109 -0.09319987 0.5331116
col8 col9 col10 col11 col12 col13
row1 0.6218033 1.6618432 0.2078401 -0.4332953 0.1917064 -0.18327759
row5 0.3421853 -0.6415915 -0.3831563 1.3331485 -1.6265226 -0.08067978
col14 col15 col16 col17 col18 col19
row1 -0.7496876 -0.5848135 -1.3345821 0.5831589 -1.40482706 1.1022806
row5 -0.3188035 -0.1039074 -0.2870822 -1.5988090 -0.07760007 -0.5051306
col20
row1 -1.251573
row5 1.399583
> tmp[,c("col6","col20")]
col6 col20
row1 -0.84794563 -1.2515727
row2 -0.96609411 -1.3882156
row3 -0.82570043 -1.6398512
row4 1.03117448 -0.1294714
row5 -0.09319987 1.3995831
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.84794563 -1.251573
row5 -0.09319987 1.399583
>
>
>
>
> 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 50.23422 49.18067 50.2 50.48679 48.95643 103.8021 50.25397 49.60697
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.52047 47.68195 51.14844 48.47479 50.37208 48.78775 47.9068 49.29417
col17 col18 col19 col20
row1 51.43635 49.51896 50.79916 104.2724
> tmp[,"col10"]
col10
row1 47.68195
row2 29.56796
row3 30.79487
row4 29.01207
row5 46.93438
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.23422 49.18067 50.20000 50.48679 48.95643 103.8021 50.25397 49.60697
row5 49.27415 50.93068 51.13882 48.56711 48.92660 106.6801 50.86578 49.10415
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.52047 47.68195 51.14844 48.47479 50.37208 48.78775 47.90680 49.29417
row5 51.42310 46.93438 49.46619 49.51569 50.32565 48.32883 48.08628 50.57387
col17 col18 col19 col20
row1 51.43635 49.51896 50.79916 104.2724
row5 50.63796 48.88968 49.16025 104.2898
> tmp[,c("col6","col20")]
col6 col20
row1 103.80212 104.27243
row2 71.72313 74.50998
row3 73.78548 76.87293
row4 75.22690 74.43454
row5 106.68009 104.28983
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 103.8021 104.2724
row5 106.6801 104.2898
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 103.8021 104.2724
row5 106.6801 104.2898
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.9144484
[2,] -0.8098312
[3,] -0.9876174
[4,] 1.7515589
[5,] -1.8122512
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.18319259 -0.5497676
[2,] 0.18989148 0.6839980
[3,] -0.04259938 -0.2806942
[4,] 0.83880399 -0.8321479
[5,] -0.16391177 1.7356768
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.1816252 0.8202691
[2,] 0.1422928 -0.9964073
[3,] 1.4109349 0.1253409
[4,] 1.2003303 0.9868190
[5,] -0.1431036 -0.8323068
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.1816252
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.1816252
[2,] 0.1422928
>
>
>
> 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 -1.1608075 0.6076032 -1.028853 -1.2137554 1.7192526 0.5077116 1.232977
row1 0.6892089 -0.1413828 1.249041 -0.1825488 -0.2977208 1.1869643 -1.027071
[,8] [,9] [,10] [,11] [,12] [,13]
row3 -0.5069974 -1.9729607 0.2970421 1.256723 2.2023696 -0.56633695
row1 -0.1802151 -0.4333251 -0.8919139 -2.842386 0.1717993 0.01723998
[,14] [,15] [,16] [,17] [,18] [,19]
row3 0.6736778 0.5987979 -0.05873249 -0.5666230 0.9293307 0.8136792
row1 -0.6095234 -0.7452325 2.11961258 -0.3743716 -0.8216198 0.6605915
[,20]
row3 0.9532788
row1 0.9700914
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.9591425 -1.627807 -0.2801145 0.03293707 1.394125 1.574516 0.9613006
[,8] [,9] [,10]
row2 -0.8537588 0.508594 -0.3718054
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.3689807 0.6166892 1.019362 -0.2427398 -0.6914355 0.2784231 1.072596
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -1.577243 1.26385 0.384982 0.2199381 0.2766866 0.9822821 -0.7803756
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -2.070585 2.70738 -0.09739114 0.3670552 -0.3792679 0.5245631
>
>
> 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: 0x6000019d4d20>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a443ce69cb"
[2] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a42483b134"
[3] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a441e6dfa6"
[4] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a41c652d17"
[5] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a436734f91"
[6] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a44c6cd484"
[7] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a47cf44d4e"
[8] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a4aff7bf9"
[9] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a4b241e13"
[10] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a47032771b"
[11] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a4129c729"
[12] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a45dd25557"
[13] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a41be0f2e0"
[14] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a44d695e6c"
[15] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM50a440b62c28"
>
>
> ### 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: 0x6000019d8300>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x6000019d8300>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x6000019d8300>
> rowMedians(tmp)
[1] -0.5269435089 0.0016479676 -0.2499792621 0.1166488272 0.1203767697
[6] -0.1870961259 0.0097678355 -0.3854182332 -0.1810897804 -0.0747229094
[11] -0.6544599269 -0.5963717339 0.0104584174 0.2553377013 0.1986673770
[16] 0.2550845182 0.1977094342 -0.5677894379 0.0972943540 -0.2736271722
[21] 0.1190422771 0.5432976642 -0.0792669076 0.0652473161 -0.3174475979
[26] 0.2859374723 -0.0614754000 -0.3934335237 0.0881201638 0.0693727855
[31] -0.4896583960 0.7201917231 0.2376611305 0.2276135758 0.5261463220
[36] -0.0026568283 -0.0703018005 -0.5186373420 0.3715989599 0.4029793613
[41] -0.0422320255 -0.4439739161 0.1570819481 0.2465414047 -0.2973232083
[46] -0.0800393463 0.0938615930 0.3151826166 -0.2617931752 -0.1613684601
[51] 0.2138731970 0.0501758369 -0.1406963672 -0.1656747779 0.3342539501
[56] 0.0549384127 -0.3816515240 -0.2883535962 -0.6341181784 -0.0006156303
[61] -0.2182542484 0.1382631989 0.4002943654 -0.1264262787 0.2962769667
[66] -0.3172420143 0.1469257381 0.6245555658 -0.6370187683 0.3769254609
[71] 0.0184814433 0.5869144452 0.2495078270 0.0467885910 -0.2296643426
[76] 0.2435109092 -0.3553186915 0.1422531468 -0.4345749180 -0.1197130311
[81] 0.2728741701 -0.4026182893 -0.3495811977 -0.6214432756 0.2865923035
[86] 0.2678262512 0.3653503578 -0.3894678304 0.1172220116 -0.0678751483
[91] 0.0461345265 0.8108825804 0.1758521911 0.2985013796 -0.4630860242
[96] 0.3973914811 -0.3692234776 -0.3452905506 0.7502486736 -0.1256775877
[101] 0.5475120905 -0.2678935157 0.3068665491 0.1738316319 -0.3568360583
[106] 0.0382417006 0.0028947092 0.2337803293 -0.0366761600 -0.0261967604
[111] -0.1044045834 0.0091187081 -0.1981085926 -0.1455571503 0.0517156626
[116] -0.5636844560 0.6436269461 0.1969538012 -0.1137006835 -0.2448390331
[121] -0.0462809530 -0.5233842588 -0.0555506951 -0.5851800492 -0.1812787918
[126] 0.4335553407 -0.2414187617 0.0371795306 0.1662518877 -0.3505812357
[131] 0.4891955352 0.1620749677 -0.0456569996 0.2353758936 0.3181040547
[136] -0.1084151928 -0.5489272448 -0.1972398925 -0.3234171515 0.2564701252
[141] -0.2639790003 -0.5764029559 0.1440029294 0.0799351719 0.3238654681
[146] -0.2502534834 -0.4327144662 -0.6005695192 -0.0000848372 -0.0705019636
[151] -0.4476295616 0.4494401872 0.2849854615 0.0211303214 0.1181198054
[156] -0.1752692840 -0.0577194311 -0.2106485395 -0.4634163066 -0.2399060047
[161] 0.0637361866 -0.0926491820 0.1158659083 0.1835588469 0.0673956795
[166] 0.0182314981 -0.5462161982 0.4151313637 0.0001250986 -0.5291794624
[171] -0.0254629739 0.1393242388 0.3048902571 -0.6145046583 0.2314551016
[176] -0.1181316130 0.4775405649 0.1808921386 0.5803889588 0.0446739209
[181] 0.4175896815 0.4261515497 -0.0990079590 0.1331765003 0.9785906188
[186] 0.3339047289 -0.2864551747 0.4847628252 -0.1135198542 -0.4610777219
[191] -0.1107315517 -0.2686471861 -0.0474750313 -0.2468832457 -0.2577486209
[196] -0.0304776915 -0.6534176027 0.3236237668 -0.3876721915 0.0476811887
[201] 0.2182288626 -0.0423543022 -0.2385792188 -0.2279851202 -0.1385729678
[206] -0.1186518038 0.1443121356 0.0251083331 0.0243136199 0.0029862459
[211] 0.1130935002 0.1370955236 0.3338650242 -0.1479393266 0.3596473067
[216] 0.0345405270 0.2176656090 0.0684023103 0.1573192833 -0.3100080061
[221] -0.3303893032 0.0834519852 0.4703353633 -0.2749815020 0.3562706908
[226] -0.4499800352 0.1326379489 0.1704270971 0.0423293511 0.1103356042
>
> proc.time()
user system elapsed
0.674 3.312 4.068
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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: 0x60000386c000>
> .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: 0x60000386c000>
> .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: 0x60000386c000>
> .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: 0x60000386c000>
> 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: 0x600003864060>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003864060>
> .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: 0x600003864060>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003864060>
> .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: 0x600003864060>
> 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: 0x600003864240>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003864240>
> .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: 0x600003864240>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600003864240>
> .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: 0x600003864240>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x600003864240>
> .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: 0x600003864240>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x600003864240>
> .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: 0x600003864240>
> 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: 0x600003864420>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x600003864420>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003864420>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003864420>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile52cc1296eefc" "BufferedMatrixFile52cc7323ebec"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile52cc1296eefc" "BufferedMatrixFile52cc7323ebec"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000038646c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000038646c0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000038646c0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000038646c0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x6000038646c0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x6000038646c0>
> .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: 0x6000038648a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000038648a0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x6000038648a0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x6000038648a0>
> 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: 0x600003860000>
> .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: 0x600003860000>
> rm(P)
>
> proc.time()
user system elapsed
0.118 0.040 0.156
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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
0.116 0.025 0.138