Ben Bolstad
| Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: 0147962 |
| git_last_commit_date: 2025-04-15 09:39:39 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-26 12:05 -0400 (Fri, 26 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4831 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4619 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4563 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 253/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.73.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.73.0 |
| 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_1.73.0.tar.gz |
| StartedAt: 2025-09-25 18:30:33 -0400 (Thu, 25 Sep 2025) |
| EndedAt: 2025-09-25 18:30:50 -0400 (Thu, 25 Sep 2025) |
| EllapsedTime: 16.2 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_1.73.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.73.0’
* 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-3.22-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 ... NOTE
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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-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/4.5-arm64/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.73.0’
** 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/4.5-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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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
0.118 0.041 0.151
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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-3.22-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 480828 25.7 1056624 56.5 NA 634340 33.9
Vcells 891019 6.8 8388608 64.0 196608 2109889 16.1
>
>
>
>
> ##
> ## 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 Sep 25 18:30:42 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 Sep 25 18:30:42 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: 0x600003834000>
>
>
>
> 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 Sep 25 18:30:43 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 Sep 25 18:30:44 2025"
>
> ColMode(tmp2)
<pointer: 0x600003834000>
>
>
>
> ### 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,] 100.0617910 -0.2953550 0.4998150 -2.3199345
[2,] 2.2186682 -0.3646605 -0.2665948 1.0098755
[3,] -0.3893817 -0.1311281 1.4221167 -0.8487052
[4,] -0.9443724 -0.5983828 0.2225003 -0.6895484
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-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,] 100.0617910 0.2953550 0.4998150 2.3199345
[2,] 2.2186682 0.3646605 0.2665948 1.0098755
[3,] 0.3893817 0.1311281 1.4221167 0.8487052
[4,] 0.9443724 0.5983828 0.2225003 0.6895484
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-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,] 10.0030891 0.5434657 0.7069759 1.5231331
[2,] 1.4895194 0.6038713 0.5163282 1.0049256
[3,] 0.6240046 0.3621161 1.1925254 0.9212519
[4,] 0.9717883 0.7735521 0.4716993 0.8303905
>
> 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-3.22-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,] 225.09268 30.73001 32.56957 42.55127
[2,] 42.11386 31.40337 30.42988 36.05913
[3,] 31.62943 28.75229 38.34737 35.06122
[4,] 35.66225 33.33390 29.93949 33.99345
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x600003838000>
> exp(tmp5)
<pointer: 0x600003838000>
> log(tmp5,2)
<pointer: 0x600003838000>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 468.5009
> Min(tmp5)
[1] 52.74109
> mean(tmp5)
[1] 73.80755
> Sum(tmp5)
[1] 14761.51
> Var(tmp5)
[1] 863.4094
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.89536 70.70754 71.43816 70.19301 71.59492 74.02101 70.49762 75.50683
[9] 70.99793 70.22308
> rowSums(tmp5)
[1] 1857.907 1414.151 1428.763 1403.860 1431.898 1480.420 1409.952 1510.137
[9] 1419.959 1404.462
> rowVars(tmp5)
[1] 7915.25480 71.37397 49.36287 46.97047 104.59465 50.82745
[7] 104.41937 121.24291 51.88991 72.23511
> rowSd(tmp5)
[1] 88.967718 8.448312 7.025871 6.853501 10.227153 7.129337 10.218580
[8] 11.011036 7.203465 8.499124
> rowMax(tmp5)
[1] 468.50093 87.65449 80.89598 84.49944 88.48817 87.44036 97.05966
[8] 99.89707 81.43824 89.31180
> rowMin(tmp5)
[1] 57.61074 52.74109 59.84412 60.68370 55.20915 61.20069 56.70836 59.38893
[9] 56.05977 55.05292
>
> colMeans(tmp5)
[1] 112.49748 66.01333 73.73151 71.69078 74.15045 69.05102 75.98587
[8] 67.06543 76.33512 72.10907 73.33837 74.55334 74.52721 67.52116
[15] 71.94648 68.83545 71.43079 72.82915 70.60310 71.93582
> colSums(tmp5)
[1] 1124.9748 660.1333 737.3151 716.9078 741.5045 690.5102 759.8587
[8] 670.6543 763.3512 721.0907 733.3837 745.5334 745.2721 675.2116
[15] 719.4648 688.3545 714.3079 728.2915 706.0310 719.3582
> colVars(tmp5)
[1] 15724.91512 56.06325 126.73900 80.48713 47.28537 64.71289
[7] 46.76690 75.23416 63.37428 164.45139 87.39813 81.83750
[13] 61.41546 75.06361 90.47221 60.23911 27.23464 85.66516
[19] 47.50546 97.70169
> colSd(tmp5)
[1] 125.399024 7.487539 11.257842 8.971462 6.876436 8.044432
[7] 6.838633 8.673763 7.960797 12.823860 9.348697 9.046408
[13] 7.836802 8.663926 9.511688 7.761386 5.218682 9.255548
[19] 6.892420 9.884416
> colMax(tmp5)
[1] 468.50093 80.48293 97.05966 88.56488 84.73594 81.43824 86.92110
[8] 83.71187 88.48817 99.89707 89.69748 90.25816 92.59210 79.86431
[15] 89.35620 78.95006 78.33905 87.44036 81.49174 84.49944
> colMin(tmp5)
[1] 59.05514 55.20915 60.41731 55.64013 59.38893 57.61074 64.37326 55.24221
[9] 61.93172 60.68370 61.68674 56.70836 66.40504 55.05292 59.99252 52.74109
[17] 65.08772 56.05977 60.80424 55.81531
>
>
> ### 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] 92.89536 70.70754 71.43816 70.19301 71.59492 74.02101 70.49762 75.50683
[9] 70.99793 NA
> rowSums(tmp5)
[1] 1857.907 1414.151 1428.763 1403.860 1431.898 1480.420 1409.952 1510.137
[9] 1419.959 NA
> rowVars(tmp5)
[1] 7915.25480 71.37397 49.36287 46.97047 104.59465 50.82745
[7] 104.41937 121.24291 51.88991 75.32865
> rowSd(tmp5)
[1] 88.967718 8.448312 7.025871 6.853501 10.227153 7.129337 10.218580
[8] 11.011036 7.203465 8.679208
> rowMax(tmp5)
[1] 468.50093 87.65449 80.89598 84.49944 88.48817 87.44036 97.05966
[8] 99.89707 81.43824 NA
> rowMin(tmp5)
[1] 57.61074 52.74109 59.84412 60.68370 55.20915 61.20069 56.70836 59.38893
[9] 56.05977 NA
>
> colMeans(tmp5)
[1] 112.49748 66.01333 73.73151 71.69078 74.15045 69.05102 75.98587
[8] 67.06543 76.33512 72.10907 73.33837 74.55334 74.52721 67.52116
[15] 71.94648 68.83545 71.43079 NA 70.60310 71.93582
> colSums(tmp5)
[1] 1124.9748 660.1333 737.3151 716.9078 741.5045 690.5102 759.8587
[8] 670.6543 763.3512 721.0907 733.3837 745.5334 745.2721 675.2116
[15] 719.4648 688.3545 714.3079 NA 706.0310 719.3582
> colVars(tmp5)
[1] 15724.91512 56.06325 126.73900 80.48713 47.28537 64.71289
[7] 46.76690 75.23416 63.37428 164.45139 87.39813 81.83750
[13] 61.41546 75.06361 90.47221 60.23911 27.23464 NA
[19] 47.50546 97.70169
> colSd(tmp5)
[1] 125.399024 7.487539 11.257842 8.971462 6.876436 8.044432
[7] 6.838633 8.673763 7.960797 12.823860 9.348697 9.046408
[13] 7.836802 8.663926 9.511688 7.761386 5.218682 NA
[19] 6.892420 9.884416
> colMax(tmp5)
[1] 468.50093 80.48293 97.05966 88.56488 84.73594 81.43824 86.92110
[8] 83.71187 88.48817 99.89707 89.69748 90.25816 92.59210 79.86431
[15] 89.35620 78.95006 78.33905 NA 81.49174 84.49944
> colMin(tmp5)
[1] 59.05514 55.20915 60.41731 55.64013 59.38893 57.61074 64.37326 55.24221
[9] 61.93172 60.68370 61.68674 56.70836 66.40504 55.05292 59.99252 52.74109
[17] 65.08772 NA 60.80424 55.81531
>
> Max(tmp5,na.rm=TRUE)
[1] 468.5009
> Min(tmp5,na.rm=TRUE)
[1] 52.74109
> mean(tmp5,na.rm=TRUE)
[1] 73.80563
> Sum(tmp5,na.rm=TRUE)
[1] 14687.32
> Var(tmp5,na.rm=TRUE)
[1] 867.7693
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.89536 70.70754 71.43816 70.19301 71.59492 74.02101 70.49762 75.50683
[9] 70.99793 70.01438
> rowSums(tmp5,na.rm=TRUE)
[1] 1857.907 1414.151 1428.763 1403.860 1431.898 1480.420 1409.952 1510.137
[9] 1419.959 1330.273
> rowVars(tmp5,na.rm=TRUE)
[1] 7915.25480 71.37397 49.36287 46.97047 104.59465 50.82745
[7] 104.41937 121.24291 51.88991 75.32865
> rowSd(tmp5,na.rm=TRUE)
[1] 88.967718 8.448312 7.025871 6.853501 10.227153 7.129337 10.218580
[8] 11.011036 7.203465 8.679208
> rowMax(tmp5,na.rm=TRUE)
[1] 468.50093 87.65449 80.89598 84.49944 88.48817 87.44036 97.05966
[8] 99.89707 81.43824 89.31180
> rowMin(tmp5,na.rm=TRUE)
[1] 57.61074 52.74109 59.84412 60.68370 55.20915 61.20069 56.70836 59.38893
[9] 56.05977 55.05292
>
> colMeans(tmp5,na.rm=TRUE)
[1] 112.49748 66.01333 73.73151 71.69078 74.15045 69.05102 75.98587
[8] 67.06543 76.33512 72.10907 73.33837 74.55334 74.52721 67.52116
[15] 71.94648 68.83545 71.43079 72.67813 70.60310 71.93582
> colSums(tmp5,na.rm=TRUE)
[1] 1124.9748 660.1333 737.3151 716.9078 741.5045 690.5102 759.8587
[8] 670.6543 763.3512 721.0907 733.3837 745.5334 745.2721 675.2116
[15] 719.4648 688.3545 714.3079 654.1031 706.0310 719.3582
> colVars(tmp5,na.rm=TRUE)
[1] 15724.91512 56.06325 126.73900 80.48713 47.28537 64.71289
[7] 46.76690 75.23416 63.37428 164.45139 87.39813 81.83750
[13] 61.41546 75.06361 90.47221 60.23911 27.23464 96.11671
[19] 47.50546 97.70169
> colSd(tmp5,na.rm=TRUE)
[1] 125.399024 7.487539 11.257842 8.971462 6.876436 8.044432
[7] 6.838633 8.673763 7.960797 12.823860 9.348697 9.046408
[13] 7.836802 8.663926 9.511688 7.761386 5.218682 9.803913
[19] 6.892420 9.884416
> colMax(tmp5,na.rm=TRUE)
[1] 468.50093 80.48293 97.05966 88.56488 84.73594 81.43824 86.92110
[8] 83.71187 88.48817 99.89707 89.69748 90.25816 92.59210 79.86431
[15] 89.35620 78.95006 78.33905 87.44036 81.49174 84.49944
> colMin(tmp5,na.rm=TRUE)
[1] 59.05514 55.20915 60.41731 55.64013 59.38893 57.61074 64.37326 55.24221
[9] 61.93172 60.68370 61.68674 56.70836 66.40504 55.05292 59.99252 52.74109
[17] 65.08772 56.05977 60.80424 55.81531
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.89536 70.70754 71.43816 70.19301 71.59492 74.02101 70.49762 75.50683
[9] 70.99793 NaN
> rowSums(tmp5,na.rm=TRUE)
[1] 1857.907 1414.151 1428.763 1403.860 1431.898 1480.420 1409.952 1510.137
[9] 1419.959 0.000
> rowVars(tmp5,na.rm=TRUE)
[1] 7915.25480 71.37397 49.36287 46.97047 104.59465 50.82745
[7] 104.41937 121.24291 51.88991 NA
> rowSd(tmp5,na.rm=TRUE)
[1] 88.967718 8.448312 7.025871 6.853501 10.227153 7.129337 10.218580
[8] 11.011036 7.203465 NA
> rowMax(tmp5,na.rm=TRUE)
[1] 468.50093 87.65449 80.89598 84.49944 88.48817 87.44036 97.05966
[8] 99.89707 81.43824 NA
> rowMin(tmp5,na.rm=TRUE)
[1] 57.61074 52.74109 59.84412 60.68370 55.20915 61.20069 56.70836 59.38893
[9] 56.05977 NA
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 116.88658 65.72543 74.10093 71.34804 74.57899 68.22200 75.62966
[8] 68.37912 77.93550 70.19765 73.39733 74.40026 74.24205 68.90652
[15] 72.17389 68.74082 72.09335 NaN 70.75319 73.72699
> colSums(tmp5,na.rm=TRUE)
[1] 1051.9792 591.5288 666.9084 642.1324 671.2109 613.9980 680.6669
[8] 615.4121 701.4195 631.7789 660.5760 669.6023 668.1784 620.1587
[15] 649.5650 618.6674 648.8401 0.0000 636.7787 663.5429
> colVars(tmp5,na.rm=TRUE)
[1] 17473.80755 62.13863 141.04606 89.22649 51.13002 65.07017
[7] 51.18527 65.22335 42.48248 143.90585 98.28379 91.80356
[13] 68.17759 62.85531 101.19945 67.66825 25.70038 NA
[19] 53.19021 73.82122
> colSd(tmp5,na.rm=TRUE)
[1] 132.188530 7.882806 11.876282 9.445977 7.150526 8.066608
[7] 7.154388 8.076097 6.517859 11.996077 9.913818 9.581417
[13] 8.256972 7.928134 10.059794 8.226071 5.069554 NA
[19] 7.293162 8.591928
> colMax(tmp5,na.rm=TRUE)
[1] 468.50093 80.48293 97.05966 88.56488 84.73594 81.43824 86.92110
[8] 83.71187 88.48817 99.89707 89.69748 90.25816 92.59210 79.86431
[15] 89.35620 78.95006 78.33905 -Inf 81.49174 84.49944
> colMin(tmp5,na.rm=TRUE)
[1] 59.05514 55.20915 60.41731 55.64013 59.38893 57.61074 64.37326 59.97544
[9] 67.85041 60.68370 61.68674 56.70836 66.40504 61.58017 59.99252 52.74109
[17] 65.08772 Inf 60.80424 60.62579
>
>
>
>
> 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] 152.7432 226.8790 247.9143 289.4254 202.2226 326.0759 216.1514 215.9299
[9] 252.2250 237.3723
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 152.7432 226.8790 247.9143 289.4254 202.2226 326.0759 216.1514 215.9299
[9] 252.2250 237.3723
>
>
>
> 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 -1.136868e-13 2.842171e-14 0.000000e+00 5.684342e-14
[6] 0.000000e+00 0.000000e+00 0.000000e+00 -8.526513e-14 5.684342e-14
[11] 1.136868e-13 -1.421085e-14 1.421085e-14 -1.278977e-13 -1.136868e-13
[16] 0.000000e+00 -5.684342e-14 -5.684342e-14 -2.842171e-14 0.000000e+00
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
3 18
1 13
1 4
6 10
10 7
5 4
6 9
4 4
8 19
6 20
2 9
7 6
8 19
4 14
10 15
9 13
6 4
9 16
7 16
8 18
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] 2.786058
> Min(tmp)
[1] -2.131211
> mean(tmp)
[1] 0.19039
> Sum(tmp)
[1] 19.039
> Var(tmp)
[1] 0.9573654
>
> rowMeans(tmp)
[1] 0.19039
> rowSums(tmp)
[1] 19.039
> rowVars(tmp)
[1] 0.9573654
> rowSd(tmp)
[1] 0.9784505
> rowMax(tmp)
[1] 2.786058
> rowMin(tmp)
[1] -2.131211
>
> colMeans(tmp)
[1] -1.665751126 -0.316366260 -0.532861132 -0.303276184 0.371497608
[6] 1.214231159 0.825315975 0.357026122 -0.442626599 0.447311342
[11] -0.499286148 -0.916596244 -1.143654983 0.827363718 0.007419401
[16] -0.081528769 1.379412700 1.168347834 0.147162764 -0.081023213
[21] 0.685578027 1.784654037 1.244884780 -0.087355257 0.447419828
[26] 0.186656907 -1.132297893 1.355469478 0.106478880 0.260433944
[31] 2.384199744 -0.050577865 -1.253973789 0.131590844 -0.646930134
[36] 0.010261690 -0.581145644 1.376713695 -1.075950051 -1.675905305
[41] 1.213939835 0.899532074 0.066966742 0.910188594 -0.069988037
[46] 1.542504140 0.731986194 -0.581646432 0.760790385 1.416467148
[51] 1.216341841 -0.358113863 0.095170960 0.055085180 -1.363912723
[56] -1.118488291 2.786057692 0.271297586 -0.132249572 0.575096954
[61] -0.817009376 0.676570381 -1.133593343 -0.234045214 -0.692374858
[66] 0.212930406 -0.543928339 -0.238591410 -0.082789424 1.785512394
[71] 1.003290008 -0.133465007 0.309956990 0.721685159 0.194437119
[76] 1.571590278 0.108714499 1.665929984 2.075271605 -0.978150084
[81] -0.070614593 -1.056272441 0.354287639 0.901341512 0.025218926
[86] 2.081457691 -1.082090581 -0.873596965 1.312398202 -0.510352292
[91] -0.497161250 -0.236600390 0.220595594 -1.115329283 1.341510678
[96] 1.168658352 0.299370084 1.379371779 -1.093278793 -2.131210902
> colSums(tmp)
[1] -1.665751126 -0.316366260 -0.532861132 -0.303276184 0.371497608
[6] 1.214231159 0.825315975 0.357026122 -0.442626599 0.447311342
[11] -0.499286148 -0.916596244 -1.143654983 0.827363718 0.007419401
[16] -0.081528769 1.379412700 1.168347834 0.147162764 -0.081023213
[21] 0.685578027 1.784654037 1.244884780 -0.087355257 0.447419828
[26] 0.186656907 -1.132297893 1.355469478 0.106478880 0.260433944
[31] 2.384199744 -0.050577865 -1.253973789 0.131590844 -0.646930134
[36] 0.010261690 -0.581145644 1.376713695 -1.075950051 -1.675905305
[41] 1.213939835 0.899532074 0.066966742 0.910188594 -0.069988037
[46] 1.542504140 0.731986194 -0.581646432 0.760790385 1.416467148
[51] 1.216341841 -0.358113863 0.095170960 0.055085180 -1.363912723
[56] -1.118488291 2.786057692 0.271297586 -0.132249572 0.575096954
[61] -0.817009376 0.676570381 -1.133593343 -0.234045214 -0.692374858
[66] 0.212930406 -0.543928339 -0.238591410 -0.082789424 1.785512394
[71] 1.003290008 -0.133465007 0.309956990 0.721685159 0.194437119
[76] 1.571590278 0.108714499 1.665929984 2.075271605 -0.978150084
[81] -0.070614593 -1.056272441 0.354287639 0.901341512 0.025218926
[86] 2.081457691 -1.082090581 -0.873596965 1.312398202 -0.510352292
[91] -0.497161250 -0.236600390 0.220595594 -1.115329283 1.341510678
[96] 1.168658352 0.299370084 1.379371779 -1.093278793 -2.131210902
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] -1.665751126 -0.316366260 -0.532861132 -0.303276184 0.371497608
[6] 1.214231159 0.825315975 0.357026122 -0.442626599 0.447311342
[11] -0.499286148 -0.916596244 -1.143654983 0.827363718 0.007419401
[16] -0.081528769 1.379412700 1.168347834 0.147162764 -0.081023213
[21] 0.685578027 1.784654037 1.244884780 -0.087355257 0.447419828
[26] 0.186656907 -1.132297893 1.355469478 0.106478880 0.260433944
[31] 2.384199744 -0.050577865 -1.253973789 0.131590844 -0.646930134
[36] 0.010261690 -0.581145644 1.376713695 -1.075950051 -1.675905305
[41] 1.213939835 0.899532074 0.066966742 0.910188594 -0.069988037
[46] 1.542504140 0.731986194 -0.581646432 0.760790385 1.416467148
[51] 1.216341841 -0.358113863 0.095170960 0.055085180 -1.363912723
[56] -1.118488291 2.786057692 0.271297586 -0.132249572 0.575096954
[61] -0.817009376 0.676570381 -1.133593343 -0.234045214 -0.692374858
[66] 0.212930406 -0.543928339 -0.238591410 -0.082789424 1.785512394
[71] 1.003290008 -0.133465007 0.309956990 0.721685159 0.194437119
[76] 1.571590278 0.108714499 1.665929984 2.075271605 -0.978150084
[81] -0.070614593 -1.056272441 0.354287639 0.901341512 0.025218926
[86] 2.081457691 -1.082090581 -0.873596965 1.312398202 -0.510352292
[91] -0.497161250 -0.236600390 0.220595594 -1.115329283 1.341510678
[96] 1.168658352 0.299370084 1.379371779 -1.093278793 -2.131210902
> colMin(tmp)
[1] -1.665751126 -0.316366260 -0.532861132 -0.303276184 0.371497608
[6] 1.214231159 0.825315975 0.357026122 -0.442626599 0.447311342
[11] -0.499286148 -0.916596244 -1.143654983 0.827363718 0.007419401
[16] -0.081528769 1.379412700 1.168347834 0.147162764 -0.081023213
[21] 0.685578027 1.784654037 1.244884780 -0.087355257 0.447419828
[26] 0.186656907 -1.132297893 1.355469478 0.106478880 0.260433944
[31] 2.384199744 -0.050577865 -1.253973789 0.131590844 -0.646930134
[36] 0.010261690 -0.581145644 1.376713695 -1.075950051 -1.675905305
[41] 1.213939835 0.899532074 0.066966742 0.910188594 -0.069988037
[46] 1.542504140 0.731986194 -0.581646432 0.760790385 1.416467148
[51] 1.216341841 -0.358113863 0.095170960 0.055085180 -1.363912723
[56] -1.118488291 2.786057692 0.271297586 -0.132249572 0.575096954
[61] -0.817009376 0.676570381 -1.133593343 -0.234045214 -0.692374858
[66] 0.212930406 -0.543928339 -0.238591410 -0.082789424 1.785512394
[71] 1.003290008 -0.133465007 0.309956990 0.721685159 0.194437119
[76] 1.571590278 0.108714499 1.665929984 2.075271605 -0.978150084
[81] -0.070614593 -1.056272441 0.354287639 0.901341512 0.025218926
[86] 2.081457691 -1.082090581 -0.873596965 1.312398202 -0.510352292
[91] -0.497161250 -0.236600390 0.220595594 -1.115329283 1.341510678
[96] 1.168658352 0.299370084 1.379371779 -1.093278793 -2.131210902
> colMedians(tmp)
[1] -1.665751126 -0.316366260 -0.532861132 -0.303276184 0.371497608
[6] 1.214231159 0.825315975 0.357026122 -0.442626599 0.447311342
[11] -0.499286148 -0.916596244 -1.143654983 0.827363718 0.007419401
[16] -0.081528769 1.379412700 1.168347834 0.147162764 -0.081023213
[21] 0.685578027 1.784654037 1.244884780 -0.087355257 0.447419828
[26] 0.186656907 -1.132297893 1.355469478 0.106478880 0.260433944
[31] 2.384199744 -0.050577865 -1.253973789 0.131590844 -0.646930134
[36] 0.010261690 -0.581145644 1.376713695 -1.075950051 -1.675905305
[41] 1.213939835 0.899532074 0.066966742 0.910188594 -0.069988037
[46] 1.542504140 0.731986194 -0.581646432 0.760790385 1.416467148
[51] 1.216341841 -0.358113863 0.095170960 0.055085180 -1.363912723
[56] -1.118488291 2.786057692 0.271297586 -0.132249572 0.575096954
[61] -0.817009376 0.676570381 -1.133593343 -0.234045214 -0.692374858
[66] 0.212930406 -0.543928339 -0.238591410 -0.082789424 1.785512394
[71] 1.003290008 -0.133465007 0.309956990 0.721685159 0.194437119
[76] 1.571590278 0.108714499 1.665929984 2.075271605 -0.978150084
[81] -0.070614593 -1.056272441 0.354287639 0.901341512 0.025218926
[86] 2.081457691 -1.082090581 -0.873596965 1.312398202 -0.510352292
[91] -0.497161250 -0.236600390 0.220595594 -1.115329283 1.341510678
[96] 1.168658352 0.299370084 1.379371779 -1.093278793 -2.131210902
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -1.665751 -0.3163663 -0.5328611 -0.3032762 0.3714976 1.214231 0.825316
[2,] -1.665751 -0.3163663 -0.5328611 -0.3032762 0.3714976 1.214231 0.825316
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.3570261 -0.4426266 0.4473113 -0.4992861 -0.9165962 -1.143655 0.8273637
[2,] 0.3570261 -0.4426266 0.4473113 -0.4992861 -0.9165962 -1.143655 0.8273637
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.007419401 -0.08152877 1.379413 1.168348 0.1471628 -0.08102321 0.685578
[2,] 0.007419401 -0.08152877 1.379413 1.168348 0.1471628 -0.08102321 0.685578
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 1.784654 1.244885 -0.08735526 0.4474198 0.1866569 -1.132298 1.355469
[2,] 1.784654 1.244885 -0.08735526 0.4474198 0.1866569 -1.132298 1.355469
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.1064789 0.2604339 2.3842 -0.05057787 -1.253974 0.1315908 -0.6469301
[2,] 0.1064789 0.2604339 2.3842 -0.05057787 -1.253974 0.1315908 -0.6469301
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.01026169 -0.5811456 1.376714 -1.07595 -1.675905 1.21394 0.8995321
[2,] 0.01026169 -0.5811456 1.376714 -1.07595 -1.675905 1.21394 0.8995321
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.06696674 0.9101886 -0.06998804 1.542504 0.7319862 -0.5816464 0.7607904
[2,] 0.06696674 0.9101886 -0.06998804 1.542504 0.7319862 -0.5816464 0.7607904
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 1.416467 1.216342 -0.3581139 0.09517096 0.05508518 -1.363913 -1.118488
[2,] 1.416467 1.216342 -0.3581139 0.09517096 0.05508518 -1.363913 -1.118488
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 2.786058 0.2712976 -0.1322496 0.575097 -0.8170094 0.6765704 -1.133593
[2,] 2.786058 0.2712976 -0.1322496 0.575097 -0.8170094 0.6765704 -1.133593
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -0.2340452 -0.6923749 0.2129304 -0.5439283 -0.2385914 -0.08278942 1.785512
[2,] -0.2340452 -0.6923749 0.2129304 -0.5439283 -0.2385914 -0.08278942 1.785512
[,71] [,72] [,73] [,74] [,75] [,76] [,77] [,78]
[1,] 1.00329 -0.133465 0.309957 0.7216852 0.1944371 1.57159 0.1087145 1.66593
[2,] 1.00329 -0.133465 0.309957 0.7216852 0.1944371 1.57159 0.1087145 1.66593
[,79] [,80] [,81] [,82] [,83] [,84] [,85]
[1,] 2.075272 -0.9781501 -0.07061459 -1.056272 0.3542876 0.9013415 0.02521893
[2,] 2.075272 -0.9781501 -0.07061459 -1.056272 0.3542876 0.9013415 0.02521893
[,86] [,87] [,88] [,89] [,90] [,91] [,92]
[1,] 2.081458 -1.082091 -0.873597 1.312398 -0.5103523 -0.4971612 -0.2366004
[2,] 2.081458 -1.082091 -0.873597 1.312398 -0.5103523 -0.4971612 -0.2366004
[,93] [,94] [,95] [,96] [,97] [,98] [,99]
[1,] 0.2205956 -1.115329 1.341511 1.168658 0.2993701 1.379372 -1.093279
[2,] 0.2205956 -1.115329 1.341511 1.168658 0.2993701 1.379372 -1.093279
[,100]
[1,] -2.131211
[2,] -2.131211
>
>
> Max(tmp2)
[1] 2.193075
> Min(tmp2)
[1] -2.294856
> mean(tmp2)
[1] 0.03309967
> Sum(tmp2)
[1] 3.309967
> Var(tmp2)
[1] 0.8281239
>
> rowMeans(tmp2)
[1] 1.05062981 -0.75705607 -0.38902601 -1.41972468 -1.36767441 1.34266964
[7] 0.22239855 1.29569093 0.79528941 0.19534597 0.11706012 0.06051512
[13] -0.29452581 -0.06004195 0.73941604 -0.09731694 -0.33695152 -0.60712012
[19] 0.75602522 0.85907756 -0.25642598 -0.82453378 -1.00524388 0.45537176
[25] -1.35616780 1.47334400 1.43440243 0.13669116 0.30130794 0.63884079
[31] 0.43095118 -0.18138933 -0.99939201 -0.41355090 1.02043609 -0.43130528
[37] -1.23994633 1.08323349 -0.34657584 -2.29485598 -0.88171170 0.22254318
[43] -0.53241389 -1.62313467 0.29655979 0.29562882 0.37912411 0.20410998
[49] 0.11206205 -0.60511536 0.15362088 -0.03510996 0.18946689 1.03492019
[55] -0.25709257 -0.07955511 1.44452045 -0.56626096 0.24365438 -1.40960858
[61] 0.30701933 0.40377875 1.72394952 1.40917682 -1.14850895 0.79030215
[67] 0.73465239 0.33425649 -0.57815385 0.12423566 -0.12453304 0.18132071
[73] -1.73380728 0.32411022 0.22706242 0.71398616 1.38182004 -0.64177535
[79] 0.38560468 -2.27710909 0.88392746 -0.91403775 0.87100201 2.19307501
[85] -0.16857415 -1.62987910 0.90797075 -1.41075930 -0.49922243 0.23806515
[91] 0.75456360 0.39388424 -1.40117584 0.56950292 -0.03357976 -1.09183278
[97] 1.34291208 0.98672450 0.82428796 -0.36035550
> rowSums(tmp2)
[1] 1.05062981 -0.75705607 -0.38902601 -1.41972468 -1.36767441 1.34266964
[7] 0.22239855 1.29569093 0.79528941 0.19534597 0.11706012 0.06051512
[13] -0.29452581 -0.06004195 0.73941604 -0.09731694 -0.33695152 -0.60712012
[19] 0.75602522 0.85907756 -0.25642598 -0.82453378 -1.00524388 0.45537176
[25] -1.35616780 1.47334400 1.43440243 0.13669116 0.30130794 0.63884079
[31] 0.43095118 -0.18138933 -0.99939201 -0.41355090 1.02043609 -0.43130528
[37] -1.23994633 1.08323349 -0.34657584 -2.29485598 -0.88171170 0.22254318
[43] -0.53241389 -1.62313467 0.29655979 0.29562882 0.37912411 0.20410998
[49] 0.11206205 -0.60511536 0.15362088 -0.03510996 0.18946689 1.03492019
[55] -0.25709257 -0.07955511 1.44452045 -0.56626096 0.24365438 -1.40960858
[61] 0.30701933 0.40377875 1.72394952 1.40917682 -1.14850895 0.79030215
[67] 0.73465239 0.33425649 -0.57815385 0.12423566 -0.12453304 0.18132071
[73] -1.73380728 0.32411022 0.22706242 0.71398616 1.38182004 -0.64177535
[79] 0.38560468 -2.27710909 0.88392746 -0.91403775 0.87100201 2.19307501
[85] -0.16857415 -1.62987910 0.90797075 -1.41075930 -0.49922243 0.23806515
[91] 0.75456360 0.39388424 -1.40117584 0.56950292 -0.03357976 -1.09183278
[97] 1.34291208 0.98672450 0.82428796 -0.36035550
> 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] 1.05062981 -0.75705607 -0.38902601 -1.41972468 -1.36767441 1.34266964
[7] 0.22239855 1.29569093 0.79528941 0.19534597 0.11706012 0.06051512
[13] -0.29452581 -0.06004195 0.73941604 -0.09731694 -0.33695152 -0.60712012
[19] 0.75602522 0.85907756 -0.25642598 -0.82453378 -1.00524388 0.45537176
[25] -1.35616780 1.47334400 1.43440243 0.13669116 0.30130794 0.63884079
[31] 0.43095118 -0.18138933 -0.99939201 -0.41355090 1.02043609 -0.43130528
[37] -1.23994633 1.08323349 -0.34657584 -2.29485598 -0.88171170 0.22254318
[43] -0.53241389 -1.62313467 0.29655979 0.29562882 0.37912411 0.20410998
[49] 0.11206205 -0.60511536 0.15362088 -0.03510996 0.18946689 1.03492019
[55] -0.25709257 -0.07955511 1.44452045 -0.56626096 0.24365438 -1.40960858
[61] 0.30701933 0.40377875 1.72394952 1.40917682 -1.14850895 0.79030215
[67] 0.73465239 0.33425649 -0.57815385 0.12423566 -0.12453304 0.18132071
[73] -1.73380728 0.32411022 0.22706242 0.71398616 1.38182004 -0.64177535
[79] 0.38560468 -2.27710909 0.88392746 -0.91403775 0.87100201 2.19307501
[85] -0.16857415 -1.62987910 0.90797075 -1.41075930 -0.49922243 0.23806515
[91] 0.75456360 0.39388424 -1.40117584 0.56950292 -0.03357976 -1.09183278
[97] 1.34291208 0.98672450 0.82428796 -0.36035550
> rowMin(tmp2)
[1] 1.05062981 -0.75705607 -0.38902601 -1.41972468 -1.36767441 1.34266964
[7] 0.22239855 1.29569093 0.79528941 0.19534597 0.11706012 0.06051512
[13] -0.29452581 -0.06004195 0.73941604 -0.09731694 -0.33695152 -0.60712012
[19] 0.75602522 0.85907756 -0.25642598 -0.82453378 -1.00524388 0.45537176
[25] -1.35616780 1.47334400 1.43440243 0.13669116 0.30130794 0.63884079
[31] 0.43095118 -0.18138933 -0.99939201 -0.41355090 1.02043609 -0.43130528
[37] -1.23994633 1.08323349 -0.34657584 -2.29485598 -0.88171170 0.22254318
[43] -0.53241389 -1.62313467 0.29655979 0.29562882 0.37912411 0.20410998
[49] 0.11206205 -0.60511536 0.15362088 -0.03510996 0.18946689 1.03492019
[55] -0.25709257 -0.07955511 1.44452045 -0.56626096 0.24365438 -1.40960858
[61] 0.30701933 0.40377875 1.72394952 1.40917682 -1.14850895 0.79030215
[67] 0.73465239 0.33425649 -0.57815385 0.12423566 -0.12453304 0.18132071
[73] -1.73380728 0.32411022 0.22706242 0.71398616 1.38182004 -0.64177535
[79] 0.38560468 -2.27710909 0.88392746 -0.91403775 0.87100201 2.19307501
[85] -0.16857415 -1.62987910 0.90797075 -1.41075930 -0.49922243 0.23806515
[91] 0.75456360 0.39388424 -1.40117584 0.56950292 -0.03357976 -1.09183278
[97] 1.34291208 0.98672450 0.82428796 -0.36035550
>
> colMeans(tmp2)
[1] 0.03309967
> colSums(tmp2)
[1] 3.309967
> colVars(tmp2)
[1] 0.8281239
> colSd(tmp2)
[1] 0.9100131
> colMax(tmp2)
[1] 2.193075
> colMin(tmp2)
[1] -2.294856
> colMedians(tmp2)
[1] 0.1674708
> colRanges(tmp2)
[,1]
[1,] -2.294856
[2,] 2.193075
>
> 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] -2.7494514 -0.5074337 0.9246587 -1.8615182 5.3682539 3.1163402
[7] 2.4167356 -2.4338849 -5.6592029 -3.3308786
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.5264772
[2,] -1.1851468
[3,] -0.3307842
[4,] 0.5145495
[5,] 1.8597992
>
> rowApply(tmp,sum)
[1] -2.6201610 -0.2454046 2.7661779 -0.6778690 2.0981669 -1.7720206
[7] 1.7914490 1.8961935 -3.5052535 -4.4476599
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 3 6 8 1 10 3 7 5 1 1
[2,] 2 1 10 10 4 5 5 3 8 8
[3,] 9 5 9 9 2 10 10 2 4 2
[4,] 8 4 4 4 3 6 1 4 10 4
[5,] 10 8 6 5 5 7 9 9 9 7
[6,] 5 9 5 7 9 9 3 6 5 6
[7,] 7 10 3 6 7 8 6 1 2 10
[8,] 6 7 2 3 8 2 2 8 7 3
[9,] 1 3 1 2 6 4 8 10 3 5
[10,] 4 2 7 8 1 1 4 7 6 9
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 0.1396398 1.5980238 1.9536108 0.1800655 1.0447793 2.0266253
[7] -1.9051051 1.8564237 -1.3523331 -0.0022580 -0.2094852 6.3844397
[13] -1.6807282 2.0070405 2.4337182 -2.6280589 -2.4707081 -1.9806908
[19] 0.6434567 -1.4662714
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.421306764
[2,] -0.405894270
[3,] -0.006638158
[4,] 0.108562785
[5,] 0.864916203
>
> rowApply(tmp,sum)
[1] 4.539337 3.265085 -2.158536 -2.742727 3.669026
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 11 15 5
[2,] 16 15 3 10 19
[3,] 11 19 13 6 17
[4,] 17 17 7 3 9
[5,] 13 12 18 5 7
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.421306764 1.1774976 0.1437103 1.3172023 0.1952122 1.93735601
[2,] 0.864916203 0.7642621 0.9877959 0.9594994 0.2959160 0.49748273
[3,] -0.006638158 -1.6659446 0.2179943 -0.8845470 1.5049692 1.00066142
[4,] 0.108562785 -0.2514806 -0.6683101 -1.0244621 -0.6728653 0.08482099
[5,] -0.405894270 1.5736892 1.2724203 -0.1876272 -0.2784529 -1.49369589
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.2767591 1.67129313 1.3281613 0.66719397 -0.6003024 0.1582781
[2,] -0.5942042 -0.55730844 -0.3981014 0.02425878 -0.2612344 0.9834344
[3,] -2.1031884 0.07818733 -0.8935514 -1.40414567 -0.9441087 2.0034518
[4,] -0.1124026 0.91332923 -0.7654545 -0.21792110 1.3871421 1.8847484
[5,] 1.1814493 -0.24907752 -0.6233871 0.92835602 0.2090181 1.3545271
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.7052955 -0.3285376 -0.5218161 -0.5906389 0.04438316 -0.6648744
[2,] -0.3055162 2.4743605 0.1202575 -1.0987956 -1.09758800 0.6991599
[3,] -0.4317321 1.1438844 1.7120299 -2.1604650 0.68223880 -0.3131826
[4,] -0.4095589 0.4729030 0.5717747 -0.4976479 -1.77666389 -0.5168852
[5,] 0.1713744 -1.7555698 0.5514722 1.7194884 -0.32307815 -1.1849086
[,19] [,20]
[1,] 0.3997225 -0.39114325
[2,] -0.4087503 -0.68475958
[3,] 0.9153807 -0.60983067
[4,] -1.2567485 0.00439249
[5,] 0.9938522 0.21506960
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-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-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 650 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 561 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-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 -0.7305871 -1.133739 0.8381012 0.4776564 -1.140253 0.02587937 1.342781
col8 col9 col10 col11 col12 col13 col14
row1 1.442921 -0.0991257 0.5337573 0.9216769 -2.001503 0.450531 -1.926376
col15 col16 col17 col18 col19 col20
row1 -1.266944 0.3479862 1.15489 1.823455 1.795977 1.676872
> tmp[,"col10"]
col10
row1 0.533757329
row2 0.800007822
row3 0.009457158
row4 -0.183244957
row5 0.225832490
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.7305871 -1.1337388 0.8381012 0.4776564 -1.140253 0.02587937 1.342781
row5 -0.3562083 -0.3046496 1.2869835 2.0240950 -0.595356 -0.53862569 -1.069192
col8 col9 col10 col11 col12 col13 col14
row1 1.442921 -0.0991257 0.5337573 0.9216769 -2.001503 0.450531 -1.9263760
row5 -1.211863 1.3914112 0.2258325 0.2590534 -1.680972 1.635482 0.5369686
col15 col16 col17 col18 col19 col20
row1 -1.26694449 0.3479862 1.154890 1.823455 1.7959769 1.6768718
row5 0.07943372 1.4258890 -1.766127 -1.097782 0.9407669 0.1587697
> tmp[,c("col6","col20")]
col6 col20
row1 0.02587937 1.676871847
row2 -0.32553144 -0.047314683
row3 -0.40439433 0.003474013
row4 -0.87776501 0.876906677
row5 -0.53862569 0.158769696
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.02587937 1.6768718
row5 -0.53862569 0.1587697
>
>
>
>
> 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 50.03332 51.03614 49.84647 51.1379 46.47379 105.8671 51.78617 49.19452
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.00979 51.62311 49.64056 49.36755 49.59383 51.39866 49.47807 50.35933
col17 col18 col19 col20
row1 51.32323 48.6714 50.04917 103.7112
> tmp[,"col10"]
col10
row1 51.62311
row2 29.77495
row3 30.22647
row4 29.30525
row5 49.65645
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.03332 51.03614 49.84647 51.13790 46.47379 105.8671 51.78617 49.19452
row5 49.79806 50.07634 50.63370 51.58884 51.22926 105.4526 48.12366 49.55633
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.00979 51.62311 49.64056 49.36755 49.59383 51.39866 49.47807 50.35933
row5 50.23350 49.65645 50.45532 49.06411 48.37830 49.41679 49.92903 49.83861
col17 col18 col19 col20
row1 51.32323 48.67140 50.04917 103.7112
row5 49.87093 50.83335 50.21361 105.9656
> tmp[,c("col6","col20")]
col6 col20
row1 105.86711 103.71120
row2 73.85302 75.51104
row3 74.18388 74.94830
row4 77.62951 75.57826
row5 105.45263 105.96563
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.8671 103.7112
row5 105.4526 105.9656
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.8671 103.7112
row5 105.4526 105.9656
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 1.7664127
[2,] -0.3568304
[3,] 0.7169406
[4,] 1.0623900
[5,] -0.2022248
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.63983260 1.7153582
[2,] 0.02994788 -0.2128302
[3,] 0.25075063 -0.3456599
[4,] -0.84296425 1.0788063
[5,] 0.22871220 1.2987774
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.6974234 -0.9217526
[2,] -0.3041210 -0.1931115
[3,] -1.7781215 -0.2154177
[4,] -1.5958936 1.3030485
[5,] -1.2047546 1.4407210
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.6974234
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.6974234
[2,] -0.3041210
>
>
>
> 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 -0.6254004 1.5001476 0.2937852 -0.96721692 0.42140315 -0.2741778 0.3958753
row1 -0.8463722 0.3903559 0.3409082 0.01069969 0.02030983 -2.7768864 1.7788589
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 0.9093839 -0.3092619 -0.9099867 -0.9187331 0.1991411 -0.9878255 0.2050122
row1 0.4393949 -0.4424246 -0.9003627 -1.0467130 -0.8563167 1.8838151 0.0706446
[,15] [,16] [,17] [,18] [,19] [,20]
row3 -0.0349667 0.2979213 -0.6297206 -0.8051079 -0.4736107 1.7675925
row1 -0.2817848 -2.0883609 0.4647875 -0.6438557 -0.8992788 0.3643654
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.2510011 1.344941 0.9755418 0.3033405 -1.170637 -0.7369468 0.1296475
[,8] [,9] [,10]
row2 -0.8924913 -2.013354 -0.05975556
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -1.025051 0.5431675 0.3443776 0.5314778 -0.4399437 0.9822149 -1.279432
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.2378992 1.165922 -1.241601 0.3989996 0.7417434 -0.7305232 1.07544
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -1.121418 -0.6171087 0.5169655 1.118943 0.9391841 0.2037958
>
>
> 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: 0x600003820300>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b325065c8c"
[2] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b344a5fe51"
[3] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b36ddb9b0c"
[4] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b36ca0692c"
[5] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b31758ff6b"
[6] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b353e8d5c6"
[7] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b35b2ae533"
[8] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b35d2da607"
[9] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b35fef455b"
[10] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b355b28a91"
[11] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b33ca7618b"
[12] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b310f50bc9"
[13] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b347d8c1d1"
[14] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b3679ca530"
[15] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMa2b35d212774"
>
>
> ### 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: 0x60000381c420>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x60000381c420>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x60000381c420>
> rowMedians(tmp)
[1] -0.307794284 -0.414521755 -0.361391799 -0.007365284 0.123586506
[6] 0.020551759 -0.120226430 0.576772097 0.155591241 0.174059512
[11] -0.628463368 -0.108495289 -0.694879895 0.139507649 -0.069373254
[16] 0.220236073 0.188179396 0.142540285 0.172677019 -0.009490285
[21] -0.136475296 0.609096069 -0.492998643 0.356424889 -0.600407225
[26] 0.223163526 -0.118602840 0.347909864 -0.180466055 -0.018199591
[31] 0.116084184 -0.174086584 0.643311483 -0.395044803 -0.048367304
[36] 0.005608576 -0.201033205 0.290471692 0.278367792 -0.025502274
[41] -0.223357504 -0.491055064 -0.153641617 -0.246761696 0.109296726
[46] 0.417050605 0.109180292 0.038761992 0.050069492 -0.923230575
[51] -0.256997470 0.255152852 -0.059332688 0.159995384 -0.353973788
[56] 0.015297755 0.344976157 -0.318448419 0.005354500 0.693126690
[61] -0.175878180 -0.342260171 0.356315387 -0.075038064 0.191690883
[66] 0.227878896 -0.348087825 -0.400689270 -0.176925608 -0.087269206
[71] -0.263522294 0.329626849 0.279012341 0.357028854 0.069742599
[76] 0.139186551 0.278074724 0.526471636 0.664492185 0.254272856
[81] -0.147726640 -0.838044004 0.303130279 0.446602357 0.156730718
[86] -0.556225210 -0.153465684 -0.545047046 -0.167682962 -0.162591230
[91] 0.044264775 0.351592613 0.132848409 0.522500540 0.220071662
[96] 0.151233346 0.105074207 -0.396763495 -0.210102221 0.124585223
[101] -0.307125574 0.159906338 0.679755715 -0.194928660 -0.450029526
[106] -0.216910932 0.212858090 -0.347170654 -0.182772647 -0.005714869
[111] 0.262530995 -0.065060818 0.710129480 0.399127374 -0.200780954
[116] -0.281458162 0.330611269 -0.159497433 0.175705541 -0.302373492
[121] 0.529845133 0.455976379 -0.468211629 0.038934156 -0.139911589
[126] -0.230121063 0.141168767 -0.105994136 -0.166774050 -0.362103178
[131] -0.242298633 0.528845204 0.207077222 0.858834040 0.110625720
[136] 0.361877944 0.275325259 0.320411895 -0.015715960 0.189051647
[141] -0.188140927 0.189840583 0.387664289 -0.395371694 0.167850147
[146] 0.034684422 0.549343144 0.264130251 -0.050034944 0.383233319
[151] -0.468155887 -0.071598279 0.166033051 0.107959116 -0.077014114
[156] -0.490350969 -0.322479651 -0.018513764 -0.274006084 -0.036484511
[161] -0.700032519 -0.180635519 0.298144870 -0.664933377 -0.214103983
[166] -0.025401161 0.240321177 0.531709462 0.347436701 -0.474192485
[171] 0.598976648 -0.182261870 -0.553185008 -0.481239962 -0.146513266
[176] -0.095675339 -0.001998717 0.359942526 0.052792691 0.226830615
[181] 0.191862787 -0.284925550 -0.114231575 -0.280329103 -0.338456803
[186] 0.176960258 0.064765224 0.388291934 0.247075755 0.045085210
[191] 0.002096194 0.092697852 0.294685132 0.031899968 0.019059126
[196] 0.460574151 0.345589456 0.147498876 -0.011294799 -0.117918456
[201] -0.054989402 -0.436485936 -0.499806417 0.043137897 -0.250065721
[206] -0.280189467 -0.108623353 0.045693402 -0.213906786 -0.454152160
[211] 0.249271160 0.072936006 0.266636136 -0.361927478 0.310249735
[216] -0.101056003 0.148617450 0.211959664 0.080578204 -0.669886697
[221] 0.406635307 0.013538167 -0.402183023 -0.169246673 -0.201743178
[226] 0.069711045 0.703501872 0.183197803 0.166750862 0.397428864
>
> proc.time()
user system elapsed
0.650 3.213 4.067
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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: 0x600003a7d020>
> .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: 0x600003a7d020>
> .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: 0x600003a7d020>
> .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: 0x600003a7d020>
> 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: 0x600003a74660>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003a74660>
> .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: 0x600003a74660>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003a74660>
> .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: 0x600003a74660>
> 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: 0x600003a74840>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003a74840>
> .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: 0x600003a74840>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600003a74840>
> .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: 0x600003a74840>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x600003a74840>
> .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: 0x600003a74840>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x600003a74840>
> .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: 0x600003a74840>
> 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: 0x600003a70000>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x600003a70000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003a70000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003a70000>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilea7043dbfd82" "BufferedMatrixFilea7045fe063c8"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilea7043dbfd82" "BufferedMatrixFilea7045fe063c8"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003a70240>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003a70240>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600003a70240>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600003a70240>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x600003a70240>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x600003a70240>
> .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: 0x600003a70420>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003a70420>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600003a70420>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x600003a70420>
> 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: 0x600003a70600>
> .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: 0x600003a70600>
> rm(P)
>
> proc.time()
user system elapsed
0.109 0.036 0.141
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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
0.114 0.028 0.138